Run revdep_details(, "envi")
for more info
checking whether package ‘envi’ can be installed ... WARNING
Found the following significant warnings:
Warning: no DISPLAY variable so Tk is not available
See ‘/wynton/home/cbi/hb/repositories/doFuture/revdep/checks/envi/new/envi.Rcheck/00install.out’ for details.
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘RStoolbox’
Run revdep_details(, "hwep")
for more info
checking installed package size ... NOTE
installed size is 28.1Mb
sub-directories of 1Mb or more:
libs 27.7Mb
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Run revdep_details(, "ldsr")
for more info
Specified C++11: please drop specification unless essential
Run revdep_details(, "multilevelcoda")
for more info
Package suggested but not available for checking: ‘cmdstanr’
Run revdep_details(, "nebula")
for more info
installed size is 9.5Mb
sub-directories of 1Mb or more:
libs 9.3Mb
Run revdep_details(, "oncomsm")
for more info
checking installed package size ... NOTE
installed size is 19.9Mb
sub-directories of 1Mb or more:
libs 19.6Mb
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Run revdep_details(, "pareg")
for more info
checking examples ... ERROR ``` Running examples in ‘pareg-Ex.R’ failed The error most likely occurred in:
Name: as.data.frame.pareg
Title: as.data.frame for an object of class 'pareg'.
Aliases: as.data.frame.pareg
** Examples
df_genes <- data.frame( ... xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h7f98852_1002 xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h0b41bf4_1003 xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h7f98852_1007 xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0 zlib conda-forge/linux-64::zlib-1.2.13-hd590300_5 zstd conda-forge/linux-64::zstd-1.5.5-hfc55251_0
Error: Error creating conda environment 'fallback' [exit code 1] Execution halted ```
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: [Errno 2] No such file or directory: '/wynton/home/cbi/hb/.cache/R/basilisk/1.14.1/0/envs/fallback/share/zoneinfo/Antarctica' [Errno 2] No such file or directory: '/wynton/home/cbi/hb/.cache/R/basilisk/1.14.1/0/envs/fallback/share/zoneinfo/America/Kentucky' [Errno 2] No such file or directory: '/wynton/home/cbi/hb/.cache/R/basilisk/1.14.1/0/envs/fallback/share/zoneinfo/America' [Errno 2] No such file or directory: '/wynton/home/cbi/hb/.cache/R/basilisk/1.14.1/0/envs/fallback/x86_64-conda-linux-gnu/include/c++/13.2.0/tr2' [Errno 2] No such file or directory: '/wynton/home/cbi/hb/.cache/R/basilisk/1.14.1/0/envs/fallback/x86_64-conda-linux-gnu/include/c++/13.2.0/pstl' [Errno 2] No such file or directory: '/wynton/home/cbi/hb/.cache/R/basilisk/1.14.1/0/envs/fallback/x86_64-conda-linux-gnu/include/c++/13.2.0/ext/pb_ds/detail/thin_heap_' ... [Errno 2] No such file or directory: '/wynton/home/cbi/hb/.cache/R/basilisk/1.14.1/0/envs/fallback/x86_64-conda-linux-gnu/sysroot/usr/include/drm' [Errno 2] No such file or directory: '/wynton/home/cbi/hb/.cache/R/basilisk/1.14.1/0/envs/fallback/x86_64-conda-linux-gnu/sysroot/usr/include/asm' [Errno 2] No such file or directory: '/wynton/home/cbi/hb/.cache/R/basilisk/1.14.1/0/envs/fallback/x86_64-conda-linux-gnu/sysroot/usr/include/asm-generic' [Errno 2] No such file or directory: '/wynton/home/cbi/hb/.cache/R/basilisk/1.14.1/0/envs/fallback/fonts'
Error: Error creating conda environment 'fallback' [exit code 1] In addition: Warning message: In check_forbidden_install("Conda Environments") : cannot install Conda Environments during R CMD check Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘pareg.Rmd’ using rmarkdown The magick package is required to crop "/wynton/home/cbi/hb/repositories/doFuture/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pareg_files/figure-html/unnamed-chunk-4-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/doFuture/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pareg_files/figure-html/unnamed-chunk-5-1.png" but not available. 2023-12-19 19:49:12.285320: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: SSE4.1 SSE4.2 AVX AVX2 AVX512F AVX512_VNNI FMA To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags. Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ... --- re-building ‘pathway_similarities.Rmd’ using rmarkdown The magick package is required to crop "/wynton/home/cbi/hb/repositories/doFuture/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pathway_similarities_files/figure-html/unnamed-chunk-2-1.png" but not available. The magick package is required to crop "/wynton/home/cbi/hb/repositories/doFuture/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pathway_similarities_files/figure-html/unnamed-chunk-3-1.png" but not available. --- finished re-building ‘pathway_similarities.Rmd’
SUMMARY: processing the following file failed: ‘pareg.Rmd’
Error: Vignette re-building failed. Execution halted ```
checking for portable file names ... NOTE ``` Found the following non-portable file paths: pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_ablation_study/config.yaml pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_ablation_study/params.csv pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_dispersion_fitting/config.yaml pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_dispersion_fitting/params.csv pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_real_datasets/config.yaml pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_real_datasets/params.csv pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_effect/config.yaml pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_effect/params.csv pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_parameter/config.yaml ... pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_response_distribution/params.csv pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_similarity_measures/config.yaml pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_similarity_measures/params.csv pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/workflow/scripts/compare_rocauc_vs_loss.R pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_parameter
Tarballs are only required to store paths of up to 100 bytes and cannot store those of more than 256 bytes, with restrictions including to 100 bytes for the final component. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. ```
checking whether package ‘pareg’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/wynton/home/cbi/hb/repositories/doFuture/revdep/checks/pareg/new/pareg.Rcheck/00install.out’ for details.
Run revdep_details(, "projpred")
for more info
Package suggested but not available for checking: ‘cmdstanr’
Run revdep_details(, "rpm")
for more info
installed size is 6.0Mb
sub-directories of 1Mb or more:
libs 5.6Mb
Run revdep_details(, "skpr")
for more info
installed size is 20.4Mb
sub-directories of 1Mb or more:
libs 20.2Mb
Run revdep_details(, "sparrpowR")
for more info
Found the following significant warnings:
Warning: no DISPLAY variable so Tk is not available
See ‘/wynton/home/cbi/hb/repositories/doFuture/revdep/checks/sparrpowR/new/sparrpowR.Rcheck/00install.out’ for details.
Run revdep_details(, "sphunif")
for more info
checking installed package size ... NOTE
installed size is 10.0Mb
sub-directories of 1Mb or more:
libs 9.8Mb
checking data for non-ASCII characters ... NOTE
Note: found 189 marked UTF-8 strings
Run revdep_details(, "sRACIPE")
for more info
checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
checking R code for possible problems ... NOTE
sracipeSimulate: no visible global function definition for
‘registerDoFuture’
sracipeSimulate: no visible global function definition for ‘plan’
sracipeSimulate: no visible global function definition for ‘%dopar%’
sracipeSimulate: no visible global function definition for ‘foreach’
sracipeSimulate: no visible binding for global variable
‘configurationTmp’
sracipeSimulate: no visible binding for global variable ‘outFileGETmp’
sracipeSimulate: no visible binding for global variable
‘outFileParamsTmp’
sracipeSimulate: no visible binding for global variable ‘outFileICTmp’
Undefined global functions or variables:
%dopar% configurationTmp foreach outFileGETmp outFileICTmp
outFileParamsTmp plan registerDoFuture
Run revdep_details(, "ssdtools")
for more info
installed size is 10.3Mb
sub-directories of 1Mb or more:
libs 10.0Mb
Run revdep_details(, "vmeasur")
for more info
Found the following significant warnings:
Warning: no DISPLAY variable so Tk is not available
See ‘/wynton/home/cbi/hb/repositories/doFuture/revdep/checks/vmeasur/new/vmeasur.Rcheck/00install.out’ for details.
Run revdep_details(, "WeightedCluster")
for more info
checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘WeightedCluster.Rnw’ using knitr --- finished re-building ‘WeightedCluster.Rnw’
--- re-building ‘WeightedClusterFR.Rnw’ using knitr Error: processing vignette 'WeightedClusterFR.Rnw' failed with diagnostics: Running 'texi2dvi' on 'WeightedClusterFR.tex' failed. LaTeX errors: ! Package babel Error: Unknown option `frenchb'. Either you misspelled it (babel) or the language definition file frenchb.ldf was not foun ... l.85 \usepackage {tikz}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘WeightedClusterPreview.Rnw’
SUMMARY: processing the following files failed: ‘WeightedClusterFR.Rnw’ ‘WeightedClusterPreview.Rnw’
Error: Vignette re-building failed. Execution halted ```
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