R version 4.1.1 (2021-08-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Pop!_OS 21.04 Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.13.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 [8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] BiocManager_1.30.16 loaded via a namespace (and not attached): [1] compiler_4.1.1 tools_4.1.1 aRbs_0.1.3.tar.gz ./aRbs.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/aRbs.Rcheck’ ./aRbs.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./aRbs.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./aRbs.Rcheck/00check.log:* using session charset: UTF-8 ./aRbs.Rcheck/00check.log:* checking for file ‘aRbs/DESCRIPTION’ ... OK ./aRbs.Rcheck/00check.log:* this is package ‘aRbs’ version ‘0.1.3’ ./aRbs.Rcheck/00check.log:* package encoding: UTF-8 ./aRbs.Rcheck/00check.log:* checking package namespace information ... OK ./aRbs.Rcheck/00check.log:* checking package dependencies ... OK ./aRbs.Rcheck/00check.log:* checking if this is a source package ... OK ./aRbs.Rcheck/00check.log:* checking if there is a namespace ... OK ./aRbs.Rcheck/00check.log:* checking for executable files ... OK ./aRbs.Rcheck/00check.log:* checking for hidden files and directories ... OK ./aRbs.Rcheck/00check.log:* checking for portable file names ... OK ./aRbs.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./aRbs.Rcheck/00check.log:* checking whether package ‘aRbs’ can be installed ... OK ./aRbs.Rcheck/00check.log:* checking installed package size ... OK ./aRbs.Rcheck/00check.log:* checking package directory ... OK ./aRbs.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./aRbs.Rcheck/00check.log:* checking top-level files ... OK ./aRbs.Rcheck/00check.log:* checking for left-over files ... OK ./aRbs.Rcheck/00check.log:* checking index information ... OK ./aRbs.Rcheck/00check.log:* checking package subdirectories ... OK ./aRbs.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./aRbs.Rcheck/00check.log:* checking R files for syntax errors ... OK ./aRbs.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./aRbs.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./aRbs.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./aRbs.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./aRbs.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./aRbs.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./aRbs.Rcheck/00check.log:* checking dependencies in R code ... OK ./aRbs.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./aRbs.Rcheck/00check.log:* checking replacement functions ... OK ./aRbs.Rcheck/00check.log:* checking foreign function calls ... OK ./aRbs.Rcheck/00check.log:* checking R code for possible problems ... OK ./aRbs.Rcheck/00check.log:* checking Rd files ... OK ./aRbs.Rcheck/00check.log:* checking Rd metadata ... OK ./aRbs.Rcheck/00check.log:* checking Rd cross-references ... OK ./aRbs.Rcheck/00check.log:* checking for missing documentation entries ... OK ./aRbs.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./aRbs.Rcheck/00check.log:* checking Rd \usage sections ... OK ./aRbs.Rcheck/00check.log:* checking Rd contents ... OK ./aRbs.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./aRbs.Rcheck/00check.log:* checking examples ... ERROR ./aRbs.Rcheck/00check.log:Running examples in ‘aRbs-Ex.R’ failed ./aRbs.Rcheck/00check.log:The error most likely occurred in: ./aRbs.Rcheck/00check.log:> ### Name: clean_links ./aRbs.Rcheck/00check.log:> ### Title: Clean links given by the 'scrape_links()' function. ./aRbs.Rcheck/00check.log:> ### Aliases: clean_links ./aRbs.Rcheck/00check.log:> ./aRbs.Rcheck/00check.log:> ### ** Examples ./aRbs.Rcheck/00check.log:> ./aRbs.Rcheck/00check.log:> links <- scrape_links("https://www.oddschecker.com/football") ./aRbs.Rcheck/00check.log:Error in open.connection(x, "rb") : HTTP error 403. ./aRbs.Rcheck/00check.log:Calls: scrape_links -> -> read_html.default ./aRbs.Rcheck/00check.log:Execution halted ./aRbs.Rcheck/00check.log:* checking PDF version of manual ... OK ./aRbs.Rcheck/00check.log:* DONE ./aRbs.Rcheck/00check.log:Status: 1 ERROR CornerstoneR_2.0.2.tar.gz ./CornerstoneR.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/CornerstoneR.Rcheck’ ./CornerstoneR.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./CornerstoneR.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./CornerstoneR.Rcheck/00check.log:* using session charset: UTF-8 ./CornerstoneR.Rcheck/00check.log:* checking for file ‘CornerstoneR/DESCRIPTION’ ... OK ./CornerstoneR.Rcheck/00check.log:* this is package ‘CornerstoneR’ version ‘2.0.2’ ./CornerstoneR.Rcheck/00check.log:* package encoding: UTF-8 ./CornerstoneR.Rcheck/00check.log:* checking package namespace information ... OK ./CornerstoneR.Rcheck/00check.log:* checking package dependencies ... OK ./CornerstoneR.Rcheck/00check.log:* checking if this is a source package ... OK ./CornerstoneR.Rcheck/00check.log:* checking if there is a namespace ... OK ./CornerstoneR.Rcheck/00check.log:* checking for executable files ... OK ./CornerstoneR.Rcheck/00check.log:* checking for hidden files and directories ... OK ./CornerstoneR.Rcheck/00check.log:* checking for portable file names ... OK ./CornerstoneR.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./CornerstoneR.Rcheck/00check.log:* checking whether package ‘CornerstoneR’ can be installed ... OK ./CornerstoneR.Rcheck/00check.log:* checking installed package size ... OK ./CornerstoneR.Rcheck/00check.log:* checking package directory ... OK ./CornerstoneR.Rcheck/00check.log:* checking ‘build’ directory ... OK ./CornerstoneR.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./CornerstoneR.Rcheck/00check.log:* checking top-level files ... OK ./CornerstoneR.Rcheck/00check.log:* checking for left-over files ... OK ./CornerstoneR.Rcheck/00check.log:* checking index information ... OK ./CornerstoneR.Rcheck/00check.log:* checking package subdirectories ... OK ./CornerstoneR.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./CornerstoneR.Rcheck/00check.log:* checking R files for syntax errors ... OK ./CornerstoneR.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./CornerstoneR.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./CornerstoneR.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./CornerstoneR.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./CornerstoneR.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./CornerstoneR.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./CornerstoneR.Rcheck/00check.log:* checking dependencies in R code ... OK ./CornerstoneR.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./CornerstoneR.Rcheck/00check.log:* checking replacement functions ... OK ./CornerstoneR.Rcheck/00check.log:* checking foreign function calls ... OK ./CornerstoneR.Rcheck/00check.log:* checking R code for possible problems ... OK ./CornerstoneR.Rcheck/00check.log:* checking Rd files ... OK ./CornerstoneR.Rcheck/00check.log:* checking Rd metadata ... OK ./CornerstoneR.Rcheck/00check.log:* checking Rd cross-references ... OK ./CornerstoneR.Rcheck/00check.log:* checking for missing documentation entries ... OK ./CornerstoneR.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./CornerstoneR.Rcheck/00check.log:* checking Rd \usage sections ... OK ./CornerstoneR.Rcheck/00check.log:* checking Rd contents ... OK ./CornerstoneR.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./CornerstoneR.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./CornerstoneR.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./CornerstoneR.Rcheck/00check.log:* checking LazyData ... OK ./CornerstoneR.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./CornerstoneR.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./CornerstoneR.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./CornerstoneR.Rcheck/00check.log:* checking examples ... ERROR ./CornerstoneR.Rcheck/00check.log:Running examples in ‘CornerstoneR-Ex.R’ failed ./CornerstoneR.Rcheck/00check.log:The error most likely occurred in: ./CornerstoneR.Rcheck/00check.log:> ### Name: fitFunction ./CornerstoneR.Rcheck/00check.log:> ### Title: Fit Function to Data via Nonlinear Regression ./CornerstoneR.Rcheck/00check.log:> ### Aliases: fitFunction ./CornerstoneR.Rcheck/00check.log:> ./CornerstoneR.Rcheck/00check.log:> ### ** Examples ./CornerstoneR.Rcheck/00check.log:> ./CornerstoneR.Rcheck/00check.log:> # Generate data from logistic function: ./CornerstoneR.Rcheck/00check.log:> fun = function(x, a, b, c, d, sigma = 1) { ./CornerstoneR.Rcheck/00check.log:+ a+(b-a) / (1+exp(-d*(x-c))) + rnorm(length(x), sd = sigma) ./CornerstoneR.Rcheck/00check.log:+ } ./CornerstoneR.Rcheck/00check.log:> library(data.table) ./CornerstoneR.Rcheck/00check.log:> dt = data.table( x1 = sample(seq(-10, 10, length.out = 100)) ./CornerstoneR.Rcheck/00check.log:+ , group1 = sample(x = c("A", "B"), replace = TRUE, size = 100) ./CornerstoneR.Rcheck/00check.log:+ ) ./CornerstoneR.Rcheck/00check.log:> dt[group1 == "A", y1 := fun(x1, 1, 10, 1, 0.6, 0.1)] ./CornerstoneR.Rcheck/00check.log:> dt[group1 == "B", y1 := fun(x1, 8, 2, -1, 0.3, 0.1)] ./CornerstoneR.Rcheck/00check.log:> # Set script variables ./CornerstoneR.Rcheck/00check.log:> scriptvars = list(math.fun = "Logistic", resp.frml = "", preds.frml = "", limits = "" ./CornerstoneR.Rcheck/00check.log:+ , start.vals = "", weights = "", max.iter = 50, max.ftol = 0 ./CornerstoneR.Rcheck/00check.log:+ ) ./CornerstoneR.Rcheck/00check.log:> # Fit the logistic function: ./CornerstoneR.Rcheck/00check.log:> res = fitFunction(dt, "x1", "y1", "group1", character(0), scriptvars, TRUE) ./CornerstoneR.Rcheck/00check.log:> # Show estimated coefficients: ./CornerstoneR.Rcheck/00check.log:> res$coeff ./CornerstoneR.Rcheck/00check.log: group1 Coeff_a Coeff_b Coeff_c Coeff_d StdErr_a StdErr_b StdErr_c StdErr_d ./CornerstoneR.Rcheck/00check.log:1: A NA NA NA NA NA NA NA NA ./CornerstoneR.Rcheck/00check.log:2: B NA NA NA NA NA NA NA NA ./CornerstoneR.Rcheck/00check.log: pseudoR2 RMSE Converged Iterations Tolerance StopCode ./CornerstoneR.Rcheck/00check.log:1: NA NA NA NA NA NA ./CornerstoneR.Rcheck/00check.log:2: NA NA NA NA NA NA ./CornerstoneR.Rcheck/00check.log: StopMessage ./CornerstoneR.Rcheck/00check.log:1: Error : When i is a data.table (or character vector), the columns to join by must be specified using 'on=' argument (see ?data.table), by keying x (i.e. sorted, and, marked as sorted, see ?setkey), or by sharing column names between x and i (i.e., a natural join). Keyed joins might have further speed benefits on very large data due to x being sorted in RAM.\n ./CornerstoneR.Rcheck/00check.log:2: Error : When i is a data.table (or character vector), the columns to join by must be specified using 'on=' argument (see ?data.table), by keying x (i.e. sorted, and, marked as sorted, see ?setkey), or by sharing column names between x and i (i.e., a natural join). Keyed joins might have further speed benefits on very large data due to x being sorted in RAM.\n ./CornerstoneR.Rcheck/00check.log:> # Variance-Covariance matrix: ./CornerstoneR.Rcheck/00check.log:> res$vcov ./CornerstoneR.Rcheck/00check.log: group1 a b c d ./CornerstoneR.Rcheck/00check.log:1: A NA NA NA NA ./CornerstoneR.Rcheck/00check.log:2: A NA NA NA NA ./CornerstoneR.Rcheck/00check.log:3: A NA NA NA NA ./CornerstoneR.Rcheck/00check.log:4: A NA NA NA NA ./CornerstoneR.Rcheck/00check.log:5: B NA NA NA NA ./CornerstoneR.Rcheck/00check.log:6: B NA NA NA NA ./CornerstoneR.Rcheck/00check.log:7: B NA NA NA NA ./CornerstoneR.Rcheck/00check.log:8: B NA NA NA NA ./CornerstoneR.Rcheck/00check.log:> # Plot fitted vs. residuals: ./CornerstoneR.Rcheck/00check.log:> plot(res$predictions$Fitted, res$predictions$Residuals) ./CornerstoneR.Rcheck/00check.log:Warning in min(x) : no non-missing arguments to min; returning Inf ./CornerstoneR.Rcheck/00check.log:Warning in max(x) : no non-missing arguments to max; returning -Inf ./CornerstoneR.Rcheck/00check.log:Warning in min(x) : no non-missing arguments to min; returning Inf ./CornerstoneR.Rcheck/00check.log:Warning in max(x) : no non-missing arguments to max; returning -Inf ./CornerstoneR.Rcheck/00check.log:Error in plot.window(...) : need finite 'xlim' values ./CornerstoneR.Rcheck/00check.log:Calls: plot -> plot.default -> localWindow -> plot.window ./CornerstoneR.Rcheck/00check.log:Execution halted ./CornerstoneR.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./CornerstoneR.Rcheck/00check.log:* checking tests ... ERROR ./CornerstoneR.Rcheck/00check.log: Running ‘testthat.R’ ./CornerstoneR.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./CornerstoneR.Rcheck/00check.log:Last 13 lines of output: ./CornerstoneR.Rcheck/00check.log: Backtrace: ./CornerstoneR.Rcheck/00check.log: █ ./CornerstoneR.Rcheck/00check.log: 1. └─checkmate::expect_data_table(...) test_fitFunction.R:654:2 ./CornerstoneR.Rcheck/00check.log: 2. └─checkmate::makeExpectation(x, res, info, label) ./CornerstoneR.Rcheck/00check.log: 3. └─testthat::expect_true(...) ./CornerstoneR.Rcheck/00check.log: ── Failure (test_fitFunction.R:657:3): Multiple Groups ───────────────────────── ./CornerstoneR.Rcheck/00check.log: round(res$coeff[, 3:5]) not equal to data.table(Coeff_a = 1:4, Coeff_b = 10:7, Coeff_c = -2:1). ./CornerstoneR.Rcheck/00check.log: Column 'Coeff_a': 'is.NA' value mismatch: 0 in current 4 in target ./CornerstoneR.Rcheck/00check.log: ── Failure (test_fitFunction.R:658:3): Multiple Groups ───────────────────────── ./CornerstoneR.Rcheck/00check.log: round(res$coeff[, 6], digits = 1) not equal to data.table(Coeff_d = seq(0.6, 0.3, -0.1)). ./CornerstoneR.Rcheck/00check.log: Column 'Coeff_d': 'is.NA' value mismatch: 0 in current 4 in target ./CornerstoneR.Rcheck/00check.log: ./CornerstoneR.Rcheck/00check.log: [ FAIL 43 | WARN 0 | SKIP 0 | PASS 297 ] ./CornerstoneR.Rcheck/00check.log: Error: Test failures ./CornerstoneR.Rcheck/00check.log: Execution halted ./CornerstoneR.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./CornerstoneR.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./CornerstoneR.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./CornerstoneR.Rcheck/00check.log: ‘fitFunction.Rmd’ using ‘UTF-8’... OK ./CornerstoneR.Rcheck/00check.log: ‘matchNearestNeighbor.Rmd’ using ‘UTF-8’... OK ./CornerstoneR.Rcheck/00check.log: ‘mosaicPlot.Rmd’ using ‘UTF-8’... OK ./CornerstoneR.Rcheck/00check.log: ‘randomForest.Rmd’ using ‘UTF-8’... OK ./CornerstoneR.Rcheck/00check.log: ‘redirectDataset.Rmd’ using ‘UTF-8’... OK ./CornerstoneR.Rcheck/00check.log: ‘reshape.Rmd’ using ‘UTF-8’... OK ./CornerstoneR.Rcheck/00check.log: ‘showVersions.Rmd’ using ‘UTF-8’... OK ./CornerstoneR.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./CornerstoneR.Rcheck/00check.log:* checking PDF version of manual ... OK ./CornerstoneR.Rcheck/00check.log:* DONE ./CornerstoneR.Rcheck/00check.log:Status: 2 ERRORs doremi_1.0.0.tar.gz ./doremi.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/doremi.Rcheck’ ./doremi.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./doremi.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./doremi.Rcheck/00check.log:* using session charset: UTF-8 ./doremi.Rcheck/00check.log:* checking for file ‘doremi/DESCRIPTION’ ... OK ./doremi.Rcheck/00check.log:* checking extension type ... Package ./doremi.Rcheck/00check.log:* this is package ‘doremi’ version ‘1.0.0’ ./doremi.Rcheck/00check.log:* package encoding: UTF-8 ./doremi.Rcheck/00check.log:* checking package namespace information ... OK ./doremi.Rcheck/00check.log:* checking package dependencies ... OK ./doremi.Rcheck/00check.log:* checking if this is a source package ... OK ./doremi.Rcheck/00check.log:* checking if there is a namespace ... OK ./doremi.Rcheck/00check.log:* checking for executable files ... OK ./doremi.Rcheck/00check.log:* checking for hidden files and directories ... OK ./doremi.Rcheck/00check.log:* checking for portable file names ... OK ./doremi.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./doremi.Rcheck/00check.log:* checking whether package ‘doremi’ can be installed ... OK ./doremi.Rcheck/00check.log:* checking installed package size ... OK ./doremi.Rcheck/00check.log:* checking package directory ... OK ./doremi.Rcheck/00check.log:* checking ‘build’ directory ... OK ./doremi.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./doremi.Rcheck/00check.log:* checking top-level files ... OK ./doremi.Rcheck/00check.log:* checking for left-over files ... OK ./doremi.Rcheck/00check.log:* checking index information ... OK ./doremi.Rcheck/00check.log:* checking package subdirectories ... OK ./doremi.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./doremi.Rcheck/00check.log:* checking R files for syntax errors ... OK ./doremi.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./doremi.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./doremi.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./doremi.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./doremi.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./doremi.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./doremi.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./doremi.Rcheck/00check.log:Namespace in Imports field not imported from: ‘gridExtra’ ./doremi.Rcheck/00check.log: All declared Imports should be used. ./doremi.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./doremi.Rcheck/00check.log:* checking replacement functions ... OK ./doremi.Rcheck/00check.log:* checking foreign function calls ... OK ./doremi.Rcheck/00check.log:* checking R code for possible problems ... OK ./doremi.Rcheck/00check.log:* checking Rd files ... OK ./doremi.Rcheck/00check.log:* checking Rd metadata ... OK ./doremi.Rcheck/00check.log:* checking Rd cross-references ... OK ./doremi.Rcheck/00check.log:* checking for missing documentation entries ... OK ./doremi.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./doremi.Rcheck/00check.log:* checking Rd \usage sections ... OK ./doremi.Rcheck/00check.log:* checking Rd contents ... OK ./doremi.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./doremi.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./doremi.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./doremi.Rcheck/00check.log:* checking LazyData ... OK ./doremi.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./doremi.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./doremi.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./doremi.Rcheck/00check.log:* checking examples ... ERROR ./doremi.Rcheck/00check.log:Running examples in ‘doremi-Ex.R’ failed ./doremi.Rcheck/00check.log:The error most likely occurred in: ./doremi.Rcheck/00check.log:> ### Name: generate.panel.1order ./doremi.Rcheck/00check.log:> ### Title: Generation of first order differential equation solutions for ./doremi.Rcheck/00check.log:> ### several individuals with intra-individual and inter-individual noise ./doremi.Rcheck/00check.log:> ### Aliases: generate.panel.1order ./doremi.Rcheck/00check.log:> ### Keywords: differential-equation first-order simulation ./doremi.Rcheck/00check.log:> ./doremi.Rcheck/00check.log:> ### ** Examples ./doremi.Rcheck/00check.log:> ./doremi.Rcheck/00check.log:> generate.panel.1order(time = generate.excitation(3, 6, 2, 1, 200, 2)$t, ./doremi.Rcheck/00check.log:+ excitation = generate.excitation(3, 6, 2, 1, 200, 2)$exc, ./doremi.Rcheck/00check.log:+ y0 = 0, ./doremi.Rcheck/00check.log:+ tau = 10, ./doremi.Rcheck/00check.log:+ k = 1, ./doremi.Rcheck/00check.log:+ yeq = 0, ./doremi.Rcheck/00check.log:+ nind = 5, ./doremi.Rcheck/00check.log:+ internoise = 0.2, ./doremi.Rcheck/00check.log:+ intranoise = 1) ./doremi.Rcheck/00check.log:Error: x is not a data.table|frame. Shallow copy is a copy of the vector of column pointers (only), so is only meaningful for data.table|frame ./doremi.Rcheck/00check.log:Execution halted ./doremi.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./doremi.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./doremi.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./doremi.Rcheck/00check.log: ‘Introduction-to-doremi.Rmd’ using ‘UTF-8’... OK ./doremi.Rcheck/00check.log: ‘derivatives.Rmd’ using ‘UTF-8’... OK ./doremi.Rcheck/00check.log: ‘first-order.Rmd’ using ‘UTF-8’... OK ./doremi.Rcheck/00check.log: ‘second-order.Rmd’ using ‘UTF-8’... OK ./doremi.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./doremi.Rcheck/00check.log:Error(s) in re-building vignettes: ./doremi.Rcheck/00check.log: ... ./doremi.Rcheck/00check.log:--- re-building ‘Introduction-to-doremi.Rmd’ using rmarkdown ./doremi.Rcheck/00check.log:--- finished re-building ‘Introduction-to-doremi.Rmd’ ./doremi.Rcheck/00check.log:--- re-building ‘derivatives.Rmd’ using rmarkdown ./doremi.Rcheck/00check.log:--- finished re-building ‘derivatives.Rmd’ ./doremi.Rcheck/00check.log:--- re-building ‘first-order.Rmd’ using rmarkdown ./doremi.Rcheck/00check.log:Quitting from lines 118-119 (first-order.Rmd) ./doremi.Rcheck/00check.log:Error: processing vignette 'first-order.Rmd' failed with diagnostics: ./doremi.Rcheck/00check.log:x is not a data.table|frame. Shallow copy is a copy of the vector of column pointers (only), so is only meaningful for data.table|frame ./doremi.Rcheck/00check.log:--- failed re-building ‘first-order.Rmd’ ./doremi.Rcheck/00check.log:--- re-building ‘second-order.Rmd’ using rmarkdown ./doremi.Rcheck/00check.log:Quitting from lines 111-122 (second-order.Rmd) ./doremi.Rcheck/00check.log:Error: processing vignette 'second-order.Rmd' failed with diagnostics: ./doremi.Rcheck/00check.log:x is not a data.table|frame. Shallow copy is a copy of the vector of column pointers (only), so is only meaningful for data.table|frame ./doremi.Rcheck/00check.log:--- failed re-building ‘second-order.Rmd’ ./doremi.Rcheck/00check.log:SUMMARY: processing the following files failed: ./doremi.Rcheck/00check.log: ‘first-order.Rmd’ ‘second-order.Rmd’ ./doremi.Rcheck/00check.log:Error: Vignette re-building failed. ./doremi.Rcheck/00check.log:Execution halted ./doremi.Rcheck/00check.log:* checking PDF version of manual ... OK ./doremi.Rcheck/00check.log:* DONE ./doremi.Rcheck/00check.log:Status: 1 ERROR, 1 WARNING, 1 NOTE dvmisc_1.1.4.tar.gz ./dvmisc.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/dvmisc.Rcheck’ ./dvmisc.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./dvmisc.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./dvmisc.Rcheck/00check.log:* using session charset: UTF-8 ./dvmisc.Rcheck/00check.log:* checking for file ‘dvmisc/DESCRIPTION’ ... OK ./dvmisc.Rcheck/00check.log:* checking extension type ... Package ./dvmisc.Rcheck/00check.log:* this is package ‘dvmisc’ version ‘1.1.4’ ./dvmisc.Rcheck/00check.log:* package encoding: UTF-8 ./dvmisc.Rcheck/00check.log:* checking package namespace information ... OK ./dvmisc.Rcheck/00check.log:* checking package dependencies ... OK ./dvmisc.Rcheck/00check.log:* checking if this is a source package ... OK ./dvmisc.Rcheck/00check.log:* checking if there is a namespace ... OK ./dvmisc.Rcheck/00check.log:* checking for executable files ... OK ./dvmisc.Rcheck/00check.log:* checking for hidden files and directories ... OK ./dvmisc.Rcheck/00check.log:* checking for portable file names ... OK ./dvmisc.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./dvmisc.Rcheck/00check.log:* checking whether package ‘dvmisc’ can be installed ... OK ./dvmisc.Rcheck/00check.log:* checking installed package size ... OK ./dvmisc.Rcheck/00check.log:* checking package directory ... OK ./dvmisc.Rcheck/00check.log:* checking ‘build’ directory ... OK ./dvmisc.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./dvmisc.Rcheck/00check.log:* checking top-level files ... OK ./dvmisc.Rcheck/00check.log:* checking for left-over files ... OK ./dvmisc.Rcheck/00check.log:* checking index information ... OK ./dvmisc.Rcheck/00check.log:* checking package subdirectories ... OK ./dvmisc.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./dvmisc.Rcheck/00check.log:* checking R files for syntax errors ... OK ./dvmisc.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./dvmisc.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./dvmisc.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./dvmisc.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./dvmisc.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./dvmisc.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./dvmisc.Rcheck/00check.log:* checking dependencies in R code ... OK ./dvmisc.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./dvmisc.Rcheck/00check.log:* checking replacement functions ... OK ./dvmisc.Rcheck/00check.log:* checking foreign function calls ... OK ./dvmisc.Rcheck/00check.log:* checking R code for possible problems ... OK ./dvmisc.Rcheck/00check.log:* checking Rd files ... OK ./dvmisc.Rcheck/00check.log:* checking Rd metadata ... OK ./dvmisc.Rcheck/00check.log:* checking Rd cross-references ... OK ./dvmisc.Rcheck/00check.log:* checking for missing documentation entries ... OK ./dvmisc.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./dvmisc.Rcheck/00check.log:* checking Rd \usage sections ... OK ./dvmisc.Rcheck/00check.log:* checking Rd contents ... OK ./dvmisc.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./dvmisc.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./dvmisc.Rcheck/00check.log:* checking compiled code ... OK ./dvmisc.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./dvmisc.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./dvmisc.Rcheck/00check.log:* checking examples ... ERROR ./dvmisc.Rcheck/00check.log:Running examples in ‘dvmisc-Ex.R’ failed ./dvmisc.Rcheck/00check.log:The error most likely occurred in: ./dvmisc.Rcheck/00check.log:> ### Name: expand_grid ./dvmisc.Rcheck/00check.log:> ### Title: Similar to expand.grid but with Sequences Reversed and Ability ./dvmisc.Rcheck/00check.log:> ### to Treat Variables as Sets ./dvmisc.Rcheck/00check.log:> ### Aliases: expand_grid ./dvmisc.Rcheck/00check.log:> ./dvmisc.Rcheck/00check.log:> ### ** Examples ./dvmisc.Rcheck/00check.log:> ./dvmisc.Rcheck/00check.log:> # Simple example of expand.grid vs. expand_grid ./dvmisc.Rcheck/00check.log:> expand.grid(x = c("a", "b", "c"), y = c(1, 2), z = c(TRUE, FALSE)) ./dvmisc.Rcheck/00check.log: x y z ./dvmisc.Rcheck/00check.log:1 a 1 TRUE ./dvmisc.Rcheck/00check.log:2 b 1 TRUE ./dvmisc.Rcheck/00check.log:3 c 1 TRUE ./dvmisc.Rcheck/00check.log:4 a 2 TRUE ./dvmisc.Rcheck/00check.log:5 b 2 TRUE ./dvmisc.Rcheck/00check.log:6 c 2 TRUE ./dvmisc.Rcheck/00check.log:7 a 1 FALSE ./dvmisc.Rcheck/00check.log:8 b 1 FALSE ./dvmisc.Rcheck/00check.log:9 c 1 FALSE ./dvmisc.Rcheck/00check.log:10 a 2 FALSE ./dvmisc.Rcheck/00check.log:11 b 2 FALSE ./dvmisc.Rcheck/00check.log:12 c 2 FALSE ./dvmisc.Rcheck/00check.log:> expand_grid(x = c("a", "b", "c"), y = c(1, 2), z = c(TRUE, FALSE)) ./dvmisc.Rcheck/00check.log:Error: x is not a data.table|frame. Shallow copy is a copy of the vector of column pointers (only), so is only meaningful for data.table|frame ./dvmisc.Rcheck/00check.log:Execution halted ./dvmisc.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./dvmisc.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./dvmisc.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./dvmisc.Rcheck/00check.log: ‘dvmisc.Rmd’ using ‘UTF-8’... OK ./dvmisc.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./dvmisc.Rcheck/00check.log:* checking PDF version of manual ... OK ./dvmisc.Rcheck/00check.log:* DONE ./dvmisc.Rcheck/00check.log:Status: 1 ERROR ecochange_2.2.tar.gz ./ecochange.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/ecochange.Rcheck’ ./ecochange.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./ecochange.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./ecochange.Rcheck/00check.log:* using session charset: UTF-8 ./ecochange.Rcheck/00check.log:* checking for file ‘ecochange/DESCRIPTION’ ... OK ./ecochange.Rcheck/00check.log:* checking extension type ... Package ./ecochange.Rcheck/00check.log:* this is package ‘ecochange’ version ‘2.2’ ./ecochange.Rcheck/00check.log:* package encoding: latin1 ./ecochange.Rcheck/00check.log:* checking package namespace information ... OK ./ecochange.Rcheck/00check.log:* checking package dependencies ... OK ./ecochange.Rcheck/00check.log:* checking if this is a source package ... OK ./ecochange.Rcheck/00check.log:* checking if there is a namespace ... OK ./ecochange.Rcheck/00check.log:* checking for executable files ... OK ./ecochange.Rcheck/00check.log:* checking for hidden files and directories ... OK ./ecochange.Rcheck/00check.log:* checking for portable file names ... OK ./ecochange.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./ecochange.Rcheck/00check.log:* checking whether package ‘ecochange’ can be installed ... OK ./ecochange.Rcheck/00check.log:* checking installed package size ... OK ./ecochange.Rcheck/00check.log:* checking package directory ... OK ./ecochange.Rcheck/00check.log:* checking ‘build’ directory ... OK ./ecochange.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./ecochange.Rcheck/00check.log:* checking top-level files ... OK ./ecochange.Rcheck/00check.log:* checking for left-over files ... OK ./ecochange.Rcheck/00check.log:* checking index information ... OK ./ecochange.Rcheck/00check.log:* checking package subdirectories ... OK ./ecochange.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./ecochange.Rcheck/00check.log:* checking R files for syntax errors ... OK ./ecochange.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./ecochange.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./ecochange.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./ecochange.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./ecochange.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./ecochange.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./ecochange.Rcheck/00check.log:* checking dependencies in R code ... OK ./ecochange.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./ecochange.Rcheck/00check.log:* checking replacement functions ... OK ./ecochange.Rcheck/00check.log:* checking foreign function calls ... OK ./ecochange.Rcheck/00check.log:* checking R code for possible problems ... OK ./ecochange.Rcheck/00check.log:* checking Rd files ... OK ./ecochange.Rcheck/00check.log:* checking Rd metadata ... OK ./ecochange.Rcheck/00check.log:* checking Rd cross-references ... OK ./ecochange.Rcheck/00check.log:* checking for missing documentation entries ... OK ./ecochange.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./ecochange.Rcheck/00check.log:* checking Rd \usage sections ... OK ./ecochange.Rcheck/00check.log:* checking Rd contents ... OK ./ecochange.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./ecochange.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./ecochange.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./ecochange.Rcheck/00check.log:* checking examples ... ERROR ./ecochange.Rcheck/00check.log:Running examples in ‘ecochange-Ex.R’ failed ./ecochange.Rcheck/00check.log:The error most likely occurred in: ./ecochange.Rcheck/00check.log:> ### Name: echanges ./ecochange.Rcheck/00check.log:> ### Title: Ecosystem changes ./ecochange.Rcheck/00check.log:> ### Aliases: echanges ./ecochange.Rcheck/00check.log:> ./ecochange.Rcheck/00check.log:> ### ** Examples ./ecochange.Rcheck/00check.log:> ./ecochange.Rcheck/00check.log:> ./ecochange.Rcheck/00check.log:> ## Warnings from GDAL/PROJ are suppressed. ./ecochange.Rcheck/00check.log:> ./ecochange.Rcheck/00check.log:> ## Brick with structural Essential Biodiversity Variables covering the ./ecochange.Rcheck/00check.log:> ## extent of a location in the northern Amazon basin (Colombia): ./ecochange.Rcheck/00check.log:> path. <- system.file('amazon.grd',package = 'ecochange') ./ecochange.Rcheck/00check.log:> amazon <- suppressWarnings(brick(path.)) ./ecochange.Rcheck/00check.log:> ./ecochange.Rcheck/00check.log:> ## Changes in layers of tree-canopy cover (TC) in the 'amazon' ./ecochange.Rcheck/00check.log:> ## brick are computed: ./ecochange.Rcheck/00check.log:> suppressWarnings( ./ecochange.Rcheck/00check.log:+ def <- echanges(amazon, eco = 'TC', ./ecochange.Rcheck/00check.log:+ change = 'lossyear', ./ecochange.Rcheck/00check.log:+ eco_range = c(1,80), ./ecochange.Rcheck/00check.log:+ get_unaffected = TRUE, ./ecochange.Rcheck/00check.log:+ binary_output = FALSE, ./ecochange.Rcheck/00check.log:+ mc.cores = 2) ./ecochange.Rcheck/00check.log:+ ) ./ecochange.Rcheck/00check.log:[1] "'eco' has length > 1: matching names of 'eco' with values in 'change_vals'..." ./ecochange.Rcheck/00check.log:> ./ecochange.Rcheck/00check.log:> ## Function 'plotebv' allows comparing rasters using a common scale bar: ./ecochange.Rcheck/00check.log:> suppressWarnings( ./ecochange.Rcheck/00check.log:+ plotebv(def) ./ecochange.Rcheck/00check.log:+ ) ./ecochange.Rcheck/00check.log:Error in (function (classes, fdef, mtable) : ./ecochange.Rcheck/00check.log: unable to find an inherited method for function ‘xmin’ for signature ‘"Extent"’ ./ecochange.Rcheck/00check.log:Execution halted ./ecochange.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./ecochange.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./ecochange.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./ecochange.Rcheck/00check.log: ‘ecochange_vignette.Rmd’ using ‘UTF-8’... OK ./ecochange.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./ecochange.Rcheck/00check.log:Error(s) in re-building vignettes: ./ecochange.Rcheck/00check.log:--- re-building ‘ecochange_vignette.Rmd’ using rmarkdown ./ecochange.Rcheck/00check.log:Loading required package: ecochange ./ecochange.Rcheck/00check.log:Loading required package: raster ./ecochange.Rcheck/00check.log:Loading required package: sp ./ecochange.Rcheck/00check.log:Loading required package: rgeos ./ecochange.Rcheck/00check.log:rgeos version: 0.5-8, (SVN revision 679) ./ecochange.Rcheck/00check.log: GEOS runtime version: 3.9.0-CAPI-1.16.2 ./ecochange.Rcheck/00check.log: Please note that rgeos will be retired by the end of 2023, ./ecochange.Rcheck/00check.log:plan transition to sf functions using GEOS at your earliest convenience. ./ecochange.Rcheck/00check.log: GEOS using OverlayNG ./ecochange.Rcheck/00check.log: Linking to sp version: 1.4-5 ./ecochange.Rcheck/00check.log: Polygon checking: TRUE ./ecochange.Rcheck/00check.log:Loading required package: ggplot2 ./ecochange.Rcheck/00check.log:Loading required package: sf ./ecochange.Rcheck/00check.log:Linking to GEOS 3.9.0, GDAL 3.2.2, PROJ 7.2.1 ./ecochange.Rcheck/00check.log:Loading required package: gdalUtils ./ecochange.Rcheck/00check.log:Attaching package: 'gdalUtils' ./ecochange.Rcheck/00check.log:The following object is masked from 'package:sf': ./ecochange.Rcheck/00check.log: gdal_rasterize ./ecochange.Rcheck/00check.log:Package 'ecochange' version 2.2 ./ecochange.Rcheck/00check.log:Type 'citation("ecochange")' for citing this R package in publications. ./ecochange.Rcheck/00check.log:Loading required package: rgdal ./ecochange.Rcheck/00check.log:Please note that rgdal will be retired by the end of 2023, ./ecochange.Rcheck/00check.log:plan transition to sf/stars/terra functions using GDAL and PROJ ./ecochange.Rcheck/00check.log:at your earliest convenience. ./ecochange.Rcheck/00check.log:rgdal: version: 1.5-27, (SVN revision 1148) ./ecochange.Rcheck/00check.log:Geospatial Data Abstraction Library extensions to R successfully loaded ./ecochange.Rcheck/00check.log:Loaded GDAL runtime: GDAL 3.2.2, released 2021/03/05 ./ecochange.Rcheck/00check.log:Path to GDAL shared files: /usr/share/gdal ./ecochange.Rcheck/00check.log:GDAL binary built with GEOS: TRUE ./ecochange.Rcheck/00check.log:Loaded PROJ runtime: Rel. 7.2.1, January 1st, 2021, [PJ_VERSION: 721] ./ecochange.Rcheck/00check.log:Path to PROJ shared files: /home/mdowle/.local/share/proj:/usr/share/proj ./ecochange.Rcheck/00check.log:PROJ CDN enabled: FALSE ./ecochange.Rcheck/00check.log:Linking to sp version:1.4-5 ./ecochange.Rcheck/00check.log:To mute warnings of possible GDAL/OSR exportToProj4() degradation, ./ecochange.Rcheck/00check.log:use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal. ./ecochange.Rcheck/00check.log:Loading required package: parallel ./ecochange.Rcheck/00check.log:Loading required package: R.utils ./ecochange.Rcheck/00check.log:Loading required package: R.oo ./ecochange.Rcheck/00check.log:Loading required package: R.methodsS3 ./ecochange.Rcheck/00check.log:R.methodsS3 v1.8.1 (2020-08-26 16:20:06 UTC) successfully loaded. See ?R.methodsS3 for help. ./ecochange.Rcheck/00check.log:R.oo v1.24.0 (2020-08-26 16:11:58 UTC) successfully loaded. See ?R.oo for help. ./ecochange.Rcheck/00check.log:Attaching package: 'R.oo' ./ecochange.Rcheck/00check.log:The following object is masked from 'package:R.methodsS3': ./ecochange.Rcheck/00check.log: throw ./ecochange.Rcheck/00check.log:The following object is masked from 'package:rgdal': ./ecochange.Rcheck/00check.log: getDescription ./ecochange.Rcheck/00check.log:The following objects are masked from 'package:raster': ./ecochange.Rcheck/00check.log: extend, trim ./ecochange.Rcheck/00check.log:The following objects are masked from 'package:methods': ./ecochange.Rcheck/00check.log: getClasses, getMethods ./ecochange.Rcheck/00check.log:The following objects are masked from 'package:base': ./ecochange.Rcheck/00check.log: attach, detach, load, save ./ecochange.Rcheck/00check.log:R.utils v2.11.0 (2021-09-26 08:30:02 UTC) successfully loaded. See ?R.utils for help. ./ecochange.Rcheck/00check.log:Attaching package: 'R.utils' ./ecochange.Rcheck/00check.log:The following objects are masked from 'package:raster': ./ecochange.Rcheck/00check.log: extract, resample ./ecochange.Rcheck/00check.log:The following object is masked from 'package:utils': ./ecochange.Rcheck/00check.log: timestamp ./ecochange.Rcheck/00check.log:The following objects are masked from 'package:base': ./ecochange.Rcheck/00check.log: cat, commandArgs, getOption, inherits, isOpen, nullfile, parse, ./ecochange.Rcheck/00check.log: warnings ./ecochange.Rcheck/00check.log:Loading required package: rvest ./ecochange.Rcheck/00check.log:Loading required package: xml2 ./ecochange.Rcheck/00check.log:Loading required package: tidyverse ./ecochange.Rcheck/00check.log:── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ── ./ecochange.Rcheck/00check.log:✔ tibble 3.1.5 ✔ dplyr 1.0.7 ./ecochange.Rcheck/00check.log:✔ tidyr 1.1.4 ✔ stringr 1.4.0 ./ecochange.Rcheck/00check.log:✔ readr 2.0.2 ✔ forcats 0.5.1 ./ecochange.Rcheck/00check.log:✔ purrr 0.3.4 ./ecochange.Rcheck/00check.log:── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ./ecochange.Rcheck/00check.log:✖ tidyr::extract() masks R.utils::extract(), raster::extract() ./ecochange.Rcheck/00check.log:✖ dplyr::filter() masks stats::filter() ./ecochange.Rcheck/00check.log:✖ readr::guess_encoding() masks rvest::guess_encoding() ./ecochange.Rcheck/00check.log:✖ dplyr::lag() masks stats::lag() ./ecochange.Rcheck/00check.log:✖ dplyr::select() masks raster::select() ./ecochange.Rcheck/00check.log:Loading required package: landscapemetrics ./ecochange.Rcheck/00check.log:Loading required package: httr ./ecochange.Rcheck/00check.log:Loading required package: getPass ./ecochange.Rcheck/00check.log:Loading required package: gdalUtilities ./ecochange.Rcheck/00check.log:Attaching package: 'gdalUtilities' ./ecochange.Rcheck/00check.log:The following objects are masked from 'package:gdalUtils': ./ecochange.Rcheck/00check.log: gdal_grid, gdal_rasterize, gdal_translate, gdalbuildvrt, gdaldem, ./ecochange.Rcheck/00check.log: gdalinfo, gdalwarp, nearblack, ogr2ogr ./ecochange.Rcheck/00check.log:The following object is masked from 'package:sf': ./ecochange.Rcheck/00check.log: gdal_rasterize ./ecochange.Rcheck/00check.log:Loading required package: viridis ./ecochange.Rcheck/00check.log:Loading required package: viridisLite ./ecochange.Rcheck/00check.log:Loading required package: rasterVis ./ecochange.Rcheck/00check.log:Loading required package: terra ./ecochange.Rcheck/00check.log:terra version 1.4.9 ./ecochange.Rcheck/00check.log:Attaching package: 'terra' ./ecochange.Rcheck/00check.log:The following object is masked from 'package:dplyr': ./ecochange.Rcheck/00check.log: src ./ecochange.Rcheck/00check.log:The following object is masked from 'package:tidyr': ./ecochange.Rcheck/00check.log: extract ./ecochange.Rcheck/00check.log:The following objects are masked from 'package:R.utils': ./ecochange.Rcheck/00check.log: draw, extract, resample, wrap ./ecochange.Rcheck/00check.log:The following objects are masked from 'package:R.oo': ./ecochange.Rcheck/00check.log: extend, trim ./ecochange.Rcheck/00check.log:The following object is masked from 'package:rgdal': ./ecochange.Rcheck/00check.log: project ./ecochange.Rcheck/00check.log:The following objects are masked from 'package:raster': ./ecochange.Rcheck/00check.log: RGB, adjacent, animate, area, boundaries, buffer, cellFromRowCol, ./ecochange.Rcheck/00check.log: cellFromRowColCombine, cellFromXY, clamp, click, colFromCell, ./ecochange.Rcheck/00check.log: colFromX, cover, crop, crosstab, crs, crs<-, distance, erase, ./ecochange.Rcheck/00check.log: extend, extract, flip, focal, freq, geom, hasValues, inMemory, ./ecochange.Rcheck/00check.log: init, interpolate, mask, modal, mosaic, ncell, ncol<-, nrow<-, ./ecochange.Rcheck/00check.log: origin, origin<-, plotRGB, rasterize, readStart, readStop, rectify, ./ecochange.Rcheck/00check.log: res, res<-, resample, rotate, rowColFromCell, rowFromCell, ./ecochange.Rcheck/00check.log: rowFromY, setMinMax, setValues, shift, stretch, symdif, terrain, ./ecochange.Rcheck/00check.log: trim, values, values<-, writeRaster, writeStart, writeStop, ./ecochange.Rcheck/00check.log: writeValues, xFromCell, xFromCol, xmax, xmax<-, xmin, xmin<-, xres, ./ecochange.Rcheck/00check.log: xyFromCell, yFromCell, yFromRow, ymax, ymax<-, ymin, ymin<-, yres, ./ecochange.Rcheck/00check.log: zonal, zoom ./ecochange.Rcheck/00check.log:Loading required package: lattice ./ecochange.Rcheck/00check.log:Loading required package: latticeExtra ./ecochange.Rcheck/00check.log:Attaching package: 'latticeExtra' ./ecochange.Rcheck/00check.log:The following object is masked from 'package:ggplot2': ./ecochange.Rcheck/00check.log: layer ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::init' by 'terra::init' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::writeStop' by 'terra::writeStop' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::extract' by 'terra::extract' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::yFromCell' by 'terra::yFromCell' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::adjacent' by 'terra::adjacent' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::cellFromRowColCombine' by 'terra::cellFromRowColCombine' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::RGB' by 'terra::RGB' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::nrow<-' by 'terra::nrow<-' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::rotate' by 'terra::rotate' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::click' by 'terra::click' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::readStart' by 'terra::readStart' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::ymax<-' by 'terra::ymax<-' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::mosaic' by 'terra::mosaic' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::yres' by 'terra::yres' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::xres' by 'terra::xres' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::ymin' by 'terra::ymin' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::mask' by 'terra::mask' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::xmin' by 'terra::xmin' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::animate' by 'terra::animate' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::cellFromRowCol' by 'terra::cellFromRowCol' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::hasValues' by 'terra::hasValues' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::rasterize' by 'terra::rasterize' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::writeStart' by 'terra::writeStart' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::setValues' by 'terra::setValues' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::resample' by 'terra::resample' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::xyFromCell' by 'terra::xyFromCell' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::stretch' by 'terra::stretch' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::cover' by 'terra::cover' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::writeValues' by 'terra::writeValues' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::values' by 'terra::values' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::cellFromXY' by 'terra::cellFromXY' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::xmin<-' by 'terra::xmin<-' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::modal' by 'terra::modal' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::res' by 'terra::res' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::freq' by 'terra::freq' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::ncell' by 'terra::ncell' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::trim' by 'terra::trim' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::area' by 'terra::area' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::erase' by 'terra::erase' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::writeRaster' by 'terra::writeRaster' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::res<-' by 'terra::res<-' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::extend' by 'terra::extend' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::yFromRow' by 'terra::yFromRow' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::crs' by 'terra::crs' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::clamp' by 'terra::clamp' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::colFromCell' by 'terra::colFromCell' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::zonal' by 'terra::zonal' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::boundaries' by 'terra::boundaries' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::symdif' by 'terra::symdif' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::ncol<-' by 'terra::ncol<-' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::origin' by 'terra::origin' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::rowColFromCell' by 'terra::rowColFromCell' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::terrain' by 'terra::terrain' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::geom' by 'terra::geom' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::xFromCell' by 'terra::xFromCell' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::crs<-' by 'terra::crs<-' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::rowFromCell' by 'terra::rowFromCell' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::inMemory' by 'terra::inMemory' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::xmax<-' by 'terra::xmax<-' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::crosstab' by 'terra::crosstab' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::zoom' by 'terra::zoom' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::values<-' by 'terra::values<-' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::setMinMax' by 'terra::setMinMax' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::distance' by 'terra::distance' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::readStop' by 'terra::readStop' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::origin<-' by 'terra::origin<-' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::flip' by 'terra::flip' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::crop' by 'terra::crop' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::xFromCol' by 'terra::xFromCol' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::interpolate' by 'terra::interpolate' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::shift' by 'terra::shift' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::focal' by 'terra::focal' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::buffer' by 'terra::buffer' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::ymin<-' by 'terra::ymin<-' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::colFromX' by 'terra::colFromX' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::ymax' by 'terra::ymax' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::rectify' by 'terra::rectify' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::xmax' by 'terra::xmax' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::rowFromY' by 'terra::rowFromY' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Warning: replacing previous import 'raster::plotRGB' by 'terra::plotRGB' when loading 'rasterVis' ./ecochange.Rcheck/00check.log:Loading required package: rlang ./ecochange.Rcheck/00check.log:Attaching package: 'rlang' ./ecochange.Rcheck/00check.log:The following objects are masked from 'package:purrr': ./ecochange.Rcheck/00check.log: %@%, as_function, flatten, flatten_chr, flatten_dbl, flatten_int, ./ecochange.Rcheck/00check.log: flatten_lgl, flatten_raw, invoke, list_along, modify, prepend, ./ecochange.Rcheck/00check.log: splice ./ecochange.Rcheck/00check.log:The following object is masked from 'package:xml2': ./ecochange.Rcheck/00check.log: as_list ./ecochange.Rcheck/00check.log:The following object is masked from 'package:R.utils': ./ecochange.Rcheck/00check.log: env ./ecochange.Rcheck/00check.log:The following objects are masked from 'package:R.oo': ./ecochange.Rcheck/00check.log: abort, ll ./ecochange.Rcheck/00check.log:Loading required package: rasterDT ./ecochange.Rcheck/00check.log:Loading required package: data.table ./ecochange.Rcheck/00check.log:Attaching package: 'data.table' ./ecochange.Rcheck/00check.log:The following object is masked from 'package:rlang': ./ecochange.Rcheck/00check.log: := ./ecochange.Rcheck/00check.log:The following objects are masked from 'package:terra': ./ecochange.Rcheck/00check.log: copy, shift ./ecochange.Rcheck/00check.log:The following objects are masked from 'package:dplyr': ./ecochange.Rcheck/00check.log: between, first, last ./ecochange.Rcheck/00check.log:The following object is masked from 'package:purrr': ./ecochange.Rcheck/00check.log: transpose ./ecochange.Rcheck/00check.log:The following object is masked from 'package:raster': ./ecochange.Rcheck/00check.log: shift ./ecochange.Rcheck/00check.log:rsp2ebv package:ecochange R Documentation ./ecochange.Rcheck/00check.log:_I_n_t_e_g_r_a_t_e _r_e_m_o_t_e _s_e_n_s_i_n_g _p_r_o_d_u_c_t_s ./ecochange.Rcheck/00check.log:_D_e_s_c_r_i_p_t_i_o_n: ./ecochange.Rcheck/00check.log: This function integrates ecosystem remote sensing products and ./ecochange.Rcheck/00check.log: produces raster-data sections with the cell values enclosed in a ./ecochange.Rcheck/00check.log: region of interest. ./ecochange.Rcheck/00check.log:_U_s_a_g_e: ./ecochange.Rcheck/00check.log: rsp2ebv(ps = NULL, ..., ./ecochange.Rcheck/00check.log: lyrs = NULL, path, ./ecochange.Rcheck/00check.log: sr, ofr = c(30, 30), ./ecochange.Rcheck/00check.log: mc.cores = round(detectCores() * ./ecochange.Rcheck/00check.log: 0.6, 0)) ./ecochange.Rcheck/00check.log: ./ecochange.Rcheck/00check.log:_A_r_g_u_m_e_n_t_s: ./ecochange.Rcheck/00check.log: ps: 'SpatialPolygonsDataFrame'; or 'character'; or 'NULL'. Region ./ecochange.Rcheck/00check.log: of interest. This can be whether 1) a polygon geometry; or 2) ./ecochange.Rcheck/00check.log: the name of a 'GADM' unit (see 'getGADM'); or 3) a 'NULL' ./ecochange.Rcheck/00check.log: value. Default 'NULL' makes the function to print a list of ./ecochange.Rcheck/00check.log: 'GADM' units. ./ecochange.Rcheck/00check.log: ...: If 'ps' is a 'GADM' unit then additional arguments in ./ecochange.Rcheck/00check.log: 'getGADM' can be specified here. ./ecochange.Rcheck/00check.log: lyrs: 'character'. Names of the ecosystem earth-observation ./ecochange.Rcheck/00check.log: products. If 'NULL' then a list of products is printed, see ./ecochange.Rcheck/00check.log: 'listGP'. Default 'NULL'. ./ecochange.Rcheck/00check.log: path: 'character'. Path name indicating where the variables are ./ecochange.Rcheck/00check.log: stored. If missing then a folder named as ''ecochange'' ./ecochange.Rcheck/00check.log: located in a current temporary directory is used. ./ecochange.Rcheck/00check.log: sr: 'character'. 'PROJ.4' description of the target coordinate ./ecochange.Rcheck/00check.log: reference system. If missing then the target layers are ./ecochange.Rcheck/00check.log: projected to metric system 'UTM'. ./ecochange.Rcheck/00check.log: ofr: 'numeric'. 'c(xres,yres)'. Output file resolution (in target ./ecochange.Rcheck/00check.log: georeferenced units). Default 'c(30,30)' m2. ./ecochange.Rcheck/00check.log:mc.cores: 'numeric'. The number of cores. Default uses around 60 ./ecochange.Rcheck/00check.log: percent of the cores. ./ecochange.Rcheck/00check.log:_D_e_t_a_i_l_s: ./ecochange.Rcheck/00check.log: This function implements ''gdalUtils'' so it assumes the user has ./ecochange.Rcheck/00check.log: a working GDAL installation on their system. From the ./ecochange.Rcheck/00check.log: documentation: "If the ''gdalUtils_gdalPath'' option has been set ./ecochange.Rcheck/00check.log: (usually by ''gdal_setInstallation''), the GDAL found in that ./ecochange.Rcheck/00check.log: 'path' will be used. If nothing is found, ''gdal_setInstallation'' ./ecochange.Rcheck/00check.log: will be executed to attempt to find a working GDAL that has the ./ecochange.Rcheck/00check.log: right drivers as specified with the ''of'' (output format) ./ecochange.Rcheck/00check.log: parameter", see example below. ./ecochange.Rcheck/00check.log:_V_a_l_u_e: ./ecochange.Rcheck/00check.log: 'RasterStack' or 'list'. ./ecochange.Rcheck/00check.log:_A_u_t_h_o_r(_s): ./ecochange.Rcheck/00check.log: Wilson Lara Henao [aut, cre], Victor ./ecochange.Rcheck/00check.log: Gutierrez-Velez [aut], Ivan Gonzalez [aut], Maria C. Londono [aut] ./ecochange.Rcheck/00check.log:_R_e_f_e_r_e_n_c_e_s: ./ecochange.Rcheck/00check.log: Jetz, W., McGeoch, M. A., Guralnick, R., Ferrier, S., Beck, J., ./ecochange.Rcheck/00check.log: Costello, M. J., ... & Meyer, C. (2019). Essential biodiversity ./ecochange.Rcheck/00check.log: variables for mapping and monitoring species populations. Nature ./ecochange.Rcheck/00check.log: Ecology & Evolution, 3(4), 539-551. ./ecochange.Rcheck/00check.log: O'Connor, B., Secades, C., Penner, J., Sonnenschein, R., Skidmore, ./ecochange.Rcheck/00check.log: A., Burgess, N. D., & Hutton, J. M. (2015). Earth observation as a ./ecochange.Rcheck/00check.log: tool for tracking progress towards the Aichi Biodiversity Targets. ./ecochange.Rcheck/00check.log: Remote sensing in ecology and conservation, 1(1), 19-28. ./ecochange.Rcheck/00check.log: Skidmore, A. K., & Pettorelli, N. (2015). Agree on biodiversity ./ecochange.Rcheck/00check.log: metrics to track from space: Ecologists and space agencies must ./ecochange.Rcheck/00check.log: forge a global monitoring strategy. Nature, 523(7561), 403-406. ./ecochange.Rcheck/00check.log:_E_x_a_m_p_l_e_s: ./ecochange.Rcheck/00check.log: ## First, we'll check to make sure there is a valid GDAL ./ecochange.Rcheck/00check.log: ## installation (from 'gdalUtils): ./ecochange.Rcheck/00check.log: ./ecochange.Rcheck/00check.log: ./ecochange.Rcheck/00check.log: gdalUtils::gdal_setInstallation() ./ecochange.Rcheck/00check.log: valid_install <- !is.null(getOption("gdalUtils_gdalPath")) ./ecochange.Rcheck/00check.log: ./ecochange.Rcheck/00check.log: ./ecochange.Rcheck/00check.log: ## Warnings from GDAL/PROJ are suppressed. ./ecochange.Rcheck/00check.log: ./ecochange.Rcheck/00check.log: ## A Global Surface Water layer ('seasonality') covering the extent of a ./ecochange.Rcheck/00check.log: ## Colombian municipality Cartagena del Chairá is formated into an ./ecochange.Rcheck/00check.log: ## spatial EBV: ./ecochange.Rcheck/00check.log: load(system.file('cchaira_roi.RData',package = 'ecochange')) ./ecochange.Rcheck/00check.log: ./ecochange.Rcheck/00check.log: ./ecochange.Rcheck/00check.log: suppressWarnings( ./ecochange.Rcheck/00check.log: rsp_cchaira <- getrsp(cchaira_roi, ./ecochange.Rcheck/00check.log: lyrs = 'seasonality', mc.cores = 2, path = tempdir()) ./ecochange.Rcheck/00check.log: ) ./ecochange.Rcheck/00check.log: ./ecochange.Rcheck/00check.log: file.exists(rsp_cchaira) ./ecochange.Rcheck/00check.log: ./ecochange.Rcheck/00check.log: suppressWarnings( ./ecochange.Rcheck/00check.log: season_cchaira <- rsp2ebv(cchaira_roi, ./ecochange.Rcheck/00check.log: lyrs = 'seasonality', path = tempdir()) ./ecochange.Rcheck/00check.log: ) ./ecochange.Rcheck/00check.log: ./ecochange.Rcheck/00check.log: suppressWarnings( ./ecochange.Rcheck/00check.log: plotebv(season_cchaira) ./ecochange.Rcheck/00check.log: ) ./ecochange.Rcheck/00check.log: ./ecochange.Rcheck/00check.log:trying URL 'https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_COL_2_sp.rds' ./ecochange.Rcheck/00check.log:Content type 'text/html; charset=iso-8859-1' length 1159816 bytes (1.1 MB) ./ecochange.Rcheck/00check.log:================================================== ./ecochange.Rcheck/00check.log:downloaded 1.1 MB ./ecochange.Rcheck/00check.log:Quitting from lines 63-66 (ecochange_vignette.Rmd) ./ecochange.Rcheck/00check.log:Error: processing vignette 'ecochange_vignette.Rmd' failed with diagnostics: ./ecochange.Rcheck/00check.log:unable to find an inherited method for function 'xmin' for signature '"Extent"' ./ecochange.Rcheck/00check.log:--- failed re-building ‘ecochange_vignette.Rmd’ ./ecochange.Rcheck/00check.log:SUMMARY: processing the following file failed: ./ecochange.Rcheck/00check.log: ‘ecochange_vignette.Rmd’ ./ecochange.Rcheck/00check.log:Error: Vignette re-building failed. ./ecochange.Rcheck/00check.log:Execution halted ./ecochange.Rcheck/00check.log:* checking PDF version of manual ... OK ./ecochange.Rcheck/00check.log:* DONE ./ecochange.Rcheck/00check.log:Status: 1 ERROR, 1 WARNING EIX_1.2.0.tar.gz ./EIX.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/EIX.Rcheck’ ./EIX.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./EIX.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./EIX.Rcheck/00check.log:* using session charset: UTF-8 ./EIX.Rcheck/00check.log:* checking for file ‘EIX/DESCRIPTION’ ... OK ./EIX.Rcheck/00check.log:* this is package ‘EIX’ version ‘1.2.0’ ./EIX.Rcheck/00check.log:* package encoding: UTF-8 ./EIX.Rcheck/00check.log:* checking package namespace information ... OK ./EIX.Rcheck/00check.log:* checking package dependencies ... OK ./EIX.Rcheck/00check.log:* checking if this is a source package ... OK ./EIX.Rcheck/00check.log:* checking if there is a namespace ... OK ./EIX.Rcheck/00check.log:* checking for executable files ... OK ./EIX.Rcheck/00check.log:* checking for hidden files and directories ... OK ./EIX.Rcheck/00check.log:* checking for portable file names ... OK ./EIX.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./EIX.Rcheck/00check.log:* checking whether package ‘EIX’ can be installed ... OK ./EIX.Rcheck/00check.log:* checking installed package size ... OK ./EIX.Rcheck/00check.log:* checking package directory ... OK ./EIX.Rcheck/00check.log:* checking ‘build’ directory ... OK ./EIX.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./EIX.Rcheck/00check.log:* checking top-level files ... OK ./EIX.Rcheck/00check.log:* checking for left-over files ... OK ./EIX.Rcheck/00check.log:* checking index information ... OK ./EIX.Rcheck/00check.log:* checking package subdirectories ... OK ./EIX.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./EIX.Rcheck/00check.log:* checking R files for syntax errors ... OK ./EIX.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./EIX.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./EIX.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./EIX.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./EIX.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./EIX.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./EIX.Rcheck/00check.log:* checking dependencies in R code ... OK ./EIX.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./EIX.Rcheck/00check.log:* checking replacement functions ... OK ./EIX.Rcheck/00check.log:* checking foreign function calls ... OK ./EIX.Rcheck/00check.log:* checking R code for possible problems ... OK ./EIX.Rcheck/00check.log:* checking Rd files ... OK ./EIX.Rcheck/00check.log:* checking Rd metadata ... OK ./EIX.Rcheck/00check.log:* checking Rd cross-references ... OK ./EIX.Rcheck/00check.log:* checking for missing documentation entries ... OK ./EIX.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./EIX.Rcheck/00check.log:* checking Rd \usage sections ... OK ./EIX.Rcheck/00check.log:* checking Rd contents ... OK ./EIX.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./EIX.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./EIX.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./EIX.Rcheck/00check.log:* checking LazyData ... OK ./EIX.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./EIX.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./EIX.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./EIX.Rcheck/00check.log:* checking examples ... ERROR ./EIX.Rcheck/00check.log:Running examples in ‘EIX-Ex.R’ failed ./EIX.Rcheck/00check.log:The error most likely occurred in: ./EIX.Rcheck/00check.log:> ### Name: importance ./EIX.Rcheck/00check.log:> ### Title: Importance of variables and interactions in the model ./EIX.Rcheck/00check.log:> ### Aliases: importance ./EIX.Rcheck/00check.log:> ./EIX.Rcheck/00check.log:> ### ** Examples ./EIX.Rcheck/00check.log:> ./EIX.Rcheck/00check.log:> library("EIX") ./EIX.Rcheck/00check.log:> library("Matrix") ./EIX.Rcheck/00check.log:> sm <- sparse.model.matrix(left ~ . - 1, data = HR_data) ./EIX.Rcheck/00check.log:> ./EIX.Rcheck/00check.log:> library("xgboost") ./EIX.Rcheck/00check.log:> param <- list(objective = "binary:logistic", max_depth = 2) ./EIX.Rcheck/00check.log:> xgb_model <- xgboost(sm, params = param, label = HR_data[, left] == 1, nrounds = 25, verbose=0) ./EIX.Rcheck/00check.log:[22:28:07] WARNING: amalgamation/../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior. ./EIX.Rcheck/00check.log:> ./EIX.Rcheck/00check.log:> imp <- importance(xgb_model, sm, option = "both") ./EIX.Rcheck/00check.log:> imp ./EIX.Rcheck/00check.log:Error: x is not a data.table|frame. Shallow copy is a copy of the vector of column pointers (only), so is only meaningful for data.table|frame ./EIX.Rcheck/00check.log:Execution halted ./EIX.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./EIX.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./EIX.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./EIX.Rcheck/00check.log: ‘EIX.Rmd’ using ‘UTF-8’... OK ./EIX.Rcheck/00check.log: ‘titanic_data.Rmd’ using ‘UTF-8’... OK ./EIX.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./EIX.Rcheck/00check.log:Error(s) in re-building vignettes: ./EIX.Rcheck/00check.log: ... ./EIX.Rcheck/00check.log:--- re-building ‘EIX.Rmd’ using rmarkdown ./EIX.Rcheck/00check.log: [[ suppressing 19 column names 'satisfaction_level', 'last_evaluation', 'number_project' ... ]] ./EIX.Rcheck/00check.log:Quitting from lines 84-87 (EIX.Rmd) ./EIX.Rcheck/00check.log:Error: processing vignette 'EIX.Rmd' failed with diagnostics: ./EIX.Rcheck/00check.log:x is not a data.table|frame. Shallow copy is a copy of the vector of column pointers (only), so is only meaningful for data.table|frame ./EIX.Rcheck/00check.log:--- failed re-building ‘EIX.Rmd’ ./EIX.Rcheck/00check.log:--- re-building ‘titanic_data.Rmd’ using rmarkdown ./EIX.Rcheck/00check.log:Warning: ggrepel: 4 unlabeled data points (too many overlaps). Consider increasing max.overlaps ./EIX.Rcheck/00check.log:Quitting from lines 59-62 (titanic_data.Rmd) ./EIX.Rcheck/00check.log:Error: processing vignette 'titanic_data.Rmd' failed with diagnostics: ./EIX.Rcheck/00check.log:x is not a data.table|frame. Shallow copy is a copy of the vector of column pointers (only), so is only meaningful for data.table|frame ./EIX.Rcheck/00check.log:--- failed re-building ‘titanic_data.Rmd’ ./EIX.Rcheck/00check.log:SUMMARY: processing the following files failed: ./EIX.Rcheck/00check.log: ‘EIX.Rmd’ ‘titanic_data.Rmd’ ./EIX.Rcheck/00check.log:Error: Vignette re-building failed. ./EIX.Rcheck/00check.log:Execution halted ./EIX.Rcheck/00check.log:* checking PDF version of manual ... OK ./EIX.Rcheck/00check.log:* DONE ./EIX.Rcheck/00check.log:Status: 1 ERROR, 1 WARNING getDTeval_0.0.2.tar.gz ./getDTeval.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/getDTeval.Rcheck’ ./getDTeval.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./getDTeval.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./getDTeval.Rcheck/00check.log:* using session charset: UTF-8 ./getDTeval.Rcheck/00check.log:* checking for file ‘getDTeval/DESCRIPTION’ ... OK ./getDTeval.Rcheck/00check.log:* this is package ‘getDTeval’ version ‘0.0.2’ ./getDTeval.Rcheck/00check.log:* package encoding: UTF-8 ./getDTeval.Rcheck/00check.log:* checking package namespace information ... OK ./getDTeval.Rcheck/00check.log:* checking package dependencies ... OK ./getDTeval.Rcheck/00check.log:* checking if this is a source package ... OK ./getDTeval.Rcheck/00check.log:* checking if there is a namespace ... OK ./getDTeval.Rcheck/00check.log:* checking for executable files ... OK ./getDTeval.Rcheck/00check.log:* checking for hidden files and directories ... OK ./getDTeval.Rcheck/00check.log:* checking for portable file names ... OK ./getDTeval.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./getDTeval.Rcheck/00check.log:* checking whether package ‘getDTeval’ can be installed ... OK ./getDTeval.Rcheck/00check.log:* checking installed package size ... OK ./getDTeval.Rcheck/00check.log:* checking package directory ... OK ./getDTeval.Rcheck/00check.log:* checking ‘build’ directory ... OK ./getDTeval.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./getDTeval.Rcheck/00check.log:* checking top-level files ... OK ./getDTeval.Rcheck/00check.log:* checking for left-over files ... OK ./getDTeval.Rcheck/00check.log:* checking index information ... OK ./getDTeval.Rcheck/00check.log:* checking package subdirectories ... OK ./getDTeval.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./getDTeval.Rcheck/00check.log:* checking R files for syntax errors ... OK ./getDTeval.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./getDTeval.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./getDTeval.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./getDTeval.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./getDTeval.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./getDTeval.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./getDTeval.Rcheck/00check.log:* checking dependencies in R code ... OK ./getDTeval.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./getDTeval.Rcheck/00check.log:* checking replacement functions ... OK ./getDTeval.Rcheck/00check.log:* checking foreign function calls ... OK ./getDTeval.Rcheck/00check.log:* checking R code for possible problems ... OK ./getDTeval.Rcheck/00check.log:* checking Rd files ... OK ./getDTeval.Rcheck/00check.log:* checking Rd metadata ... OK ./getDTeval.Rcheck/00check.log:* checking Rd cross-references ... OK ./getDTeval.Rcheck/00check.log:* checking for missing documentation entries ... OK ./getDTeval.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./getDTeval.Rcheck/00check.log:* checking Rd \usage sections ... OK ./getDTeval.Rcheck/00check.log:* checking Rd contents ... OK ./getDTeval.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./getDTeval.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./getDTeval.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./getDTeval.Rcheck/00check.log:* checking examples ... OK ./getDTeval.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./getDTeval.Rcheck/00check.log:* checking tests ... ERROR ./getDTeval.Rcheck/00check.log: Running ‘testthat.R’ ./getDTeval.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./getDTeval.Rcheck/00check.log:Complete output: ./getDTeval.Rcheck/00check.log: > library(testthat) ./getDTeval.Rcheck/00check.log: > library(getDTeval) ./getDTeval.Rcheck/00check.log: > ./getDTeval.Rcheck/00check.log: > test_check("getDTeval") ./getDTeval.Rcheck/00check.log: ══ Failed tests ════════════════════════════════════════════════════════════════ ./getDTeval.Rcheck/00check.log: ── Failure (test-getDteval.R:68:2): create a new column ──────────────────────── ./getDTeval.Rcheck/00check.log: getDTeval(...) not equal to formulaic::snack.dat[, `:=`(age_decades, floor(get(age.name)/10))]. ./getDTeval.Rcheck/00check.log: Datasets has different number of (non-excluded) attributes: target 2, current 3 ./getDTeval.Rcheck/00check.log: ./getDTeval.Rcheck/00check.log: [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ] ./getDTeval.Rcheck/00check.log: Error: Test failures ./getDTeval.Rcheck/00check.log: Execution halted ./getDTeval.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./getDTeval.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./getDTeval.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./getDTeval.Rcheck/00check.log: ‘Introduction_to_getDTeval.Rmd’ using ‘UTF-8’... OK ./getDTeval.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./getDTeval.Rcheck/00check.log:* checking PDF version of manual ... OK ./getDTeval.Rcheck/00check.log:* DONE ./getDTeval.Rcheck/00check.log:Status: 1 ERROR iemisc_0.9.9.tar.gz ./iemisc.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/iemisc.Rcheck’ ./iemisc.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./iemisc.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./iemisc.Rcheck/00check.log:* using session charset: UTF-8 ./iemisc.Rcheck/00check.log:* checking for file ‘iemisc/DESCRIPTION’ ... OK ./iemisc.Rcheck/00check.log:* this is package ‘iemisc’ version ‘0.9.9’ ./iemisc.Rcheck/00check.log:* package encoding: UTF-8 ./iemisc.Rcheck/00check.log:* checking package namespace information ... OK ./iemisc.Rcheck/00check.log:* checking package dependencies ... OK ./iemisc.Rcheck/00check.log:* checking if this is a source package ... OK ./iemisc.Rcheck/00check.log:* checking if there is a namespace ... OK ./iemisc.Rcheck/00check.log:* checking for executable files ... OK ./iemisc.Rcheck/00check.log:* checking for hidden files and directories ... OK ./iemisc.Rcheck/00check.log:* checking for portable file names ... OK ./iemisc.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./iemisc.Rcheck/00check.log:* checking whether package ‘iemisc’ can be installed ... OK ./iemisc.Rcheck/00check.log:* checking installed package size ... OK ./iemisc.Rcheck/00check.log:* checking package directory ... OK ./iemisc.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./iemisc.Rcheck/00check.log:* checking top-level files ... OK ./iemisc.Rcheck/00check.log:* checking for left-over files ... OK ./iemisc.Rcheck/00check.log:* checking index information ... OK ./iemisc.Rcheck/00check.log:* checking package subdirectories ... OK ./iemisc.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./iemisc.Rcheck/00check.log:* checking R files for syntax errors ... OK ./iemisc.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./iemisc.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./iemisc.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./iemisc.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./iemisc.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./iemisc.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./iemisc.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./iemisc.Rcheck/00check.log:Namespace in Imports field not imported from: ‘testit’ ./iemisc.Rcheck/00check.log: All declared Imports should be used. ./iemisc.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./iemisc.Rcheck/00check.log:* checking replacement functions ... OK ./iemisc.Rcheck/00check.log:* checking foreign function calls ... OK ./iemisc.Rcheck/00check.log:* checking R code for possible problems ... OK ./iemisc.Rcheck/00check.log:* checking Rd files ... OK ./iemisc.Rcheck/00check.log:* checking Rd metadata ... OK ./iemisc.Rcheck/00check.log:* checking Rd cross-references ... OK ./iemisc.Rcheck/00check.log:* checking for missing documentation entries ... OK ./iemisc.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./iemisc.Rcheck/00check.log:* checking Rd \usage sections ... OK ./iemisc.Rcheck/00check.log:* checking Rd contents ... OK ./iemisc.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./iemisc.Rcheck/00check.log:* checking LazyData ... NOTE ./iemisc.Rcheck/00check.log: 'LazyData' is specified without a 'data' directory ./iemisc.Rcheck/00check.log:* checking examples ... ERROR ./iemisc.Rcheck/00check.log:Running examples in ‘iemisc-Ex.R’ failed ./iemisc.Rcheck/00check.log:The error most likely occurred in: ./iemisc.Rcheck/00check.log:> ### Name: benefitcost ./iemisc.Rcheck/00check.log:> ### Title: Benefit-Cost Ratio (Engineering Economics) ./iemisc.Rcheck/00check.log:> ### Aliases: benefitcost ./iemisc.Rcheck/00check.log:> ./iemisc.Rcheck/00check.log:> ### ** Examples ./iemisc.Rcheck/00check.log:> ./iemisc.Rcheck/00check.log:> library("iemisc") ./iemisc.Rcheck/00check.log:> # Example from Lindeburg Reference text (page 14-4) ./iemisc.Rcheck/00check.log:> benefitcost(ic1 = 300000, n1 = 10, ac1 = 45000, ab1 = 150000, i1 = 10, ./iemisc.Rcheck/00check.log:+ salvage1 = 0, ic2 = 400000, n2 = 10, ac2 = 35000, ab2 = 200000, i2 = 10, ./iemisc.Rcheck/00check.log:+ salvage2 = 10000, option1 = "A", option2 = "B", table = "rtable") ./iemisc.Rcheck/00check.log: The Benefit-Cost ratio of B to A is 8.85 thus choose B. ./iemisc.Rcheck/00check.log:Error: x is not a data.table|frame. Shallow copy is a copy of the vector of column pointers (only), so is only meaningful for data.table|frame ./iemisc.Rcheck/00check.log:Execution halted ./iemisc.Rcheck/00check.log:* checking PDF version of manual ... OK ./iemisc.Rcheck/00check.log:* DONE ./iemisc.Rcheck/00check.log:Status: 1 ERROR, 2 NOTEs iml_0.10.1.tar.gz ./iml.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/iml.Rcheck’ ./iml.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./iml.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./iml.Rcheck/00check.log:* using session charset: UTF-8 ./iml.Rcheck/00check.log:* checking for file ‘iml/DESCRIPTION’ ... OK ./iml.Rcheck/00check.log:* checking extension type ... Package ./iml.Rcheck/00check.log:* this is package ‘iml’ version ‘0.10.1’ ./iml.Rcheck/00check.log:* package encoding: UTF-8 ./iml.Rcheck/00check.log:* checking package namespace information ... OK ./iml.Rcheck/00check.log:* checking package dependencies ... OK ./iml.Rcheck/00check.log:* checking if this is a source package ... OK ./iml.Rcheck/00check.log:* checking if there is a namespace ... OK ./iml.Rcheck/00check.log:* checking for executable files ... OK ./iml.Rcheck/00check.log:* checking for hidden files and directories ... OK ./iml.Rcheck/00check.log:* checking for portable file names ... OK ./iml.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./iml.Rcheck/00check.log:* checking whether package ‘iml’ can be installed ... OK ./iml.Rcheck/00check.log:* checking installed package size ... OK ./iml.Rcheck/00check.log:* checking package directory ... OK ./iml.Rcheck/00check.log:* checking ‘build’ directory ... OK ./iml.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./iml.Rcheck/00check.log:* checking top-level files ... OK ./iml.Rcheck/00check.log:* checking for left-over files ... OK ./iml.Rcheck/00check.log:* checking index information ... OK ./iml.Rcheck/00check.log:* checking package subdirectories ... OK ./iml.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./iml.Rcheck/00check.log:* checking R files for syntax errors ... OK ./iml.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./iml.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./iml.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./iml.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./iml.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./iml.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./iml.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./iml.Rcheck/00check.log:Namespace in Imports field not imported from: ‘keras’ ./iml.Rcheck/00check.log: All declared Imports should be used. ./iml.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./iml.Rcheck/00check.log:* checking replacement functions ... OK ./iml.Rcheck/00check.log:* checking foreign function calls ... OK ./iml.Rcheck/00check.log:* checking R code for possible problems ... OK ./iml.Rcheck/00check.log:* checking Rd files ... OK ./iml.Rcheck/00check.log:* checking Rd metadata ... OK ./iml.Rcheck/00check.log:* checking Rd cross-references ... OK ./iml.Rcheck/00check.log:* checking for missing documentation entries ... OK ./iml.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./iml.Rcheck/00check.log:* checking Rd \usage sections ... OK ./iml.Rcheck/00check.log:* checking Rd contents ... OK ./iml.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./iml.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./iml.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./iml.Rcheck/00check.log:* checking examples ... ERROR ./iml.Rcheck/00check.log:Running examples in ‘iml-Ex.R’ failed ./iml.Rcheck/00check.log:The error most likely occurred in: ./iml.Rcheck/00check.log:> ### Name: FeatureEffect ./iml.Rcheck/00check.log:> ### Title: Effect of a feature on predictions ./iml.Rcheck/00check.log:> ### Aliases: FeatureEffect ./iml.Rcheck/00check.log:> ./iml.Rcheck/00check.log:> ### ** Examples ./iml.Rcheck/00check.log:> ./iml.Rcheck/00check.log:> # We train a random forest on the Boston dataset: ./iml.Rcheck/00check.log:> data("Boston", package = "MASS") ./iml.Rcheck/00check.log:> library("randomForest") ./iml.Rcheck/00check.log:randomForest 4.6-14 ./iml.Rcheck/00check.log:Type rfNews() to see new features/changes/bug fixes. ./iml.Rcheck/00check.log:> rf <- randomForest(medv ~ ., data = Boston, ntree = 50) ./iml.Rcheck/00check.log:> mod <- Predictor$new(rf, data = Boston) ./iml.Rcheck/00check.log:> ./iml.Rcheck/00check.log:> # Compute the accumulated local effects for the first feature ./iml.Rcheck/00check.log:> eff <- FeatureEffect$new(mod, feature = "rm", grid.size = 30) ./iml.Rcheck/00check.log:Error in `[.data.table`(deltas, , list(.yhat.diff = mean(.yhat.diff)), : ./iml.Rcheck/00check.log: fastmean was passed type NULL, not numeric or logical ./iml.Rcheck/00check.log:Calls: ... calculate.ale.num -> [ -> [.data.table -> .External ./iml.Rcheck/00check.log:Execution halted ./iml.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./iml.Rcheck/00check.log:* checking tests ... ERROR ./iml.Rcheck/00check.log: Running ‘testthat.R’ ./iml.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./iml.Rcheck/00check.log:Last 13 lines of output: ./iml.Rcheck/00check.log: 3. ├─base::suppressPackageStartupMessages(private$run()) ./iml.Rcheck/00check.log: 4. │ └─base::withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage")) ./iml.Rcheck/00check.log: 5. └─private$run() ./iml.Rcheck/00check.log: 6. └─future.apply::future_lapply(...) ./iml.Rcheck/00check.log: 7. └─future.apply:::future_xapply(...) ./iml.Rcheck/00check.log: 8. ├─future::value(fs) ./iml.Rcheck/00check.log: 9. └─future:::value.list(fs) ./iml.Rcheck/00check.log: 10. ├─future::resolve(...) ./iml.Rcheck/00check.log: 11. └─future:::resolve.list(...) ./iml.Rcheck/00check.log: 12. └─future:::signalConditionsASAP(obj, resignal = FALSE, pos = ii) ./iml.Rcheck/00check.log: 13. └─future:::signalConditions(...) ./iml.Rcheck/00check.log: ./iml.Rcheck/00check.log: [ FAIL 4 | WARN 2 | SKIP 11 | PASS 458 ] ./iml.Rcheck/00check.log: Error: Test failures ./iml.Rcheck/00check.log: Execution halted ./iml.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./iml.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./iml.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./iml.Rcheck/00check.log: ‘intro.Rmd’ using ‘UTF-8’... OK ./iml.Rcheck/00check.log: ‘parallel.Rmd’ using ‘UTF-8’... OK ./iml.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./iml.Rcheck/00check.log:Error(s) in re-building vignettes: ./iml.Rcheck/00check.log: ... ./iml.Rcheck/00check.log:--- re-building ‘intro.Rmd’ using rmarkdown ./iml.Rcheck/00check.log:randomForest 4.6-14 ./iml.Rcheck/00check.log:Type rfNews() to see new features/changes/bug fixes. ./iml.Rcheck/00check.log:Quitting from lines 94-96 (intro.Rmd) ./iml.Rcheck/00check.log:Error: processing vignette 'intro.Rmd' failed with diagnostics: ./iml.Rcheck/00check.log:fastmean was passed type NULL, not numeric or logical ./iml.Rcheck/00check.log:--- failed re-building ‘intro.Rmd’ ./iml.Rcheck/00check.log:--- re-building ‘parallel.Rmd’ using rmarkdown ./iml.Rcheck/00check.log:Quitting from lines 102-110 (parallel.Rmd) ./iml.Rcheck/00check.log:Error: processing vignette 'parallel.Rmd' failed with diagnostics: ./iml.Rcheck/00check.log:fastmean was passed type NULL, not numeric or logical ./iml.Rcheck/00check.log:--- failed re-building ‘parallel.Rmd’ ./iml.Rcheck/00check.log:SUMMARY: processing the following files failed: ./iml.Rcheck/00check.log: ‘intro.Rmd’ ‘parallel.Rmd’ ./iml.Rcheck/00check.log:Error: Vignette re-building failed. ./iml.Rcheck/00check.log:Execution halted ./iml.Rcheck/00check.log:* checking PDF version of manual ... OK ./iml.Rcheck/00check.log:* DONE ./iml.Rcheck/00check.log:Status: 2 ERRORs, 1 WARNING, 1 NOTE LMMstar_0.3.2.tar.gz ./LMMstar.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/LMMstar.Rcheck’ ./LMMstar.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./LMMstar.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./LMMstar.Rcheck/00check.log:* using session charset: UTF-8 ./LMMstar.Rcheck/00check.log:* checking for file ‘LMMstar/DESCRIPTION’ ... OK ./LMMstar.Rcheck/00check.log:* checking extension type ... Package ./LMMstar.Rcheck/00check.log:* this is package ‘LMMstar’ version ‘0.3.2’ ./LMMstar.Rcheck/00check.log:* package encoding: UTF-8 ./LMMstar.Rcheck/00check.log:* checking package namespace information ... OK ./LMMstar.Rcheck/00check.log:* checking package dependencies ... OK ./LMMstar.Rcheck/00check.log:* checking if this is a source package ... OK ./LMMstar.Rcheck/00check.log:* checking if there is a namespace ... OK ./LMMstar.Rcheck/00check.log:* checking for executable files ... OK ./LMMstar.Rcheck/00check.log:* checking for hidden files and directories ... OK ./LMMstar.Rcheck/00check.log:* checking for portable file names ... OK ./LMMstar.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./LMMstar.Rcheck/00check.log:* checking whether package ‘LMMstar’ can be installed ... OK ./LMMstar.Rcheck/00check.log:* checking installed package size ... OK ./LMMstar.Rcheck/00check.log:* checking package directory ... OK ./LMMstar.Rcheck/00check.log:* checking ‘build’ directory ... OK ./LMMstar.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./LMMstar.Rcheck/00check.log:* checking top-level files ... OK ./LMMstar.Rcheck/00check.log:* checking for left-over files ... OK ./LMMstar.Rcheck/00check.log:* checking index information ... OK ./LMMstar.Rcheck/00check.log:* checking package subdirectories ... OK ./LMMstar.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./LMMstar.Rcheck/00check.log:* checking R files for syntax errors ... OK ./LMMstar.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./LMMstar.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./LMMstar.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./LMMstar.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./LMMstar.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./LMMstar.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./LMMstar.Rcheck/00check.log:* checking dependencies in R code ... OK ./LMMstar.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./LMMstar.Rcheck/00check.log:* checking replacement functions ... OK ./LMMstar.Rcheck/00check.log:* checking foreign function calls ... OK ./LMMstar.Rcheck/00check.log:* checking R code for possible problems ... OK ./LMMstar.Rcheck/00check.log:* checking Rd files ... OK ./LMMstar.Rcheck/00check.log:* checking Rd metadata ... OK ./LMMstar.Rcheck/00check.log:* checking Rd cross-references ... OK ./LMMstar.Rcheck/00check.log:* checking for missing documentation entries ... OK ./LMMstar.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./LMMstar.Rcheck/00check.log:* checking Rd \usage sections ... OK ./LMMstar.Rcheck/00check.log:* checking Rd contents ... OK ./LMMstar.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./LMMstar.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./LMMstar.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./LMMstar.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./LMMstar.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./LMMstar.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./LMMstar.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./LMMstar.Rcheck/00check.log:* checking examples ... OK ./LMMstar.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./LMMstar.Rcheck/00check.log:* checking tests ... ERROR ./LMMstar.Rcheck/00check.log: Running ‘testthat.R’ ./LMMstar.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./LMMstar.Rcheck/00check.log:Last 13 lines of output: ./LMMstar.Rcheck/00check.log: > ./LMMstar.Rcheck/00check.log: > ## * run tests ./LMMstar.Rcheck/00check.log: > ## setwd("~/Documents/GitHub/LMMstar/tests/") ./LMMstar.Rcheck/00check.log: > test_check("LMMstar") ./LMMstar.Rcheck/00check.log: ══ Skipped tests ═══════════════════════════════════════════════════════════════ ./LMMstar.Rcheck/00check.log: • empty test (5) ./LMMstar.Rcheck/00check.log: ./LMMstar.Rcheck/00check.log: ══ Failed tests ════════════════════════════════════════════════════════════════ ./LMMstar.Rcheck/00check.log: ── Failure (test-previous-bug.R:62:5): getCoef - Non-positive definite approximate variance-covariance ── ./LMMstar.Rcheck/00check.log: `GS` not equivalent to `test`. ./LMMstar.Rcheck/00check.log: Component "p.value": Mean relative difference: 1.055542e-05 ./LMMstar.Rcheck/00check.log: ./LMMstar.Rcheck/00check.log: [ FAIL 1 | WARN 0 | SKIP 5 | PASS 201 ] ./LMMstar.Rcheck/00check.log: Error: Test failures ./LMMstar.Rcheck/00check.log: Execution halted ./LMMstar.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./LMMstar.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./LMMstar.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./LMMstar.Rcheck/00check.log: ‘overview.pdf.asis’ using ‘UTF-8’... OK ./LMMstar.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./LMMstar.Rcheck/00check.log:* checking PDF version of manual ... OK ./LMMstar.Rcheck/00check.log:* DONE ./LMMstar.Rcheck/00check.log:Status: 1 ERROR maditr_0.8.2.tar.gz ./maditr.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/maditr.Rcheck’ ./maditr.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./maditr.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./maditr.Rcheck/00check.log:* using session charset: UTF-8 ./maditr.Rcheck/00check.log:* checking for file ‘maditr/DESCRIPTION’ ... OK ./maditr.Rcheck/00check.log:* checking extension type ... Package ./maditr.Rcheck/00check.log:* this is package ‘maditr’ version ‘0.8.2’ ./maditr.Rcheck/00check.log:* package encoding: UTF-8 ./maditr.Rcheck/00check.log:* checking package namespace information ... OK ./maditr.Rcheck/00check.log:* checking package dependencies ... OK ./maditr.Rcheck/00check.log:* checking if this is a source package ... OK ./maditr.Rcheck/00check.log:* checking if there is a namespace ... OK ./maditr.Rcheck/00check.log:* checking for executable files ... OK ./maditr.Rcheck/00check.log:* checking for hidden files and directories ... OK ./maditr.Rcheck/00check.log:* checking for portable file names ... OK ./maditr.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./maditr.Rcheck/00check.log:* checking whether package ‘maditr’ can be installed ... OK ./maditr.Rcheck/00check.log:* checking installed package size ... OK ./maditr.Rcheck/00check.log:* checking package directory ... OK ./maditr.Rcheck/00check.log:* checking ‘build’ directory ... OK ./maditr.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./maditr.Rcheck/00check.log:* checking top-level files ... OK ./maditr.Rcheck/00check.log:* checking for left-over files ... OK ./maditr.Rcheck/00check.log:* checking index information ... OK ./maditr.Rcheck/00check.log:* checking package subdirectories ... OK ./maditr.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./maditr.Rcheck/00check.log:* checking R files for syntax errors ... OK ./maditr.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./maditr.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./maditr.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./maditr.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./maditr.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./maditr.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./maditr.Rcheck/00check.log:* checking dependencies in R code ... OK ./maditr.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./maditr.Rcheck/00check.log:* checking replacement functions ... OK ./maditr.Rcheck/00check.log:* checking foreign function calls ... OK ./maditr.Rcheck/00check.log:* checking R code for possible problems ... OK ./maditr.Rcheck/00check.log:* checking Rd files ... OK ./maditr.Rcheck/00check.log:* checking Rd metadata ... OK ./maditr.Rcheck/00check.log:* checking Rd cross-references ... OK ./maditr.Rcheck/00check.log:* checking for missing documentation entries ... OK ./maditr.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./maditr.Rcheck/00check.log:* checking Rd \usage sections ... OK ./maditr.Rcheck/00check.log:* checking Rd contents ... OK ./maditr.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./maditr.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./maditr.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./maditr.Rcheck/00check.log:* checking examples ... OK ./maditr.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./maditr.Rcheck/00check.log:* checking tests ... ERROR ./maditr.Rcheck/00check.log: Running ‘tinytest.R’ ./maditr.Rcheck/00check.log:Running the tests in ‘tests/tinytest.R’ failed. ./maditr.Rcheck/00check.log:Last 13 lines of output: ./maditr.Rcheck/00check.log: test_vlookup.R................ 22 tests OK ./maditr.Rcheck/00check.log: test_vlookup.R................ 22 tests OK ./maditr.Rcheck/00check.log: test_vlookup.R................ 23 tests OK ./maditr.Rcheck/00check.log: test_vlookup.R................ 24 tests OK ./maditr.Rcheck/00check.log: test_vlookup.R................ 25 tests OK 14ms ./maditr.Rcheck/00check.log: ----- FAILED[attr]: test_take_all.R<117--124> ./maditr.Rcheck/00check.log: call| expect_equal(current = take_all(iris, mean = mean, keyby = Species, ./maditr.Rcheck/00check.log: call| suffix = FALSE, .SDcols = -(1:2)), target = { ./maditr.Rcheck/00check.log: call| res = dt_iris[, lapply(.SD, mean), keyby = Species, .SDcols = -(1:2)] ./maditr.Rcheck/00check.log: call| names(res)[-1] = paste0("mean_", names(res)[-1]) ./maditr.Rcheck/00check.log: call| res ./maditr.Rcheck/00check.log: call| }) ./maditr.Rcheck/00check.log: diff| Datasets have different keys. 'target': has no key. 'current': [Species]. ./maditr.Rcheck/00check.log: Error: 1 out of 391 tests failed ./maditr.Rcheck/00check.log: Execution halted ./maditr.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./maditr.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./maditr.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./maditr.Rcheck/00check.log: ‘Introduction.Rmd’ using ‘utf8’... OK ./maditr.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./maditr.Rcheck/00check.log:* checking PDF version of manual ... OK ./maditr.Rcheck/00check.log:* DONE ./maditr.Rcheck/00check.log:Status: 1 ERROR mlr3proba_0.4.1.tar.gz ./mlr3proba.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/mlr3proba.Rcheck’ ./mlr3proba.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./mlr3proba.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./mlr3proba.Rcheck/00check.log:* using session charset: UTF-8 ./mlr3proba.Rcheck/00check.log:* checking for file ‘mlr3proba/DESCRIPTION’ ... OK ./mlr3proba.Rcheck/00check.log:* this is package ‘mlr3proba’ version ‘0.4.1’ ./mlr3proba.Rcheck/00check.log:* package encoding: UTF-8 ./mlr3proba.Rcheck/00check.log:* checking package namespace information ... OK ./mlr3proba.Rcheck/00check.log:* checking package dependencies ... OK ./mlr3proba.Rcheck/00check.log:* checking if this is a source package ... OK ./mlr3proba.Rcheck/00check.log:* checking if there is a namespace ... OK ./mlr3proba.Rcheck/00check.log:* checking for executable files ... OK ./mlr3proba.Rcheck/00check.log:* checking for hidden files and directories ... OK ./mlr3proba.Rcheck/00check.log:* checking for portable file names ... OK ./mlr3proba.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./mlr3proba.Rcheck/00check.log:* checking whether package ‘mlr3proba’ can be installed ... OK ./mlr3proba.Rcheck/00check.log:* checking installed package size ... OK ./mlr3proba.Rcheck/00check.log:* checking package directory ... OK ./mlr3proba.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./mlr3proba.Rcheck/00check.log:* checking top-level files ... OK ./mlr3proba.Rcheck/00check.log:* checking for left-over files ... OK ./mlr3proba.Rcheck/00check.log:* checking index information ... OK ./mlr3proba.Rcheck/00check.log:* checking package subdirectories ... OK ./mlr3proba.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./mlr3proba.Rcheck/00check.log:* checking R files for syntax errors ... OK ./mlr3proba.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./mlr3proba.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./mlr3proba.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./mlr3proba.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./mlr3proba.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./mlr3proba.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./mlr3proba.Rcheck/00check.log:* checking dependencies in R code ... OK ./mlr3proba.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./mlr3proba.Rcheck/00check.log:* checking replacement functions ... OK ./mlr3proba.Rcheck/00check.log:* checking foreign function calls ... OK ./mlr3proba.Rcheck/00check.log:* checking R code for possible problems ... OK ./mlr3proba.Rcheck/00check.log:* checking Rd files ... OK ./mlr3proba.Rcheck/00check.log:* checking Rd metadata ... OK ./mlr3proba.Rcheck/00check.log:* checking Rd cross-references ... OK ./mlr3proba.Rcheck/00check.log:* checking for missing documentation entries ... OK ./mlr3proba.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./mlr3proba.Rcheck/00check.log:* checking Rd \usage sections ... OK ./mlr3proba.Rcheck/00check.log:* checking Rd contents ... OK ./mlr3proba.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./mlr3proba.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./mlr3proba.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./mlr3proba.Rcheck/00check.log:* checking LazyData ... OK ./mlr3proba.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./mlr3proba.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./mlr3proba.Rcheck/00check.log:* checking compiled code ... OK ./mlr3proba.Rcheck/00check.log:* checking examples ... OK ./mlr3proba.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./mlr3proba.Rcheck/00check.log:* checking tests ... ERROR ./mlr3proba.Rcheck/00check.log: Running ‘testthat.R’ ./mlr3proba.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./mlr3proba.Rcheck/00check.log:Complete output: ./mlr3proba.Rcheck/00check.log: > library(testthat) ./mlr3proba.Rcheck/00check.log: > library(checkmate) # for more expect_*() functions ./mlr3proba.Rcheck/00check.log: > library(mlr3proba) ./mlr3proba.Rcheck/00check.log: Loading required package: mlr3 ./mlr3proba.Rcheck/00check.log: > ./mlr3proba.Rcheck/00check.log: > test_check("mlr3proba") ./mlr3proba.Rcheck/00check.log: Error: C stack usage 7974628 is too close to the limit ./mlr3proba.Rcheck/00check.log: Execution halted ./mlr3proba.Rcheck/00check.log:* checking PDF version of manual ... OK ./mlr3proba.Rcheck/00check.log:* DONE ./mlr3proba.Rcheck/00check.log:Status: 1 ERROR mlr3viz_0.5.6.tar.gz ./mlr3viz.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/mlr3viz.Rcheck’ ./mlr3viz.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./mlr3viz.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./mlr3viz.Rcheck/00check.log:* using session charset: UTF-8 ./mlr3viz.Rcheck/00check.log:* checking for file ‘mlr3viz/DESCRIPTION’ ... OK ./mlr3viz.Rcheck/00check.log:* this is package ‘mlr3viz’ version ‘0.5.6’ ./mlr3viz.Rcheck/00check.log:* package encoding: UTF-8 ./mlr3viz.Rcheck/00check.log:* checking package namespace information ... OK ./mlr3viz.Rcheck/00check.log:* checking package dependencies ... OK ./mlr3viz.Rcheck/00check.log:* checking if this is a source package ... OK ./mlr3viz.Rcheck/00check.log:* checking if there is a namespace ... OK ./mlr3viz.Rcheck/00check.log:* checking for executable files ... OK ./mlr3viz.Rcheck/00check.log:* checking for hidden files and directories ... OK ./mlr3viz.Rcheck/00check.log:* checking for portable file names ... OK ./mlr3viz.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./mlr3viz.Rcheck/00check.log:* checking whether package ‘mlr3viz’ can be installed ... OK ./mlr3viz.Rcheck/00check.log:* checking installed package size ... OK ./mlr3viz.Rcheck/00check.log:* checking package directory ... OK ./mlr3viz.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./mlr3viz.Rcheck/00check.log:* checking top-level files ... OK ./mlr3viz.Rcheck/00check.log:* checking for left-over files ... OK ./mlr3viz.Rcheck/00check.log:* checking index information ... OK ./mlr3viz.Rcheck/00check.log:* checking package subdirectories ... OK ./mlr3viz.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./mlr3viz.Rcheck/00check.log:* checking R files for syntax errors ... OK ./mlr3viz.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./mlr3viz.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./mlr3viz.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./mlr3viz.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./mlr3viz.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./mlr3viz.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./mlr3viz.Rcheck/00check.log:* checking dependencies in R code ... OK ./mlr3viz.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./mlr3viz.Rcheck/00check.log:* checking replacement functions ... OK ./mlr3viz.Rcheck/00check.log:* checking foreign function calls ... OK ./mlr3viz.Rcheck/00check.log:* checking R code for possible problems ... OK ./mlr3viz.Rcheck/00check.log:* checking Rd files ... OK ./mlr3viz.Rcheck/00check.log:* checking Rd metadata ... OK ./mlr3viz.Rcheck/00check.log:* checking Rd cross-references ... OK ./mlr3viz.Rcheck/00check.log:* checking for missing documentation entries ... OK ./mlr3viz.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./mlr3viz.Rcheck/00check.log:* checking Rd \usage sections ... OK ./mlr3viz.Rcheck/00check.log:* checking Rd contents ... OK ./mlr3viz.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./mlr3viz.Rcheck/00check.log:* checking examples ... OK ./mlr3viz.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./mlr3viz.Rcheck/00check.log:* checking tests ... ERROR ./mlr3viz.Rcheck/00check.log: Running ‘testthat.R’ ./mlr3viz.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./mlr3viz.Rcheck/00check.log:Last 13 lines of output: ./mlr3viz.Rcheck/00check.log: > test_check("mlr3viz") ./mlr3viz.Rcheck/00check.log: Starting 2 test processes ./mlr3viz.Rcheck/00check.log: ══ Skipped tests ═══════════════════════════════════════════════════════════════ ./mlr3viz.Rcheck/00check.log: • On CRAN (23) ./mlr3viz.Rcheck/00check.log: ./mlr3viz.Rcheck/00check.log: ══ Failed tests ════════════════════════════════════════════════════════════════ ./mlr3viz.Rcheck/00check.log: ── Failure (test_PredictionClust.R:13:3): autoplot.PredictionClust ───────────── ./mlr3viz.Rcheck/00check.log: is.ggplot(p) is not TRUE ./mlr3viz.Rcheck/00check.log: ./mlr3viz.Rcheck/00check.log: `actual`: FALSE ./mlr3viz.Rcheck/00check.log: `expected`: TRUE ./mlr3viz.Rcheck/00check.log: ./mlr3viz.Rcheck/00check.log: [ FAIL 1 | WARN 1 | SKIP 23 | PASS 87 ] ./mlr3viz.Rcheck/00check.log: Error: Test failures ./mlr3viz.Rcheck/00check.log: Execution halted ./mlr3viz.Rcheck/00check.log:* checking PDF version of manual ... OK ./mlr3viz.Rcheck/00check.log:* DONE ./mlr3viz.Rcheck/00check.log:Status: 1 ERROR NADIA_0.4.1.tar.gz ./NADIA.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/NADIA.Rcheck’ ./NADIA.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./NADIA.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./NADIA.Rcheck/00check.log:* using session charset: UTF-8 ./NADIA.Rcheck/00check.log:* checking for file ‘NADIA/DESCRIPTION’ ... OK ./NADIA.Rcheck/00check.log:* checking extension type ... Package ./NADIA.Rcheck/00check.log:* this is package ‘NADIA’ version ‘0.4.1’ ./NADIA.Rcheck/00check.log:* package encoding: UTF-8 ./NADIA.Rcheck/00check.log:* checking package namespace information ... OK ./NADIA.Rcheck/00check.log:* checking package dependencies ... OK ./NADIA.Rcheck/00check.log:* checking if this is a source package ... OK ./NADIA.Rcheck/00check.log:* checking if there is a namespace ... OK ./NADIA.Rcheck/00check.log:* checking for executable files ... OK ./NADIA.Rcheck/00check.log:* checking for hidden files and directories ... OK ./NADIA.Rcheck/00check.log:* checking for portable file names ... OK ./NADIA.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./NADIA.Rcheck/00check.log:* checking whether package ‘NADIA’ can be installed ... OK ./NADIA.Rcheck/00check.log:* checking installed package size ... OK ./NADIA.Rcheck/00check.log:* checking package directory ... OK ./NADIA.Rcheck/00check.log:* checking ‘build’ directory ... OK ./NADIA.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./NADIA.Rcheck/00check.log:* checking top-level files ... OK ./NADIA.Rcheck/00check.log:* checking for left-over files ... OK ./NADIA.Rcheck/00check.log:* checking index information ... OK ./NADIA.Rcheck/00check.log:* checking package subdirectories ... OK ./NADIA.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./NADIA.Rcheck/00check.log:* checking R files for syntax errors ... OK ./NADIA.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./NADIA.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./NADIA.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./NADIA.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./NADIA.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./NADIA.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./NADIA.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./NADIA.Rcheck/00check.log:Namespaces in Imports field not imported from: ./NADIA.Rcheck/00check.log: ‘glmnet’ ‘mlr3learners’ ./NADIA.Rcheck/00check.log: All declared Imports should be used. ./NADIA.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./NADIA.Rcheck/00check.log:* checking replacement functions ... OK ./NADIA.Rcheck/00check.log:* checking foreign function calls ... OK ./NADIA.Rcheck/00check.log:* checking R code for possible problems ... OK ./NADIA.Rcheck/00check.log:* checking Rd files ... OK ./NADIA.Rcheck/00check.log:* checking Rd metadata ... OK ./NADIA.Rcheck/00check.log:* checking Rd cross-references ... OK ./NADIA.Rcheck/00check.log:* checking for missing documentation entries ... OK ./NADIA.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./NADIA.Rcheck/00check.log:* checking Rd \usage sections ... OK ./NADIA.Rcheck/00check.log:* checking Rd contents ... OK ./NADIA.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./NADIA.Rcheck/00check.log:* checking LazyData ... NOTE ./NADIA.Rcheck/00check.log: 'LazyData' is specified without a 'data' directory ./NADIA.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./NADIA.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./NADIA.Rcheck/00check.log:* checking examples ... ERROR ./NADIA.Rcheck/00check.log:Running examples in ‘NADIA-Ex.R’ failed ./NADIA.Rcheck/00check.log:The error most likely occurred in: ./NADIA.Rcheck/00check.log:> ### Name: PipeOpVIM_HD ./NADIA.Rcheck/00check.log:> ### Title: PipeOpVIM_HD ./NADIA.Rcheck/00check.log:> ### Aliases: PipeOpVIM_HD ./NADIA.Rcheck/00check.log:> ./NADIA.Rcheck/00check.log:> ### ** Examples ./NADIA.Rcheck/00check.log:> ./NADIA.Rcheck/00check.log:> { ./NADIA.Rcheck/00check.log:+ graph <- PipeOpVIM_HD$new() %>>% mlr3learners::LearnerClassifGlmnet$new() ./NADIA.Rcheck/00check.log:+ graph_learner <- GraphLearner$new(graph) ./NADIA.Rcheck/00check.log:+ ./NADIA.Rcheck/00check.log:+ # Task with NA ./NADIA.Rcheck/00check.log:+ ./NADIA.Rcheck/00check.log:+ resample(tsk("pima"), graph_learner, rsmp("cv", folds = 3)) ./NADIA.Rcheck/00check.log:+ } ./NADIA.Rcheck/00check.log:INFO [00:33:04.841] [mlr3] Applying learner 'impute_VIM_HD_B.classif.glmnet' on task 'pima' (iter 2/3) ./NADIA.Rcheck/00check.log:Error: nomatch= must be either NA or NULL (or 0 for backwards compatibility which is the same as NULL but please use NULL) ./NADIA.Rcheck/00check.log:Execution halted ./NADIA.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./NADIA.Rcheck/00check.log:* checking tests ... ERROR ./NADIA.Rcheck/00check.log: Running ‘testthat.R’ ./NADIA.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./NADIA.Rcheck/00check.log:Last 13 lines of output: ./NADIA.Rcheck/00check.log: Error: nomatch= must be either NA or NULL (or 0 for backwards compatibility which is the same as NULL but please use NULL) ./NADIA.Rcheck/00check.log: Backtrace: ./NADIA.Rcheck/00check.log: █ ./NADIA.Rcheck/00check.log: 1. ├─testthat::expect_equal(...) test_autotune.R:324:2 ./NADIA.Rcheck/00check.log: 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") ./NADIA.Rcheck/00check.log: 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) ./NADIA.Rcheck/00check.log: 4. └─NADIA::autotune_VIM_hotdeck(test_set) ./NADIA.Rcheck/00check.log: 5. └─base::tryCatch(...) ./NADIA.Rcheck/00check.log: 6. └─base:::tryCatchList(expr, classes, parentenv, handlers) ./NADIA.Rcheck/00check.log: 7. └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]]) ./NADIA.Rcheck/00check.log: 8. └─value[[3L]](cond) ./NADIA.Rcheck/00check.log: ./NADIA.Rcheck/00check.log: [ FAIL 5 | WARN 7 | SKIP 18 | PASS 74 ] ./NADIA.Rcheck/00check.log: Error: Test failures ./NADIA.Rcheck/00check.log: Execution halted ./NADIA.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./NADIA.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./NADIA.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./NADIA.Rcheck/00check.log: ‘Errors_Statistic_and_Handling.Rmd’ using ‘UTF-8’... OK ./NADIA.Rcheck/00check.log: ‘NADIA_examples_and_motivation.Rmd’ using ‘UTF-8’... OK ./NADIA.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./NADIA.Rcheck/00check.log:* checking PDF version of manual ... OK ./NADIA.Rcheck/00check.log:* DONE ./NADIA.Rcheck/00check.log:Status: 2 ERRORs, 2 NOTEs rasterDT_0.3.1.tar.gz ./rasterDT.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/rasterDT.Rcheck’ ./rasterDT.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./rasterDT.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./rasterDT.Rcheck/00check.log:* using session charset: UTF-8 ./rasterDT.Rcheck/00check.log:* checking for file ‘rasterDT/DESCRIPTION’ ... OK ./rasterDT.Rcheck/00check.log:* checking extension type ... Package ./rasterDT.Rcheck/00check.log:* this is package ‘rasterDT’ version ‘0.3.1’ ./rasterDT.Rcheck/00check.log:* package encoding: UTF-8 ./rasterDT.Rcheck/00check.log:* checking package namespace information ... OK ./rasterDT.Rcheck/00check.log:* checking package dependencies ... OK ./rasterDT.Rcheck/00check.log:* checking if this is a source package ... OK ./rasterDT.Rcheck/00check.log:* checking if there is a namespace ... OK ./rasterDT.Rcheck/00check.log:* checking for executable files ... OK ./rasterDT.Rcheck/00check.log:* checking for hidden files and directories ... OK ./rasterDT.Rcheck/00check.log:* checking for portable file names ... OK ./rasterDT.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./rasterDT.Rcheck/00check.log:* checking whether package ‘rasterDT’ can be installed ... OK ./rasterDT.Rcheck/00check.log:* checking installed package size ... OK ./rasterDT.Rcheck/00check.log:* checking package directory ... OK ./rasterDT.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./rasterDT.Rcheck/00check.log:* checking top-level files ... OK ./rasterDT.Rcheck/00check.log:* checking for left-over files ... OK ./rasterDT.Rcheck/00check.log:* checking index information ... OK ./rasterDT.Rcheck/00check.log:* checking package subdirectories ... OK ./rasterDT.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./rasterDT.Rcheck/00check.log:* checking R files for syntax errors ... OK ./rasterDT.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./rasterDT.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./rasterDT.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./rasterDT.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./rasterDT.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./rasterDT.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./rasterDT.Rcheck/00check.log:* checking dependencies in R code ... OK ./rasterDT.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./rasterDT.Rcheck/00check.log:* checking replacement functions ... OK ./rasterDT.Rcheck/00check.log:* checking foreign function calls ... OK ./rasterDT.Rcheck/00check.log:* checking R code for possible problems ... OK ./rasterDT.Rcheck/00check.log:* checking Rd files ... OK ./rasterDT.Rcheck/00check.log:* checking Rd metadata ... OK ./rasterDT.Rcheck/00check.log:* checking Rd cross-references ... OK ./rasterDT.Rcheck/00check.log:* checking for missing documentation entries ... OK ./rasterDT.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./rasterDT.Rcheck/00check.log:* checking Rd \usage sections ... OK ./rasterDT.Rcheck/00check.log:* checking Rd contents ... OK ./rasterDT.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./rasterDT.Rcheck/00check.log:* checking LazyData ... NOTE ./rasterDT.Rcheck/00check.log: 'LazyData' is specified without a 'data' directory ./rasterDT.Rcheck/00check.log:* checking examples ... ERROR ./rasterDT.Rcheck/00check.log:Running examples in ‘rasterDT-Ex.R’ failed ./rasterDT.Rcheck/00check.log:The error most likely occurred in: ./rasterDT.Rcheck/00check.log:> ### Name: fasterizeDT ./rasterDT.Rcheck/00check.log:> ### Title: Polygon Rasterization Using Numeric, Factor, or Character Fields ./rasterDT.Rcheck/00check.log:> ### Aliases: fasterizeDT ./rasterDT.Rcheck/00check.log:> ./rasterDT.Rcheck/00check.log:> ### ** Examples ./rasterDT.Rcheck/00check.log:> ./rasterDT.Rcheck/00check.log:> ## Load example polygons and prepare a template raster ./rasterDT.Rcheck/00check.log:> SPDF <- rgdal::readOGR(system.file("external", package = "raster"), "lux") ./rasterDT.Rcheck/00check.log:OGR data source with driver: ESRI Shapefile ./rasterDT.Rcheck/00check.log:Source: "/home/mdowle/build/revdeplib/raster/external", layer: "lux" ./rasterDT.Rcheck/00check.log:with 12 features ./rasterDT.Rcheck/00check.log:It has 5 fields ./rasterDT.Rcheck/00check.log:> llratio <- 1/cos(pi * mean(coordinates(SPDF)[, 2])/180) ./rasterDT.Rcheck/00check.log:> rr <- raster(extent(SPDF), ./rasterDT.Rcheck/00check.log:+ resolution = c(llratio * 0.01, 0.01), ./rasterDT.Rcheck/00check.log:+ crs = proj4string(SPDF)) ./rasterDT.Rcheck/00check.log:Warning in proj4string(SPDF) : ./rasterDT.Rcheck/00check.log: CRS object has comment, which is lost in output ./rasterDT.Rcheck/00check.log:> ./rasterDT.Rcheck/00check.log:> ## An integer-valued field produces a numeric raster ./rasterDT.Rcheck/00check.log:> rInt <- fasterizeDT(SPDF, rr, field = "ID_2") ./rasterDT.Rcheck/00check.log:> plot(rInt, col = colorRampPalette(blues9)(12)) ./rasterDT.Rcheck/00check.log:> ./rasterDT.Rcheck/00check.log:> ## A character-valued field returns a factor raster ./rasterDT.Rcheck/00check.log:> rFac <- fasterizeDT(SPDF, rr, field = "NAME_2") ./rasterDT.Rcheck/00check.log:> if (require(rasterVis)) { ./rasterDT.Rcheck/00check.log:+ levelplot(rFac) ./rasterDT.Rcheck/00check.log:+ } ./rasterDT.Rcheck/00check.log:Loading required package: rasterVis ./rasterDT.Rcheck/00check.log:Loading required package: terra ./rasterDT.Rcheck/00check.log:terra version 1.4.9 ./rasterDT.Rcheck/00check.log:Attaching package: ‘terra’ ./rasterDT.Rcheck/00check.log:The following objects are masked from ‘package:data.table’: ./rasterDT.Rcheck/00check.log: copy, shift ./rasterDT.Rcheck/00check.log:The following objects are masked from ‘package:raster’: ./rasterDT.Rcheck/00check.log: RGB, adjacent, animate, area, boundaries, buffer, cellFromRowCol, ./rasterDT.Rcheck/00check.log: cellFromRowColCombine, cellFromXY, clamp, click, colFromCell, ./rasterDT.Rcheck/00check.log: colFromX, cover, crop, crosstab, crs, crs<-, distance, erase, ./rasterDT.Rcheck/00check.log: extend, extract, flip, focal, freq, geom, hasValues, inMemory, ./rasterDT.Rcheck/00check.log: init, interpolate, mask, modal, mosaic, ncell, ncol<-, nrow<-, ./rasterDT.Rcheck/00check.log: origin, origin<-, plotRGB, rasterize, readStart, readStop, rectify, ./rasterDT.Rcheck/00check.log: res, res<-, resample, rotate, rowColFromCell, rowFromCell, ./rasterDT.Rcheck/00check.log: rowFromY, setMinMax, setValues, shift, stretch, symdif, terrain, ./rasterDT.Rcheck/00check.log: trim, values, values<-, writeRaster, writeStart, writeStop, ./rasterDT.Rcheck/00check.log: writeValues, xFromCell, xFromCol, xmax, xmax<-, xmin, xmin<-, xres, ./rasterDT.Rcheck/00check.log: xyFromCell, yFromCell, yFromRow, ymax, ymax<-, ymin, ymin<-, yres, ./rasterDT.Rcheck/00check.log: zonal, zoom ./rasterDT.Rcheck/00check.log:Loading required package: lattice ./rasterDT.Rcheck/00check.log:Loading required package: latticeExtra ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::init’ by ‘terra::init’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::writeStop’ by ‘terra::writeStop’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::extract’ by ‘terra::extract’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::yFromCell’ by ‘terra::yFromCell’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::adjacent’ by ‘terra::adjacent’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::cellFromRowColCombine’ by ‘terra::cellFromRowColCombine’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::RGB’ by ‘terra::RGB’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::nrow<-’ by ‘terra::nrow<-’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::rotate’ by ‘terra::rotate’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::click’ by ‘terra::click’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::readStart’ by ‘terra::readStart’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::ymax<-’ by ‘terra::ymax<-’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::mosaic’ by ‘terra::mosaic’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::yres’ by ‘terra::yres’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::xres’ by ‘terra::xres’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::ymin’ by ‘terra::ymin’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::mask’ by ‘terra::mask’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::xmin’ by ‘terra::xmin’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::animate’ by ‘terra::animate’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::cellFromRowCol’ by ‘terra::cellFromRowCol’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::hasValues’ by ‘terra::hasValues’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::rasterize’ by ‘terra::rasterize’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::writeStart’ by ‘terra::writeStart’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::setValues’ by ‘terra::setValues’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::resample’ by ‘terra::resample’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::xyFromCell’ by ‘terra::xyFromCell’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::stretch’ by ‘terra::stretch’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::cover’ by ‘terra::cover’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::writeValues’ by ‘terra::writeValues’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::values’ by ‘terra::values’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::cellFromXY’ by ‘terra::cellFromXY’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::xmin<-’ by ‘terra::xmin<-’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::modal’ by ‘terra::modal’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::res’ by ‘terra::res’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::freq’ by ‘terra::freq’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::ncell’ by ‘terra::ncell’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::trim’ by ‘terra::trim’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::area’ by ‘terra::area’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::erase’ by ‘terra::erase’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::writeRaster’ by ‘terra::writeRaster’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::res<-’ by ‘terra::res<-’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::extend’ by ‘terra::extend’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::yFromRow’ by ‘terra::yFromRow’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::crs’ by ‘terra::crs’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::clamp’ by ‘terra::clamp’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::colFromCell’ by ‘terra::colFromCell’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::zonal’ by ‘terra::zonal’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::boundaries’ by ‘terra::boundaries’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::symdif’ by ‘terra::symdif’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::ncol<-’ by ‘terra::ncol<-’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::origin’ by ‘terra::origin’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::rowColFromCell’ by ‘terra::rowColFromCell’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::terrain’ by ‘terra::terrain’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::geom’ by ‘terra::geom’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::xFromCell’ by ‘terra::xFromCell’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::crs<-’ by ‘terra::crs<-’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::rowFromCell’ by ‘terra::rowFromCell’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::inMemory’ by ‘terra::inMemory’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::xmax<-’ by ‘terra::xmax<-’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::crosstab’ by ‘terra::crosstab’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::zoom’ by ‘terra::zoom’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::values<-’ by ‘terra::values<-’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::setMinMax’ by ‘terra::setMinMax’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::distance’ by ‘terra::distance’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::readStop’ by ‘terra::readStop’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::origin<-’ by ‘terra::origin<-’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::flip’ by ‘terra::flip’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::crop’ by ‘terra::crop’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::xFromCol’ by ‘terra::xFromCol’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::interpolate’ by ‘terra::interpolate’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::shift’ by ‘terra::shift’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::focal’ by ‘terra::focal’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::buffer’ by ‘terra::buffer’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::ymin<-’ by ‘terra::ymin<-’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::colFromX’ by ‘terra::colFromX’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::ymax’ by ‘terra::ymax’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::rectify’ by ‘terra::rectify’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::xmax’ by ‘terra::xmax’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::rowFromY’ by ‘terra::rowFromY’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Warning: replacing previous import ‘raster::plotRGB’ by ‘terra::plotRGB’ when loading ‘rasterVis’ ./rasterDT.Rcheck/00check.log:Error in (function (classes, fdef, mtable) : ./rasterDT.Rcheck/00check.log: unable to find an inherited method for function ‘xmin’ for signature ‘"Extent"’ ./rasterDT.Rcheck/00check.log:Calls: levelplot ... levelplot -> .local -> .levelplot -> xmin -> ./rasterDT.Rcheck/00check.log:Execution halted ./rasterDT.Rcheck/00check.log:* checking PDF version of manual ... OK ./rasterDT.Rcheck/00check.log:* DONE ./rasterDT.Rcheck/00check.log:Status: 1 ERROR, 1 NOTE mstrio_11.3.0.1.tar.gz rio_0.5.27.tar.gz ./rio.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/rio.Rcheck’ ./rio.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./rio.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./rio.Rcheck/00check.log:* using session charset: UTF-8 ./rio.Rcheck/00check.log:* checking for file ‘rio/DESCRIPTION’ ... OK ./rio.Rcheck/00check.log:* checking extension type ... Package ./rio.Rcheck/00check.log:* this is package ‘rio’ version ‘0.5.27’ ./rio.Rcheck/00check.log:* package encoding: UTF-8 ./rio.Rcheck/00check.log:* checking package namespace information ... OK ./rio.Rcheck/00check.log:* checking package dependencies ... OK ./rio.Rcheck/00check.log:* checking if this is a source package ... OK ./rio.Rcheck/00check.log:* checking if there is a namespace ... OK ./rio.Rcheck/00check.log:* checking for executable files ... OK ./rio.Rcheck/00check.log:* checking for hidden files and directories ... OK ./rio.Rcheck/00check.log:* checking for portable file names ... OK ./rio.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./rio.Rcheck/00check.log:* checking whether package ‘rio’ can be installed ... OK ./rio.Rcheck/00check.log:* checking installed package size ... OK ./rio.Rcheck/00check.log:* checking package directory ... OK ./rio.Rcheck/00check.log:* checking ‘build’ directory ... OK ./rio.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./rio.Rcheck/00check.log:* checking top-level files ... OK ./rio.Rcheck/00check.log:* checking for left-over files ... OK ./rio.Rcheck/00check.log:* checking index information ... OK ./rio.Rcheck/00check.log:* checking package subdirectories ... OK ./rio.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./rio.Rcheck/00check.log:* checking R files for syntax errors ... OK ./rio.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./rio.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./rio.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./rio.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./rio.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./rio.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./rio.Rcheck/00check.log:* checking dependencies in R code ... OK ./rio.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./rio.Rcheck/00check.log:* checking replacement functions ... OK ./rio.Rcheck/00check.log:* checking foreign function calls ... OK ./rio.Rcheck/00check.log:* checking R code for possible problems ... OK ./rio.Rcheck/00check.log:* checking Rd files ... OK ./rio.Rcheck/00check.log:* checking Rd metadata ... OK ./rio.Rcheck/00check.log:* checking Rd cross-references ... OK ./rio.Rcheck/00check.log:* checking for missing documentation entries ... OK ./rio.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./rio.Rcheck/00check.log:* checking Rd \usage sections ... OK ./rio.Rcheck/00check.log:* checking Rd contents ... OK ./rio.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./rio.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./rio.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./rio.Rcheck/00check.log:* checking examples ... OK ./rio.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./rio.Rcheck/00check.log:* checking tests ... ERROR ./rio.Rcheck/00check.log: Running ‘test-all.R’ ./rio.Rcheck/00check.log:Running the tests in ‘tests/test-all.R’ failed. ./rio.Rcheck/00check.log:Last 13 lines of output: ./rio.Rcheck/00check.log: 49: test_code(NULL, exprs, env) ./rio.Rcheck/00check.log: 50: source_file(path, child_env(env), wrap = wrap) ./rio.Rcheck/00check.log: 51: FUN(X[[i]], ...) ./rio.Rcheck/00check.log: 52: lapply(test_paths, test_one_file, env = env, wrap = wrap) ./rio.Rcheck/00check.log: 53: doTryCatch(return(expr), name, parentenv, handler) ./rio.Rcheck/00check.log: 54: tryCatchOne(expr, names, parentenv, handlers[[1L]]) ./rio.Rcheck/00check.log: 55: tryCatchList(expr, classes, parentenv, handlers) ./rio.Rcheck/00check.log: 56: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL}) ./rio.Rcheck/00check.log: 57: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap)) ./rio.Rcheck/00check.log: 58: test_files(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package) ./rio.Rcheck/00check.log: 59: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package, parallel = parallel) ./rio.Rcheck/00check.log: 60: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") ./rio.Rcheck/00check.log: 61: test_check("rio", reporter = "summary") ./rio.Rcheck/00check.log: An irrecoverable exception occurred. R is aborting now ... ./rio.Rcheck/00check.log: Segmentation fault (core dumped) ./rio.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./rio.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./rio.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./rio.Rcheck/00check.log: ‘rio.Rmd’ using ‘UTF-8’... OK ./rio.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./rio.Rcheck/00check.log:* checking PDF version of manual ... OK ./rio.Rcheck/00check.log:* DONE ./rio.Rcheck/00check.log:Status: 1 ERROR riskRegression_2020.12.08.tar.gz ./riskRegression.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/riskRegression.Rcheck’ ./riskRegression.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./riskRegression.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./riskRegression.Rcheck/00check.log:* using session charset: UTF-8 ./riskRegression.Rcheck/00check.log:* checking for file ‘riskRegression/DESCRIPTION’ ... OK ./riskRegression.Rcheck/00check.log:* checking extension type ... Package ./riskRegression.Rcheck/00check.log:* this is package ‘riskRegression’ version ‘2020.12.08’ ./riskRegression.Rcheck/00check.log:* package encoding: UTF-8 ./riskRegression.Rcheck/00check.log:* checking package namespace information ... OK ./riskRegression.Rcheck/00check.log:* checking package dependencies ... OK ./riskRegression.Rcheck/00check.log:* checking if this is a source package ... OK ./riskRegression.Rcheck/00check.log:* checking if there is a namespace ... OK ./riskRegression.Rcheck/00check.log:* checking for executable files ... OK ./riskRegression.Rcheck/00check.log:* checking for hidden files and directories ... OK ./riskRegression.Rcheck/00check.log:* checking for portable file names ... OK ./riskRegression.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./riskRegression.Rcheck/00check.log:* checking whether package ‘riskRegression’ can be installed ... OK ./riskRegression.Rcheck/00check.log:* checking installed package size ... NOTE ./riskRegression.Rcheck/00check.log: installed size is 12.0Mb ./riskRegression.Rcheck/00check.log: sub-directories of 1Mb or more: ./riskRegression.Rcheck/00check.log: libs 10.6Mb ./riskRegression.Rcheck/00check.log:* checking package directory ... OK ./riskRegression.Rcheck/00check.log:* checking ‘build’ directory ... OK ./riskRegression.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./riskRegression.Rcheck/00check.log:* checking top-level files ... OK ./riskRegression.Rcheck/00check.log:* checking for left-over files ... OK ./riskRegression.Rcheck/00check.log:* checking index information ... OK ./riskRegression.Rcheck/00check.log:* checking package subdirectories ... OK ./riskRegression.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./riskRegression.Rcheck/00check.log:* checking R files for syntax errors ... OK ./riskRegression.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./riskRegression.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./riskRegression.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./riskRegression.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./riskRegression.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./riskRegression.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./riskRegression.Rcheck/00check.log:* checking dependencies in R code ... OK ./riskRegression.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./riskRegression.Rcheck/00check.log:* checking replacement functions ... OK ./riskRegression.Rcheck/00check.log:* checking foreign function calls ... OK ./riskRegression.Rcheck/00check.log:* checking R code for possible problems ... OK ./riskRegression.Rcheck/00check.log:* checking Rd files ... OK ./riskRegression.Rcheck/00check.log:* checking Rd metadata ... OK ./riskRegression.Rcheck/00check.log:* checking Rd cross-references ... OK ./riskRegression.Rcheck/00check.log:* checking for missing documentation entries ... OK ./riskRegression.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./riskRegression.Rcheck/00check.log:* checking Rd \usage sections ... OK ./riskRegression.Rcheck/00check.log:* checking Rd contents ... OK ./riskRegression.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./riskRegression.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./riskRegression.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./riskRegression.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./riskRegression.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./riskRegression.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./riskRegression.Rcheck/00check.log:* checking compilation flags in Makevars ... OK ./riskRegression.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./riskRegression.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./riskRegression.Rcheck/00check.log:* checking use of PKG_*FLAGS in Makefiles ... OK ./riskRegression.Rcheck/00check.log:* checking compiled code ... OK ./riskRegression.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./riskRegression.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./riskRegression.Rcheck/00check.log:* checking examples ... OK ./riskRegression.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./riskRegression.Rcheck/00check.log:* checking tests ... ERROR ./riskRegression.Rcheck/00check.log: Running ‘test-AUC.R’ ./riskRegression.Rcheck/00check.log: Running ‘test-BinomialRegression.R’ ./riskRegression.Rcheck/00check.log:Running the tests in ‘tests/test-BinomialRegression.R’ failed. ./riskRegression.Rcheck/00check.log:Last 13 lines of output: ./riskRegression.Rcheck/00check.log: + expect_success(ARR(Hist(time,status)~thick+strata(invasion)+epicel,data=Melanoma,cens.model="cox",cause=1)) ./riskRegression.Rcheck/00check.log: + expect_success(ARR(Hist(time,status)~thick+strata(invasion)+epicel,data=Melanoma,cens.model="cox",cens.formula=~thick+strat(invasion)+epicel,cause=1)) ./riskRegression.Rcheck/00check.log: + expect_success(ARR(Hist(time,status)~sex+strata(invasion)+epicel,data=Melanoma,cens.model="cox",cens.formula=~logthick+age,cause=1)) ./riskRegression.Rcheck/00check.log: + }) ./riskRegression.Rcheck/00check.log: ── Failure (???): Censoring model ────────────────────────────────────────────── ./riskRegression.Rcheck/00check.log: no expectation used. ./riskRegression.Rcheck/00check.log: ./riskRegression.Rcheck/00check.log: ── Failure (???): Censoring model ────────────────────────────────────────────── ./riskRegression.Rcheck/00check.log: no expectation used. ./riskRegression.Rcheck/00check.log: ./riskRegression.Rcheck/00check.log: ── Failure (???): Censoring model ────────────────────────────────────────────── ./riskRegression.Rcheck/00check.log: no expectation used. ./riskRegression.Rcheck/00check.log: ./riskRegression.Rcheck/00check.log: Error: Test failed ./riskRegression.Rcheck/00check.log: Execution halted ./riskRegression.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./riskRegression.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./riskRegression.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./riskRegression.Rcheck/00check.log: ‘IPA.html.asis’ using ‘UTF-8’... OK ./riskRegression.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./riskRegression.Rcheck/00check.log:* checking PDF version of manual ... OK ./riskRegression.Rcheck/00check.log:* DONE ./riskRegression.Rcheck/00check.log:Status: 1 ERROR, 1 NOTE SpaDES.core_1.0.9.tar.gz ./SpaDES.core.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/SpaDES.core.Rcheck’ ./SpaDES.core.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./SpaDES.core.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./SpaDES.core.Rcheck/00check.log:* using session charset: UTF-8 ./SpaDES.core.Rcheck/00check.log:* checking for file ‘SpaDES.core/DESCRIPTION’ ... OK ./SpaDES.core.Rcheck/00check.log:* checking extension type ... Package ./SpaDES.core.Rcheck/00check.log:* this is package ‘SpaDES.core’ version ‘1.0.9’ ./SpaDES.core.Rcheck/00check.log:* package encoding: UTF-8 ./SpaDES.core.Rcheck/00check.log:* checking package namespace information ... OK ./SpaDES.core.Rcheck/00check.log:* checking package dependencies ... OK ./SpaDES.core.Rcheck/00check.log:* checking if this is a source package ... OK ./SpaDES.core.Rcheck/00check.log:* checking if there is a namespace ... OK ./SpaDES.core.Rcheck/00check.log:* checking for executable files ... OK ./SpaDES.core.Rcheck/00check.log:* checking for hidden files and directories ... OK ./SpaDES.core.Rcheck/00check.log:* checking for portable file names ... OK ./SpaDES.core.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./SpaDES.core.Rcheck/00check.log:* checking whether package ‘SpaDES.core’ can be installed ... OK ./SpaDES.core.Rcheck/00check.log:* checking installed package size ... OK ./SpaDES.core.Rcheck/00check.log:* checking package directory ... OK ./SpaDES.core.Rcheck/00check.log:* checking ‘build’ directory ... OK ./SpaDES.core.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./SpaDES.core.Rcheck/00check.log:* checking top-level files ... OK ./SpaDES.core.Rcheck/00check.log:* checking for left-over files ... OK ./SpaDES.core.Rcheck/00check.log:* checking index information ... OK ./SpaDES.core.Rcheck/00check.log:* checking package subdirectories ... OK ./SpaDES.core.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./SpaDES.core.Rcheck/00check.log:* checking R files for syntax errors ... OK ./SpaDES.core.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./SpaDES.core.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./SpaDES.core.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./SpaDES.core.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./SpaDES.core.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./SpaDES.core.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./SpaDES.core.Rcheck/00check.log:* checking dependencies in R code ... OK ./SpaDES.core.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./SpaDES.core.Rcheck/00check.log:* checking replacement functions ... OK ./SpaDES.core.Rcheck/00check.log:* checking foreign function calls ... OK ./SpaDES.core.Rcheck/00check.log:* checking R code for possible problems ... OK ./SpaDES.core.Rcheck/00check.log:* checking Rd files ... OK ./SpaDES.core.Rcheck/00check.log:* checking Rd metadata ... OK ./SpaDES.core.Rcheck/00check.log:* checking Rd cross-references ... OK ./SpaDES.core.Rcheck/00check.log:* checking for missing documentation entries ... OK ./SpaDES.core.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./SpaDES.core.Rcheck/00check.log:* checking Rd \usage sections ... OK ./SpaDES.core.Rcheck/00check.log:* checking Rd contents ... OK ./SpaDES.core.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./SpaDES.core.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./SpaDES.core.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./SpaDES.core.Rcheck/00check.log:* checking examples ... ERROR ./SpaDES.core.Rcheck/00check.log:Running examples in ‘SpaDES.core-Ex.R’ failed ./SpaDES.core.Rcheck/00check.log:The error most likely occurred in: ./SpaDES.core.Rcheck/00check.log:> ### Name: moduleMetadata ./SpaDES.core.Rcheck/00check.log:> ### Title: Parse and extract module metadata ./SpaDES.core.Rcheck/00check.log:> ### Aliases: moduleMetadata ./SpaDES.core.Rcheck/00check.log:> ### moduleMetadata,missing,character,character-method ./SpaDES.core.Rcheck/00check.log:> ### moduleMetadata,missing,character,missing-method ./SpaDES.core.Rcheck/00check.log:> ### moduleMetadata,ANY,ANY,ANY-method ./SpaDES.core.Rcheck/00check.log:> ./SpaDES.core.Rcheck/00check.log:> ### ** Examples ./SpaDES.core.Rcheck/00check.log:> ./SpaDES.core.Rcheck/00check.log:> path <- system.file("sampleModules", package = "SpaDES.core") ./SpaDES.core.Rcheck/00check.log:> sampleModules <- dir(path) ./SpaDES.core.Rcheck/00check.log:> # turn off code checking -- don't need it here ./SpaDES.core.Rcheck/00check.log:> opts <- options("spades.moduleCodeChecks" = FALSE, ./SpaDES.core.Rcheck/00check.log:+ "spades.useRequire" = FALSE) ./SpaDES.core.Rcheck/00check.log:> ./SpaDES.core.Rcheck/00check.log:> x <- moduleMetadata(sampleModules[3], path = path) ./SpaDES.core.Rcheck/00check.log:Assuming sim is a module name ./SpaDES.core.Rcheck/00check.log:> ./SpaDES.core.Rcheck/00check.log:> # using simList ./SpaDES.core.Rcheck/00check.log:> mySim <- simInit( ./SpaDES.core.Rcheck/00check.log:+ times = list(start = 2000.0, end = 2001.0, timeunit = "year"), ./SpaDES.core.Rcheck/00check.log:+ params = list( ./SpaDES.core.Rcheck/00check.log:+ .globals = list(stackName = "landscape") ./SpaDES.core.Rcheck/00check.log:+ ), ./SpaDES.core.Rcheck/00check.log:+ modules = list("caribouMovement"), ./SpaDES.core.Rcheck/00check.log:+ paths = list(modulePath = system.file("sampleModules", package = "SpaDES.core")) ./SpaDES.core.Rcheck/00check.log:+ ) ./SpaDES.core.Rcheck/00check.log:Setting: ./SpaDES.core.Rcheck/00check.log: options( ./SpaDES.core.Rcheck/00check.log: spades.modulePath = '/home/mdowle/build/revdeplib/SpaDES.core.Rcheck/SpaDES.core/sampleModules' ./SpaDES.core.Rcheck/00check.log: ) ./SpaDES.core.Rcheck/00check.log:Paths set to: ./SpaDES.core.Rcheck/00check.log: options( ./SpaDES.core.Rcheck/00check.log: rasterTmpDir = '/tmp/Rtmpe0Ud1S/raster' ./SpaDES.core.Rcheck/00check.log: reproducible.cachePath = '/tmp/Rtmpe0Ud1S/Require/cache' ./SpaDES.core.Rcheck/00check.log: spades.inputPath = '/tmp/Rtmppta9Zz/SpaDES/inputs' ./SpaDES.core.Rcheck/00check.log: spades.outputPath = '/tmp/Rtmppta9Zz/SpaDES/outputs' ./SpaDES.core.Rcheck/00check.log: spades.modulePath = '/home/mdowle/build/revdeplib/SpaDES.core.Rcheck/SpaDES.core/sampleModules' ./SpaDES.core.Rcheck/00check.log: ) ./SpaDES.core.Rcheck/00check.log:options('spades.useRequire' = FALSE), so not checking minimum package version requirements ./SpaDES.core.Rcheck/00check.log:Loading required package: SpaDES.tools ./SpaDES.core.Rcheck/00check.log:Loading required package: grid ./SpaDES.core.Rcheck/00check.log:Attaching package: ‘grid’ ./SpaDES.core.Rcheck/00check.log:The following object is masked from ‘package:quickPlot’: ./SpaDES.core.Rcheck/00check.log: gpar ./SpaDES.core.Rcheck/00check.log:Loading required package: raster ./SpaDES.core.Rcheck/00check.log:Loading required package: sp ./SpaDES.core.Rcheck/00check.log:The following .globals were used: ./SpaDES.core.Rcheck/00check.log: module global ./SpaDES.core.Rcheck/00check.log:1: caribouMovement stackName ./SpaDES.core.Rcheck/00check.log:Error in h(simpleError(msg, call)) : ./SpaDES.core.Rcheck/00check.log: error in evaluating the argument 'simGraph' in selecting a method for function '.depsLoadOrder': error in evaluating the argument 'simEdgeList' in selecting a method for function '.depsPruneEdges': INTEGER() can only be applied to a 'integer', not a 'character' ./SpaDES.core.Rcheck/00check.log:Calls: simInit ... bmerge -> .handleSimpleError -> h -> .handleSimpleError -> h ./SpaDES.core.Rcheck/00check.log:Execution halted ./SpaDES.core.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./SpaDES.core.Rcheck/00check.log:* checking tests ... ERROR ./SpaDES.core.Rcheck/00check.log: Running ‘test-all.R’ ./SpaDES.core.Rcheck/00check.log:Running the tests in ‘tests/test-all.R’ failed. ./SpaDES.core.Rcheck/00check.log:Last 13 lines of output: ./SpaDES.core.Rcheck/00check.log: 15. │ │ └─base::eval(mc, parent.frame()) ./SpaDES.core.Rcheck/00check.log: 16. │ └─(function (deps, plot) ... ./SpaDES.core.Rcheck/00check.log: 17. │ ├─sim.out[sim.in, nomatch = NA_character_, allow.cartesian = TRUE] ./SpaDES.core.Rcheck/00check.log: 18. │ └─data.table::`[.data.table`(...) ./SpaDES.core.Rcheck/00check.log: 19. │ └─data.table:::bmerge(...) ./SpaDES.core.Rcheck/00check.log: 20. ├─SpaDES.core::.depsLoadOrder(sim, .) ./SpaDES.core.Rcheck/00check.log: 21. ├─SpaDES.core::.depsPruneEdges(.) ./SpaDES.core.Rcheck/00check.log: 22. ├─base::.handleSimpleError(...) ./SpaDES.core.Rcheck/00check.log: 23. │ └─base:::h(simpleError(msg, call)) ./SpaDES.core.Rcheck/00check.log: 24. └─base::.handleSimpleError(...) ./SpaDES.core.Rcheck/00check.log: 25. └─base:::h(simpleError(msg, call)) ./SpaDES.core.Rcheck/00check.log: ./SpaDES.core.Rcheck/00check.log: [ FAIL 27 | WARN 0 | SKIP 21 | PASS 228 ] ./SpaDES.core.Rcheck/00check.log: Error: Test failures ./SpaDES.core.Rcheck/00check.log: Execution halted ./SpaDES.core.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./SpaDES.core.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./SpaDES.core.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./SpaDES.core.Rcheck/00check.log: ‘i-introduction.Rmd’ using ‘UTF-8’... OK ./SpaDES.core.Rcheck/00check.log: ‘ii-modules.Rmd’ using ‘UTF-8’... OK ./SpaDES.core.Rcheck/00check.log: ‘iii-cache.Rmd’ using ‘UTF-8’... OK ./SpaDES.core.Rcheck/00check.log: ‘iv-advanced.Rmd’ using ‘UTF-8’... OK ./SpaDES.core.Rcheck/00check.log: ‘v-automated-testing.Rmd’ using ‘UTF-8’... OK ./SpaDES.core.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./SpaDES.core.Rcheck/00check.log:Error(s) in re-building vignettes: ./SpaDES.core.Rcheck/00check.log:--- re-building ‘i-introduction.Rmd’ using rmarkdown ./SpaDES.core.Rcheck/00check.log:--- finished re-building ‘i-introduction.Rmd’ ./SpaDES.core.Rcheck/00check.log:--- re-building ‘ii-modules.Rmd’ using rmarkdown ./SpaDES.core.Rcheck/00check.log:Quitting from lines 202-227 (ii-modules.Rmd) ./SpaDES.core.Rcheck/00check.log:Error: processing vignette 'ii-modules.Rmd' failed with diagnostics: ./SpaDES.core.Rcheck/00check.log:error in evaluating the argument 'simGraph' in selecting a method for function '.depsLoadOrder': error in evaluating the argument 'simEdgeList' in selecting a method for function '.depsPruneEdges': INTEGER() can only be applied to a 'integer', not a 'character' ./SpaDES.core.Rcheck/00check.log:--- failed re-building ‘ii-modules.Rmd’ ./SpaDES.core.Rcheck/00check.log:--- re-building ‘iii-cache.Rmd’ using rmarkdown ./SpaDES.core.Rcheck/00check.log:Attaching package: 'raster' ./SpaDES.core.Rcheck/00check.log:The following object is masked from 'package:magrittr': ./SpaDES.core.Rcheck/00check.log: extract ./SpaDES.core.Rcheck/00check.log:Loading required package: quickPlot ./SpaDES.core.Rcheck/00check.log:Attaching package: 'SpaDES.core' ./SpaDES.core.Rcheck/00check.log:The following objects are masked from 'package:stats': ./SpaDES.core.Rcheck/00check.log: end, start ./SpaDES.core.Rcheck/00check.log:The following object is masked from 'package:utils': ./SpaDES.core.Rcheck/00check.log: citation ./SpaDES.core.Rcheck/00check.log:Setting: ./SpaDES.core.Rcheck/00check.log: options( ./SpaDES.core.Rcheck/00check.log: spades.modulePath = '/home/mdowle/build/revdeplib/SpaDES.core.Rcheck/SpaDES.core/sampleModules' ./SpaDES.core.Rcheck/00check.log: ) ./SpaDES.core.Rcheck/00check.log:Paths set to: ./SpaDES.core.Rcheck/00check.log: options( ./SpaDES.core.Rcheck/00check.log: rasterTmpDir = '/tmp/Rtmp2wSadt/raster' ./SpaDES.core.Rcheck/00check.log: reproducible.cachePath = '/tmp/Rtmp2wSadt/Require/cache' ./SpaDES.core.Rcheck/00check.log: spades.inputPath = '/tmp/Rtmppta9Zz/SpaDES/inputs' ./SpaDES.core.Rcheck/00check.log: spades.outputPath = '/tmp/Rtmppta9Zz/SpaDES/outputs' ./SpaDES.core.Rcheck/00check.log: spades.modulePath = '/home/mdowle/build/revdeplib/SpaDES.core.Rcheck/SpaDES.core/sampleModules' ./SpaDES.core.Rcheck/00check.log: ) ./SpaDES.core.Rcheck/00check.log:options('spades.useRequire' = FALSE), so not checking minimum package version requirements ./SpaDES.core.Rcheck/00check.log:Loading required package: RColorBrewer ./SpaDES.core.Rcheck/00check.log:The following .globals were used: ./SpaDES.core.Rcheck/00check.log: module global ./SpaDES.core.Rcheck/00check.log:1: fireSpread stackName ./SpaDES.core.Rcheck/00check.log:2: randomLandscapes stackName ./SpaDES.core.Rcheck/00check.log:Quitting from lines 59-74 (iii-cache.Rmd) ./SpaDES.core.Rcheck/00check.log:Error: processing vignette 'iii-cache.Rmd' failed with diagnostics: ./SpaDES.core.Rcheck/00check.log:error in evaluating the argument 'simGraph' in selecting a method for function '.depsLoadOrder': error in evaluating the argument 'simEdgeList' in selecting a method for function '.depsPruneEdges': INTEGER() can only be applied to a 'integer', not a 'character' ./SpaDES.core.Rcheck/00check.log:--- failed re-building ‘iii-cache.Rmd’ ./SpaDES.core.Rcheck/00check.log:--- re-building ‘iv-advanced.Rmd’ using rmarkdown ./SpaDES.core.Rcheck/00check.log:--- finished re-building ‘iv-advanced.Rmd’ ./SpaDES.core.Rcheck/00check.log:--- re-building ‘v-automated-testing.Rmd’ using rmarkdown ./SpaDES.core.Rcheck/00check.log:--- finished re-building ‘v-automated-testing.Rmd’ ./SpaDES.core.Rcheck/00check.log:SUMMARY: processing the following files failed: ./SpaDES.core.Rcheck/00check.log: ‘ii-modules.Rmd’ ‘iii-cache.Rmd’ ./SpaDES.core.Rcheck/00check.log:Error: Vignette re-building failed. ./SpaDES.core.Rcheck/00check.log:Execution halted ./SpaDES.core.Rcheck/00check.log:* checking PDF version of manual ... OK ./SpaDES.core.Rcheck/00check.log:* DONE ./SpaDES.core.Rcheck/00check.log:Status: 2 ERRORs, 1 WARNING txshift_0.3.5.tar.gz ./txshift.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/txshift.Rcheck’ ./txshift.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./txshift.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./txshift.Rcheck/00check.log:* using session charset: UTF-8 ./txshift.Rcheck/00check.log:* checking for file ‘txshift/DESCRIPTION’ ... OK ./txshift.Rcheck/00check.log:* this is package ‘txshift’ version ‘0.3.5’ ./txshift.Rcheck/00check.log:* package encoding: UTF-8 ./txshift.Rcheck/00check.log:* checking package namespace information ... OK ./txshift.Rcheck/00check.log:* checking package dependencies ... NOTE ./txshift.Rcheck/00check.log:Package which this enhances but not available for checking: ‘sl3’ ./txshift.Rcheck/00check.log:* checking if this is a source package ... OK ./txshift.Rcheck/00check.log:* checking if there is a namespace ... OK ./txshift.Rcheck/00check.log:* checking for executable files ... OK ./txshift.Rcheck/00check.log:* checking for hidden files and directories ... OK ./txshift.Rcheck/00check.log:* checking for portable file names ... OK ./txshift.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./txshift.Rcheck/00check.log:* checking whether package ‘txshift’ can be installed ... OK ./txshift.Rcheck/00check.log:* checking installed package size ... OK ./txshift.Rcheck/00check.log:* checking package directory ... OK ./txshift.Rcheck/00check.log:* checking ‘build’ directory ... OK ./txshift.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./txshift.Rcheck/00check.log:* checking top-level files ... OK ./txshift.Rcheck/00check.log:* checking for left-over files ... OK ./txshift.Rcheck/00check.log:* checking index information ... OK ./txshift.Rcheck/00check.log:* checking package subdirectories ... OK ./txshift.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./txshift.Rcheck/00check.log:* checking R files for syntax errors ... OK ./txshift.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./txshift.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./txshift.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./txshift.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./txshift.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./txshift.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./txshift.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./txshift.Rcheck/00check.log:Namespace in Imports field not imported from: ‘tibble’ ./txshift.Rcheck/00check.log: All declared Imports should be used. ./txshift.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./txshift.Rcheck/00check.log:* checking replacement functions ... OK ./txshift.Rcheck/00check.log:* checking foreign function calls ... OK ./txshift.Rcheck/00check.log:* checking R code for possible problems ... OK ./txshift.Rcheck/00check.log:* checking Rd files ... OK ./txshift.Rcheck/00check.log:* checking Rd metadata ... OK ./txshift.Rcheck/00check.log:* checking Rd cross-references ... OK ./txshift.Rcheck/00check.log:* checking for missing documentation entries ... OK ./txshift.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./txshift.Rcheck/00check.log:* checking Rd \usage sections ... OK ./txshift.Rcheck/00check.log:* checking Rd contents ... OK ./txshift.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./txshift.Rcheck/00check.log:* checking LazyData ... NOTE ./txshift.Rcheck/00check.log: 'LazyData' is specified without a 'data' directory ./txshift.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./txshift.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./txshift.Rcheck/00check.log:* checking examples ... OK ./txshift.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./txshift.Rcheck/00check.log:* checking tests ... ERROR ./txshift.Rcheck/00check.log: Running ‘testthat.R’ ./txshift.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./txshift.Rcheck/00check.log:Last 13 lines of output: ./txshift.Rcheck/00check.log: ── Error (test-tmle_comparison.R:124:1): (code run outside of `test_that()`) ─── ./txshift.Rcheck/00check.log: Error in `hal9001::fit_hal(X = as.matrix(data_internal[, ..v_names]), Y = as.numeric(eif_eval$eif_unweighted[C_samp == ./txshift.Rcheck/00check.log: 1]), max_degree = NULL, fit_type = "glmnet", family = "gaussian", ./txshift.Rcheck/00check.log: return_lasso = FALSE, standardize = FALSE, type.measure = "mse", ./txshift.Rcheck/00check.log: nlambda = 1000, lambda.min.ratio = 1/nrow(data_internal), ./txshift.Rcheck/00check.log: yolo = FALSE)`: unused arguments (fit_type = "glmnet", standardize = FALSE, type.measure = "mse", nlambda = 1000, lambda.min.ratio = 1/nrow(data_internal)) ./txshift.Rcheck/00check.log: Backtrace: ./txshift.Rcheck/00check.log: █ ./txshift.Rcheck/00check.log: 1. └─txshift::txshift(...) test-tmle_comparison.R:124:0 ./txshift.Rcheck/00check.log: 2. └─txshift:::tmle_txshift(...) ./txshift.Rcheck/00check.log: 3. └─txshift:::ipcw_eif_update(...) ./txshift.Rcheck/00check.log: ./txshift.Rcheck/00check.log: [ FAIL 2 | WARN 3 | SKIP 0 | PASS 7 ] ./txshift.Rcheck/00check.log: Error: Test failures ./txshift.Rcheck/00check.log: Execution halted ./txshift.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./txshift.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./txshift.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./txshift.Rcheck/00check.log: ‘intro_txshift.Rmd’ using ‘UTF-8’... OK ./txshift.Rcheck/00check.log: ‘ipcw_txshift.Rmd’ using ‘UTF-8’... OK ./txshift.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./txshift.Rcheck/00check.log:* checking PDF version of manual ... OK ./txshift.Rcheck/00check.log:* DONE ./txshift.Rcheck/00check.log:Status: 1 ERROR, 3 NOTEs VIM_6.1.1.tar.gz ./VIM.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/VIM.Rcheck’ ./VIM.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./VIM.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./VIM.Rcheck/00check.log:* using session charset: UTF-8 ./VIM.Rcheck/00check.log:* checking for file ‘VIM/DESCRIPTION’ ... OK ./VIM.Rcheck/00check.log:* this is package ‘VIM’ version ‘6.1.1’ ./VIM.Rcheck/00check.log:* package encoding: UTF-8 ./VIM.Rcheck/00check.log:* checking package namespace information ... OK ./VIM.Rcheck/00check.log:* checking package dependencies ... OK ./VIM.Rcheck/00check.log:* checking if this is a source package ... OK ./VIM.Rcheck/00check.log:* checking if there is a namespace ... OK ./VIM.Rcheck/00check.log:* checking for executable files ... OK ./VIM.Rcheck/00check.log:* checking for hidden files and directories ... OK ./VIM.Rcheck/00check.log:* checking for portable file names ... OK ./VIM.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./VIM.Rcheck/00check.log:* checking whether package ‘VIM’ can be installed ... OK ./VIM.Rcheck/00check.log:* checking installed package size ... NOTE ./VIM.Rcheck/00check.log: installed size is 5.8Mb ./VIM.Rcheck/00check.log: sub-directories of 1Mb or more: ./VIM.Rcheck/00check.log: doc 3.1Mb ./VIM.Rcheck/00check.log: libs 1.3Mb ./VIM.Rcheck/00check.log:* checking package directory ... OK ./VIM.Rcheck/00check.log:* checking ‘build’ directory ... OK ./VIM.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./VIM.Rcheck/00check.log:* checking top-level files ... OK ./VIM.Rcheck/00check.log:* checking for left-over files ... OK ./VIM.Rcheck/00check.log:* checking index information ... OK ./VIM.Rcheck/00check.log:* checking package subdirectories ... OK ./VIM.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./VIM.Rcheck/00check.log:* checking R files for syntax errors ... OK ./VIM.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./VIM.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./VIM.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./VIM.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./VIM.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./VIM.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./VIM.Rcheck/00check.log:* checking dependencies in R code ... NOTE ./VIM.Rcheck/00check.log:Namespace in Imports field not imported from: ‘magrittr’ ./VIM.Rcheck/00check.log: All declared Imports should be used. ./VIM.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./VIM.Rcheck/00check.log:* checking replacement functions ... OK ./VIM.Rcheck/00check.log:* checking foreign function calls ... OK ./VIM.Rcheck/00check.log:* checking R code for possible problems ... OK ./VIM.Rcheck/00check.log:* checking Rd files ... OK ./VIM.Rcheck/00check.log:* checking Rd metadata ... OK ./VIM.Rcheck/00check.log:* checking Rd cross-references ... OK ./VIM.Rcheck/00check.log:* checking for missing documentation entries ... OK ./VIM.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./VIM.Rcheck/00check.log:* checking Rd \usage sections ... OK ./VIM.Rcheck/00check.log:* checking Rd contents ... OK ./VIM.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./VIM.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./VIM.Rcheck/00check.log:* checking data for non-ASCII characters ... NOTE ./VIM.Rcheck/00check.log: Note: found 2754 marked UTF-8 strings ./VIM.Rcheck/00check.log:* checking LazyData ... OK ./VIM.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./VIM.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./VIM.Rcheck/00check.log:* checking compiled code ... OK ./VIM.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./VIM.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./VIM.Rcheck/00check.log:* checking examples ... ERROR ./VIM.Rcheck/00check.log:Running examples in ‘VIM-Ex.R’ failed ./VIM.Rcheck/00check.log:The error most likely occurred in: ./VIM.Rcheck/00check.log:> ### Name: hotdeck ./VIM.Rcheck/00check.log:> ### Title: Hot-Deck Imputation ./VIM.Rcheck/00check.log:> ### Aliases: hotdeck ./VIM.Rcheck/00check.log:> ### Keywords: manip ./VIM.Rcheck/00check.log:> ./VIM.Rcheck/00check.log:> ### ** Examples ./VIM.Rcheck/00check.log:> ./VIM.Rcheck/00check.log:> ./VIM.Rcheck/00check.log:> data(sleep) ./VIM.Rcheck/00check.log:> sleepI <- hotdeck(sleep) ./VIM.Rcheck/00check.log:Error: nomatch= must be either NA or NULL (or 0 for backwards compatibility which is the same as NULL but please use NULL) ./VIM.Rcheck/00check.log:Execution halted ./VIM.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./VIM.Rcheck/00check.log:* checking tests ... ERROR ./VIM.Rcheck/00check.log: Running ‘testthat.R’ ./VIM.Rcheck/00check.log:Running the tests in ‘tests/testthat.R’ failed. ./VIM.Rcheck/00check.log:Last 13 lines of output: ./VIM.Rcheck/00check.log: Backtrace: ./VIM.Rcheck/00check.log: █ ./VIM.Rcheck/00check.log: 1. └─VIM::hotdeck(...) test_impNA.R:26:2 ./VIM.Rcheck/00check.log: 2. ├─...[] ./VIM.Rcheck/00check.log: 3. └─data.table::`[.data.table`(...) ./VIM.Rcheck/00check.log: 4. └─base::eval(jsub, SDenv, parent.frame()) ./VIM.Rcheck/00check.log: 5. └─base::eval(jsub, SDenv, parent.frame()) ./VIM.Rcheck/00check.log: 6. └─VIM:::imputeHD(...) ./VIM.Rcheck/00check.log: 7. ├─xx[J(NA_real_), .I, nomatch = FALSE] ./VIM.Rcheck/00check.log: 8. └─data.table::`[.data.table`(xx, J(NA_real_), .I, nomatch = FALSE) ./VIM.Rcheck/00check.log: 9. └─data.table:::stopf("nomatch= must be either NA or NULL (or 0 for backwards compatibility which is the same as NULL but please use NULL)") ./VIM.Rcheck/00check.log: ./VIM.Rcheck/00check.log: [ FAIL 12 | WARN 0 | SKIP 0 | PASS 160 ] ./VIM.Rcheck/00check.log: Error: Test failures ./VIM.Rcheck/00check.log: Execution halted ./VIM.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./VIM.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./VIM.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./VIM.Rcheck/00check.log: ‘VIM.Rmd’ using ‘UTF-8’... OK ./VIM.Rcheck/00check.log: ‘VisualImp.Rmd’ using ‘UTF-8’... OK ./VIM.Rcheck/00check.log: ‘donorImp.Rmd’ using ‘UTF-8’... OK ./VIM.Rcheck/00check.log: ‘irmi.Rmd’ using ‘UTF-8’... OK ./VIM.Rcheck/00check.log: ‘modelImp.Rmd’ using ‘UTF-8’... OK ./VIM.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./VIM.Rcheck/00check.log:Error(s) in re-building vignettes: ./VIM.Rcheck/00check.log:--- re-building ‘VIM.Rmd’ using rmarkdown ./VIM.Rcheck/00check.log:Loading required package: colorspace ./VIM.Rcheck/00check.log:Loading required package: grid ./VIM.Rcheck/00check.log:VIM is ready to use. ./VIM.Rcheck/00check.log:Suggestions and bug-reports can be submitted at: https://github.com/statistikat/VIM/issues ./VIM.Rcheck/00check.log:Attaching package: 'VIM' ./VIM.Rcheck/00check.log:The following object is masked from 'package:datasets': ./VIM.Rcheck/00check.log: sleep ./VIM.Rcheck/00check.log:--- finished re-building ‘VIM.Rmd’ ./VIM.Rcheck/00check.log:--- re-building ‘VisualImp.Rmd’ using rmarkdown ./VIM.Rcheck/00check.log:Loading required package: colorspace ./VIM.Rcheck/00check.log:Loading required package: grid ./VIM.Rcheck/00check.log:VIM is ready to use. ./VIM.Rcheck/00check.log:Suggestions and bug-reports can be submitted at: https://github.com/statistikat/VIM/issues ./VIM.Rcheck/00check.log:Attaching package: 'VIM' ./VIM.Rcheck/00check.log:The following object is masked from 'package:datasets': ./VIM.Rcheck/00check.log: sleep ./VIM.Rcheck/00check.log:--- finished re-building ‘VisualImp.Rmd’ ./VIM.Rcheck/00check.log:--- re-building ‘donorImp.Rmd’ using rmarkdown ./VIM.Rcheck/00check.log:Loading required package: colorspace ./VIM.Rcheck/00check.log:Loading required package: grid ./VIM.Rcheck/00check.log:VIM is ready to use. ./VIM.Rcheck/00check.log:Suggestions and bug-reports can be submitted at: https://github.com/statistikat/VIM/issues ./VIM.Rcheck/00check.log:Attaching package: 'VIM' ./VIM.Rcheck/00check.log:The following object is masked from 'package:datasets': ./VIM.Rcheck/00check.log: sleep ./VIM.Rcheck/00check.log:Quitting from lines 53-58 (donorImp.Rmd) ./VIM.Rcheck/00check.log:Error: processing vignette 'donorImp.Rmd' failed with diagnostics: ./VIM.Rcheck/00check.log:nomatch= must be either NA or NULL (or 0 for backwards compatibility which is the same as NULL but please use NULL) ./VIM.Rcheck/00check.log:--- failed re-building ‘donorImp.Rmd’ ./VIM.Rcheck/00check.log:--- re-building ‘irmi.Rmd’ using rmarkdown ./VIM.Rcheck/00check.log:Loading required package: colorspace ./VIM.Rcheck/00check.log:Loading required package: grid ./VIM.Rcheck/00check.log:VIM is ready to use. ./VIM.Rcheck/00check.log:Suggestions and bug-reports can be submitted at: https://github.com/statistikat/VIM/issues ./VIM.Rcheck/00check.log:Attaching package: 'VIM' ./VIM.Rcheck/00check.log:The following object is masked from 'package:datasets': ./VIM.Rcheck/00check.log: sleep ./VIM.Rcheck/00check.log:Warning in cbind(TRUE1 = as.numeric(iris[as.matrix(y[which(y$col == 1), : ./VIM.Rcheck/00check.log: number of rows of result is not a multiple of vector length (arg 1) ./VIM.Rcheck/00check.log:--- finished re-building ‘irmi.Rmd’ ./VIM.Rcheck/00check.log:--- re-building ‘modelImp.Rmd’ using rmarkdown ./VIM.Rcheck/00check.log:Loading required package: colorspace ./VIM.Rcheck/00check.log:Loading required package: grid ./VIM.Rcheck/00check.log:VIM is ready to use. ./VIM.Rcheck/00check.log:Suggestions and bug-reports can be submitted at: https://github.com/statistikat/VIM/issues ./VIM.Rcheck/00check.log:Attaching package: 'VIM' ./VIM.Rcheck/00check.log:The following object is masked from 'package:datasets': ./VIM.Rcheck/00check.log: sleep ./VIM.Rcheck/00check.log:Warning in cbind(TRUE1 = as.numeric(iris[as.matrix(y[which(y$col == 1), : ./VIM.Rcheck/00check.log: number of rows of result is not a multiple of vector length (arg 1) ./VIM.Rcheck/00check.log:--- finished re-building ‘modelImp.Rmd’ ./VIM.Rcheck/00check.log:SUMMARY: processing the following file failed: ./VIM.Rcheck/00check.log: ‘donorImp.Rmd’ ./VIM.Rcheck/00check.log:Error: Vignette re-building failed. ./VIM.Rcheck/00check.log:Execution halted ./VIM.Rcheck/00check.log:* checking PDF version of manual ... OK ./VIM.Rcheck/00check.log:* DONE ./VIM.Rcheck/00check.log:Status: 2 ERRORs, 1 WARNING, 3 NOTEs BTSPAS_2021.1.1.tar.gz ./BTSPAS.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/BTSPAS.Rcheck’ ./BTSPAS.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./BTSPAS.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./BTSPAS.Rcheck/00check.log:* using session charset: UTF-8 ./BTSPAS.Rcheck/00check.log:* checking for file ‘BTSPAS/DESCRIPTION’ ... OK ./BTSPAS.Rcheck/00check.log:* this is package ‘BTSPAS’ version ‘2021.1.1’ ./BTSPAS.Rcheck/00check.log:* checking package namespace information ... OK ./BTSPAS.Rcheck/00check.log:* checking package dependencies ... OK ./BTSPAS.Rcheck/00check.log:* checking if this is a source package ... OK ./BTSPAS.Rcheck/00check.log:* checking if there is a namespace ... OK ./BTSPAS.Rcheck/00check.log:* checking for executable files ... OK ./BTSPAS.Rcheck/00check.log:* checking for hidden files and directories ... OK ./BTSPAS.Rcheck/00check.log:* checking for portable file names ... OK ./BTSPAS.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./BTSPAS.Rcheck/00check.log:* checking whether package ‘BTSPAS’ can be installed ... WARNING ./BTSPAS.Rcheck/00check.log:Found the following significant warnings: ./BTSPAS.Rcheck/00check.log: Warning: replacing previous import ‘actuar::sd’ by ‘stats::sd’ when loading ‘BTSPAS’ ./BTSPAS.Rcheck/00check.log: Warning: replacing previous import ‘actuar::var’ by ‘stats::var’ when loading ‘BTSPAS’ ./BTSPAS.Rcheck/00check.log:See ‘/home/mdowle/build/revdeplib/BTSPAS.Rcheck/00install.out’ for details. ./BTSPAS.Rcheck/00check.log:* checking installed package size ... NOTE ./BTSPAS.Rcheck/00check.log: installed size is 5.2Mb ./BTSPAS.Rcheck/00check.log: sub-directories of 1Mb or more: ./BTSPAS.Rcheck/00check.log: doc 4.8Mb ./BTSPAS.Rcheck/00check.log:* checking package directory ... OK ./BTSPAS.Rcheck/00check.log:* checking ‘build’ directory ... OK ./BTSPAS.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./BTSPAS.Rcheck/00check.log:* checking top-level files ... OK ./BTSPAS.Rcheck/00check.log:* checking for left-over files ... OK ./BTSPAS.Rcheck/00check.log:* checking index information ... OK ./BTSPAS.Rcheck/00check.log:* checking package subdirectories ... OK ./BTSPAS.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./BTSPAS.Rcheck/00check.log:* checking R files for syntax errors ... OK ./BTSPAS.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./BTSPAS.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./BTSPAS.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./BTSPAS.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./BTSPAS.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./BTSPAS.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./BTSPAS.Rcheck/00check.log:* checking dependencies in R code ... OK ./BTSPAS.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./BTSPAS.Rcheck/00check.log:* checking replacement functions ... OK ./BTSPAS.Rcheck/00check.log:* checking foreign function calls ... OK ./BTSPAS.Rcheck/00check.log:* checking R code for possible problems ... OK ./BTSPAS.Rcheck/00check.log:* checking Rd files ... OK ./BTSPAS.Rcheck/00check.log:* checking Rd metadata ... OK ./BTSPAS.Rcheck/00check.log:* checking Rd cross-references ... OK ./BTSPAS.Rcheck/00check.log:* checking for missing documentation entries ... OK ./BTSPAS.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./BTSPAS.Rcheck/00check.log:* checking Rd \usage sections ... OK ./BTSPAS.Rcheck/00check.log:* checking Rd contents ... OK ./BTSPAS.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./BTSPAS.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./BTSPAS.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./BTSPAS.Rcheck/00check.log:* checking examples ... OK ./BTSPAS.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./BTSPAS.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./BTSPAS.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./BTSPAS.Rcheck/00check.log: ‘a-Diagonal-model.html.asis’... OK ./BTSPAS.Rcheck/00check.log: ‘b-Diagonal-model-with-multiple-ages.html.asis’... OK ./BTSPAS.Rcheck/00check.log: ‘c-Non-diagonal-model.html.asis’... OK ./BTSPAS.Rcheck/00check.log: ‘d-Non-diagonal-with-fall-back-model.html.asis’... OK ./BTSPAS.Rcheck/00check.log: ‘e-Bias-from-incomplete-sampling.html.asis’... OK ./BTSPAS.Rcheck/00check.log: ‘f-Interpolating-run-earlier-and-later.html.asis’... OK ./BTSPAS.Rcheck/00check.log:* checking re-building of vignette outputs ... OK ./BTSPAS.Rcheck/00check.log:* checking PDF version of manual ... OK ./BTSPAS.Rcheck/00check.log:* DONE ./BTSPAS.Rcheck/00check.log:Status: 1 WARNING, 1 NOTE LexisNexisTools_0.3.4.tar.gz ./LexisNexisTools.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/LexisNexisTools.Rcheck’ ./LexisNexisTools.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./LexisNexisTools.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./LexisNexisTools.Rcheck/00check.log:* using session charset: UTF-8 ./LexisNexisTools.Rcheck/00check.log:* checking for file ‘LexisNexisTools/DESCRIPTION’ ... OK ./LexisNexisTools.Rcheck/00check.log:* this is package ‘LexisNexisTools’ version ‘0.3.4’ ./LexisNexisTools.Rcheck/00check.log:* package encoding: UTF-8 ./LexisNexisTools.Rcheck/00check.log:* checking package namespace information ... OK ./LexisNexisTools.Rcheck/00check.log:* checking package dependencies ... OK ./LexisNexisTools.Rcheck/00check.log:* checking if this is a source package ... OK ./LexisNexisTools.Rcheck/00check.log:* checking if there is a namespace ... OK ./LexisNexisTools.Rcheck/00check.log:* checking for executable files ... OK ./LexisNexisTools.Rcheck/00check.log:* checking for hidden files and directories ... OK ./LexisNexisTools.Rcheck/00check.log:* checking for portable file names ... OK ./LexisNexisTools.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./LexisNexisTools.Rcheck/00check.log:* checking whether package ‘LexisNexisTools’ can be installed ... OK ./LexisNexisTools.Rcheck/00check.log:* checking installed package size ... OK ./LexisNexisTools.Rcheck/00check.log:* checking package directory ... OK ./LexisNexisTools.Rcheck/00check.log:* checking ‘build’ directory ... OK ./LexisNexisTools.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./LexisNexisTools.Rcheck/00check.log:* checking top-level files ... OK ./LexisNexisTools.Rcheck/00check.log:* checking for left-over files ... OK ./LexisNexisTools.Rcheck/00check.log:* checking index information ... OK ./LexisNexisTools.Rcheck/00check.log:* checking package subdirectories ... OK ./LexisNexisTools.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./LexisNexisTools.Rcheck/00check.log:* checking R files for syntax errors ... OK ./LexisNexisTools.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./LexisNexisTools.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./LexisNexisTools.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./LexisNexisTools.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./LexisNexisTools.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./LexisNexisTools.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./LexisNexisTools.Rcheck/00check.log:* checking dependencies in R code ... OK ./LexisNexisTools.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./LexisNexisTools.Rcheck/00check.log:* checking replacement functions ... OK ./LexisNexisTools.Rcheck/00check.log:* checking foreign function calls ... OK ./LexisNexisTools.Rcheck/00check.log:* checking R code for possible problems ... OK ./LexisNexisTools.Rcheck/00check.log:* checking Rd files ... OK ./LexisNexisTools.Rcheck/00check.log:* checking Rd metadata ... OK ./LexisNexisTools.Rcheck/00check.log:* checking Rd cross-references ... OK ./LexisNexisTools.Rcheck/00check.log:* checking for missing documentation entries ... OK ./LexisNexisTools.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./LexisNexisTools.Rcheck/00check.log:* checking Rd \usage sections ... OK ./LexisNexisTools.Rcheck/00check.log:* checking Rd contents ... OK ./LexisNexisTools.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./LexisNexisTools.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./LexisNexisTools.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./LexisNexisTools.Rcheck/00check.log:* checking examples ... OK ./LexisNexisTools.Rcheck/00check.log:* checking for unstated dependencies in ‘tests’ ... OK ./LexisNexisTools.Rcheck/00check.log:* checking tests ... OK ./LexisNexisTools.Rcheck/00check.log: Running ‘spelling.R’ ./LexisNexisTools.Rcheck/00check.log: Running ‘testthat.R’ ./LexisNexisTools.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./LexisNexisTools.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./LexisNexisTools.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./LexisNexisTools.Rcheck/00check.log: ‘demo.Rmd’ using ‘UTF-8’... OK ./LexisNexisTools.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./LexisNexisTools.Rcheck/00check.log:Error(s) in re-building vignettes: ./LexisNexisTools.Rcheck/00check.log: ... ./LexisNexisTools.Rcheck/00check.log:--- re-building ‘demo.Rmd’ using rmarkdown ./LexisNexisTools.Rcheck/00check.log:Quitting from lines 13-21 (demo.Rmd) ./LexisNexisTools.Rcheck/00check.log:Error: processing vignette 'demo.Rmd' failed with diagnostics: ./LexisNexisTools.Rcheck/00check.log:attempt to use zero-length variable name ./LexisNexisTools.Rcheck/00check.log:--- failed re-building ‘demo.Rmd’ ./LexisNexisTools.Rcheck/00check.log:SUMMARY: processing the following file failed: ./LexisNexisTools.Rcheck/00check.log: ‘demo.Rmd’ ./LexisNexisTools.Rcheck/00check.log:Error: Vignette re-building failed. ./LexisNexisTools.Rcheck/00check.log:Execution halted ./LexisNexisTools.Rcheck/00check.log:* checking PDF version of manual ... OK ./LexisNexisTools.Rcheck/00check.log:* DONE ./LexisNexisTools.Rcheck/00check.log:Status: 1 WARNING sitree_0.1-10.tar.gz ./sitree.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/sitree.Rcheck’ ./sitree.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./sitree.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./sitree.Rcheck/00check.log:* using session charset: UTF-8 ./sitree.Rcheck/00check.log:* checking for file ‘sitree/DESCRIPTION’ ... OK ./sitree.Rcheck/00check.log:* this is package ‘sitree’ version ‘0.1-10’ ./sitree.Rcheck/00check.log:* package encoding: UTF-8 ./sitree.Rcheck/00check.log:* checking package namespace information ... OK ./sitree.Rcheck/00check.log:* checking package dependencies ... OK ./sitree.Rcheck/00check.log:* checking if this is a source package ... OK ./sitree.Rcheck/00check.log:* checking if there is a namespace ... OK ./sitree.Rcheck/00check.log:* checking for executable files ... OK ./sitree.Rcheck/00check.log:* checking for hidden files and directories ... OK ./sitree.Rcheck/00check.log:* checking for portable file names ... OK ./sitree.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./sitree.Rcheck/00check.log:* checking whether package ‘sitree’ can be installed ... OK ./sitree.Rcheck/00check.log:* checking installed package size ... OK ./sitree.Rcheck/00check.log:* checking package directory ... OK ./sitree.Rcheck/00check.log:* checking ‘build’ directory ... OK ./sitree.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./sitree.Rcheck/00check.log:* checking top-level files ... OK ./sitree.Rcheck/00check.log:* checking for left-over files ... OK ./sitree.Rcheck/00check.log:* checking index information ... OK ./sitree.Rcheck/00check.log:* checking package subdirectories ... OK ./sitree.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./sitree.Rcheck/00check.log:* checking R files for syntax errors ... OK ./sitree.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./sitree.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./sitree.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./sitree.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./sitree.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./sitree.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./sitree.Rcheck/00check.log:* checking dependencies in R code ... OK ./sitree.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./sitree.Rcheck/00check.log:* checking replacement functions ... OK ./sitree.Rcheck/00check.log:* checking foreign function calls ... OK ./sitree.Rcheck/00check.log:* checking R code for possible problems ... OK ./sitree.Rcheck/00check.log:* checking Rd files ... OK ./sitree.Rcheck/00check.log:* checking Rd metadata ... OK ./sitree.Rcheck/00check.log:* checking Rd cross-references ... OK ./sitree.Rcheck/00check.log:* checking for missing documentation entries ... OK ./sitree.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./sitree.Rcheck/00check.log:* checking Rd \usage sections ... OK ./sitree.Rcheck/00check.log:* checking Rd contents ... OK ./sitree.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./sitree.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./sitree.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./sitree.Rcheck/00check.log:* checking LazyData ... OK ./sitree.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./sitree.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./sitree.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./sitree.Rcheck/00check.log:* checking examples ... OK ./sitree.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./sitree.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./sitree.Rcheck/00check.log:* checking running R code from vignettes ... NONE ./sitree.Rcheck/00check.log: ‘SiTree.Rmd’ using ‘UTF-8’... OK ./sitree.Rcheck/00check.log: ‘TestEquations.Rmd’ using ‘UTF-8’... OK ./sitree.Rcheck/00check.log:* checking re-building of vignette outputs ... WARNING ./sitree.Rcheck/00check.log:Error(s) in re-building vignettes: ./sitree.Rcheck/00check.log: ... ./sitree.Rcheck/00check.log:--- re-building ‘SiTree.Rmd’ using rmarkdown ./sitree.Rcheck/00check.log:--- finished re-building ‘SiTree.Rmd’ ./sitree.Rcheck/00check.log:--- re-building ‘TestEquations.Rmd’ using rmarkdown ./sitree.Rcheck/00check.log:Quitting from lines 79-167 (TestEquations.Rmd) ./sitree.Rcheck/00check.log:Error: processing vignette 'TestEquations.Rmd' failed with diagnostics: ./sitree.Rcheck/00check.log:attempt to use zero-length variable name ./sitree.Rcheck/00check.log:--- failed re-building ‘TestEquations.Rmd’ ./sitree.Rcheck/00check.log:SUMMARY: processing the following file failed: ./sitree.Rcheck/00check.log: ‘TestEquations.Rmd’ ./sitree.Rcheck/00check.log:Error: Vignette re-building failed. ./sitree.Rcheck/00check.log:Execution halted ./sitree.Rcheck/00check.log:* checking PDF version of manual ... OK ./sitree.Rcheck/00check.log:* DONE ./sitree.Rcheck/00check.log:Status: 1 WARNING twang_2.4.tar.gz ./twang.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/twang.Rcheck’ ./twang.Rcheck/00check.log:* using R version 4.1.1 (2021-08-10) ./twang.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit) ./twang.Rcheck/00check.log:* using session charset: UTF-8 ./twang.Rcheck/00check.log:* checking for file ‘twang/DESCRIPTION’ ... OK ./twang.Rcheck/00check.log:* this is package ‘twang’ version ‘2.4’ ./twang.Rcheck/00check.log:* package encoding: UTF-8 ./twang.Rcheck/00check.log:* checking package namespace information ... OK ./twang.Rcheck/00check.log:* checking package dependencies ... NOTE ./twang.Rcheck/00check.log:Package suggested but not available for checking: ‘OVtool’ ./twang.Rcheck/00check.log:* checking if this is a source package ... OK ./twang.Rcheck/00check.log:* checking if there is a namespace ... OK ./twang.Rcheck/00check.log:* checking for executable files ... OK ./twang.Rcheck/00check.log:* checking for hidden files and directories ... OK ./twang.Rcheck/00check.log:* checking for portable file names ... OK ./twang.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK ./twang.Rcheck/00check.log:* checking whether package ‘twang’ can be installed ... OK ./twang.Rcheck/00check.log:* checking installed package size ... OK ./twang.Rcheck/00check.log:* checking package directory ... OK ./twang.Rcheck/00check.log:* checking ‘build’ directory ... OK ./twang.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK ./twang.Rcheck/00check.log:* checking top-level files ... OK ./twang.Rcheck/00check.log:* checking for left-over files ... OK ./twang.Rcheck/00check.log:* checking index information ... OK ./twang.Rcheck/00check.log:* checking package subdirectories ... OK ./twang.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK ./twang.Rcheck/00check.log:* checking R files for syntax errors ... OK ./twang.Rcheck/00check.log:* checking whether the package can be loaded ... OK ./twang.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK ./twang.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK ./twang.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK ./twang.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK ./twang.Rcheck/00check.log:* checking loading without being on the library search path ... OK ./twang.Rcheck/00check.log:* checking dependencies in R code ... OK ./twang.Rcheck/00check.log:* checking S3 generic/method consistency ... OK ./twang.Rcheck/00check.log:* checking replacement functions ... OK ./twang.Rcheck/00check.log:* checking foreign function calls ... OK ./twang.Rcheck/00check.log:* checking R code for possible problems ... OK ./twang.Rcheck/00check.log:* checking Rd files ... OK ./twang.Rcheck/00check.log:* checking Rd metadata ... OK ./twang.Rcheck/00check.log:* checking Rd cross-references ... OK ./twang.Rcheck/00check.log:* checking for missing documentation entries ... OK ./twang.Rcheck/00check.log:* checking for code/documentation mismatches ... OK ./twang.Rcheck/00check.log:* checking Rd \usage sections ... OK ./twang.Rcheck/00check.log:* checking Rd contents ... OK ./twang.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK ./twang.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK ./twang.Rcheck/00check.log:* checking data for non-ASCII characters ... OK ./twang.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK ./twang.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK ./twang.Rcheck/00check.log:* checking line endings in Makefiles ... OK ./twang.Rcheck/00check.log:* checking compilation flags in Makevars ... OK ./twang.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK ./twang.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK ./twang.Rcheck/00check.log:* checking use of PKG_*FLAGS in Makefiles ... OK ./twang.Rcheck/00check.log:* checking compiled code ... OK ./twang.Rcheck/00check.log:* checking sizes of PDF files under ‘inst/doc’ ... OK ./twang.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK ./twang.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK ./twang.Rcheck/00check.log:* checking examples ... OK ./twang.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK ./twang.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK ./twang.Rcheck/00check.log:* checking running R code from vignettes ... WARNING ./twang.Rcheck/00check.log:Errors in running code in vignettes: ./twang.Rcheck/00check.log:when running code in ‘twang.rnw’ ./twang.Rcheck/00check.log: ... ./twang.Rcheck/00check.log:> glm5 <- lm(sqrt(re78) ~ treat + age + educ + black + ./twang.Rcheck/00check.log:+ hispan + nodegree + married + sqrt(re74) + sqrt(re75), data = lalonde) ./twang.Rcheck/00check.log:> library(OVtool) ./twang.Rcheck/00check.log: When sourcing ‘twang.R’: ./twang.Rcheck/00check.log:Error: there is no package called ‘OVtool’ ./twang.Rcheck/00check.log:Execution halted ./twang.Rcheck/00check.log: ‘iptw.rnw’ using ‘UTF-8’... OK ./twang.Rcheck/00check.log: ‘mnps.rnw’ using ‘UTF-8’... OK ./twang.Rcheck/00check.log: ‘twang.rnw’ using ‘UTF-8’... failed ./twang.Rcheck/00check.log:* checking re-building of vignette outputs ... NOTE ./twang.Rcheck/00check.log:Error(s) in re-building vignettes: ./twang.Rcheck/00check.log:--- re-building ‘iptw.rnw’ using Sweave ./twang.Rcheck/00check.log:To reproduce results from prior versions of the twang package, please see the version="legacy" option described in the documentation. ./twang.Rcheck/00check.log:Loading required package: grid ./twang.Rcheck/00check.log:Loading required package: Matrix ./twang.Rcheck/00check.log:Loading required package: survival ./twang.Rcheck/00check.log:Attaching package: ‘survey’ ./twang.Rcheck/00check.log:The following object is masked from ‘package:graphics’: ./twang.Rcheck/00check.log: dotchart ./twang.Rcheck/00check.log:--- finished re-building ‘iptw.rnw’ ./twang.Rcheck/00check.log:--- re-building ‘mnps.rnw’ using Sweave ./twang.Rcheck/00check.log:To reproduce results from prior versions of the twang package, please see the version="legacy" option described in the documentation. ./twang.Rcheck/00check.log:Loading required package: grid ./twang.Rcheck/00check.log:Loading required package: Matrix ./twang.Rcheck/00check.log:Loading required package: survival ./twang.Rcheck/00check.log:Attaching package: ‘survey’ ./twang.Rcheck/00check.log:The following object is masked from ‘package:graphics’: ./twang.Rcheck/00check.log: dotchart ./twang.Rcheck/00check.log:--- finished re-building ‘mnps.rnw’ ./twang.Rcheck/00check.log:--- re-building ‘twang.rnw’ using Sweave ./twang.Rcheck/00check.log:To reproduce results from prior versions of the twang package, please see the version="legacy" option described in the documentation. ./twang.Rcheck/00check.log:Loading required package: grid ./twang.Rcheck/00check.log:Loading required package: Matrix ./twang.Rcheck/00check.log:Loading required package: survival ./twang.Rcheck/00check.log:Attaching package: ‘survey’ ./twang.Rcheck/00check.log:The following object is masked from ‘package:graphics’: ./twang.Rcheck/00check.log: dotchart ./twang.Rcheck/00check.log:Error: processing vignette 'twang.rnw' failed with diagnostics: ./twang.Rcheck/00check.log: chunk 24 ./twang.Rcheck/00check.log:Error in library(OVtool) : there is no package called ‘OVtool’ ./twang.Rcheck/00check.log:--- failed re-building ‘twang.rnw’ ./twang.Rcheck/00check.log:SUMMARY: processing the following file failed: ./twang.Rcheck/00check.log: ‘twang.rnw’ ./twang.Rcheck/00check.log:Error: Vignette re-building failed. ./twang.Rcheck/00check.log:Execution halted ./twang.Rcheck/00check.log:* checking PDF version of manual ... OK ./twang.Rcheck/00check.log:* DONE ./twang.Rcheck/00check.log:Status: 1 WARNING, 2 NOTEs