Running with gitlab-runner 16.4.0 (6e766faf)  on bscearth001 texyjxyB, system ID: s_1a2f074804b7 section_start:1731583581:prepare_executor Preparing the "ssh" executor Using SSH executor... section_end:1731583583:prepare_executor section_start:1731583583:prepare_script Preparing environment Running on bscearth001 via bscearth001... section_end:1731583583:prepare_script section_start:1731583583:get_sources Getting source from Git repository Fetching changes... warning: templates not found builds/texyjxyB/0/gitlab/external/cstools.tmp/git-template Reinitialized existing Git repository in /home/Earth/fbeninca/builds/texyjxyB/0/gitlab/external/cstools/.git/ Checking out 3ec5fecf as detached HEAD (ref is dev-cross-indices)... Skipping Git submodules setup section_end:1731583595:get_sources section_start:1731583595:step_script Executing "step_script" stage of the job script $ module load R/4.1.2-foss-2015a-bare $ R CMD build --resave-data . * checking for file ‘./DESCRIPTION’ ... OK * preparing ‘CSTools’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to process help pages * saving partial Rd database * creating vignettes ... OK * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * re-saving image files * building ‘CSTools_5.2.0.tar.gz’ $ R CMD check --as-cran --no-manual --run-donttest CSTools_*.tar.gz * using log directory ‘/home/Earth/fbeninca/builds/texyjxyB/0/gitlab/external/cstools/CSTools.Rcheck’ * using R version 4.1.2 (2021-11-01) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using options ‘--run-donttest --no-manual --as-cran’ * checking for file ‘CSTools/DESCRIPTION’ ... OK * this is package ‘CSTools’ version ‘5.2.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... WARNING Maintainer: ‘Eva Rifà ’ Insufficient package version (submitted: 5.2.0, existing: 5.2.0) New maintainer: Eva Rifà Old maintainer(s): Victoria Agudetse Found the following (possibly) invalid URLs: URL: https://doi.org/10.1002/2014GL061146 From: man/CST_Calibration.Rd man/Calibration.Rd Status: 403 Message: Forbidden URL: https://doi.org/10.1002/qj.2397 From: man/CST_Calibration.Rd man/Calibration.Rd Status: 403 Message: Forbidden URL: https://doi.org/10.1002/qj.828 From: inst/doc/WeatherRegimes_vignette.html Status: 403 Message: Forbidden URL: https://doi.org/10.1007/s00382-018-4404-z From: man/CST_MultiMetric.Rd man/MultiMetric.Rd inst/doc/MultiModelSkill_vignette.html Status: Error Message: libcurl error code 60: SSL certificate problem: unable to get local issuer certificate (Status without verification: OK) URL: https://doi.org/10.1007/s00382-019-04839-5 From: man/CST_WeatherRegimes.Rd man/WeatherRegimes.Rd Status: Error Message: libcurl error code 60: SSL certificate problem: unable to get local issuer certificate (Status without verification: OK) URL: https://doi.org/10.1029/2003WR002504 From: inst/doc/RainFARM_vignette.html Status: 403 Message: Forbidden URL: https://doi.org/10.1038/s41467-019-09305-8 From: man/CST_DynBiasCorrection.Rd man/CST_ProxiesAttractor.Rd man/DynBiasCorrection.Rd man/Predictability.Rd man/ProxiesAttractor.Rd Status: Error Message: libcurl error code 60: SSL certificate problem: unable to get local issuer certificate (Status without verification: OK) URL: https://doi.org/10.1111/j.1600-0870.2005.00104.x From: man/CST_Calibration.Rd Status: 403 Message: Forbidden URL: https://gdal.org/ From: man/CST_RFWeights.Rd inst/doc/RainFARM_vignette.html Status: Error Message: libcurl error code 60: SSL certificate problem: unable to get local issuer certificate (Status without verification: OK) URL: https://stat.ethz.ch/R-manual/R-devel/library/stats/html/kmeans.html From: inst/doc/WeatherRegimes_vignette.html Status: Error Message: libcurl error code 60: SSL certificate problem: unable to get local issuer certificate (Status without verification: OK) URL: https://www.medscope-project.eu/products/tool-box/cstools-video-tutorials/ From: README.md Status: Error Message: libcurl error code 60: SSL certificate problem: self signed certificate in certificate chain (Status without verification: OK) URL: https://www.medscope-project.eu/the-project/deliverables-reports/ From: man/CST_RFTemp.Rd man/RFTemp.Rd Status: Error Message: libcurl error code 60: SSL certificate problem: self signed certificate in certificate chain (Status without verification: OK) Found the following (possibly) invalid DOIs: DOI: 10.1007/s00382-012-1626-3 From: DESCRIPTION Status: libcurl error code 60: SSL certificate problem: unable to get local issuer certificate Message: Error DOI: 10.1007/s00382-018-4404-z From: DESCRIPTION Status: libcurl error code 60: SSL certificate problem: unable to get local issuer certificate Message: Error DOI: 10.1111/j.1600-0870.2005.00104.x From: DESCRIPTION Status: Forbidden Message: 403 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘CSTools’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... NOTE unable to verify current time * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'Calibration': Calibration Code: function(exp, obs, exp_cor = NULL, cal.method = "mse_min", eval.method = "leave-one-out", multi.model = FALSE, na.fill = TRUE, na.rm = TRUE, apply_to = NULL, alpha = NULL, memb_dim = "member", sdate_dim = "sdate", dat_dim = NULL, ncores = NULL, k = 1, tail.out = TRUE) Docs: function(exp, obs, exp_cor = NULL, cal.method = "mse_min", eval.method = "leave-one-out", multi.model = FALSE, na.fill = TRUE, na.rm = TRUE, apply_to = NULL, alpha = NULL, memb_dim = "member", sdate_dim = "sdate", dat_dim = NULL, ncores = NULL) Argument names in code not in docs: k tail.out Codoc mismatches from documentation object 'CategoricalEnsCombination': CategoricalEnsCombination Code: function(fc, obs, cat.method, eval.method, amt.cat, k, tail.out, ...) Docs: function(fc, obs, cat.method, eval.method, amt.cat, ...) Argument names in code not in docs: k tail.out Mismatches in argument names: Position: 6 Code: k Docs: ... * checking Rd \usage sections ... WARNING Undocumented arguments in documentation object 'CST_Calibration' ‘k’ ‘tail.out’ Undocumented arguments in documentation object 'CST_CategoricalEnsCombination' ‘k’ ‘tail.out’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... NOTE Compilation used the following non-portable flag(s): ‘-march=native’ * checking compiled code ... OK WARNING ‘qpdf’ is needed for checks on size reduction of PDFs * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 4 WARNINGs, 2 NOTEs See ‘/home/Earth/fbeninca/builds/texyjxyB/0/gitlab/external/cstools/CSTools.Rcheck/00check.log’ for details. $ R -e 'covr::package_coverage()' R version 4.1.2 (2021-11-01) -- "Bird Hippie" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > covr::package_coverage() Error: Failure in `/tmp/RtmpZA4K3U/R_LIBS1dd03dc79eee/CSTools/CSTools-tests/testthat.Rout.fail` ) ── Error ('test-make-eval-train-dexes.R:63:3'): 2. Output checks: k-fold ─────── Error in `.make.eval.train.dexes(eval.method = "leave-one-out", 10, NULL)`: argument "k" is missing, with no default Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-make-eval-train-dexes.R:63:3 2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─CSTools:::.make.eval.train.dexes(...) [ FAIL 3 | WARN 30 | SKIP 0 | PASS 671 ] Error: Test failures Execution halted Execution halted section_end:1731584108:step_script section_start:1731584108:cleanup_file_variables Cleaning up project directory and file based variables section_end:1731584108:cleanup_file_variables ERROR: Job failed: Process exited with status 1