Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:40 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 347/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
chromVAR 1.27.0 (landing page) Alicia Schep
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the chromVAR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chromVAR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: chromVAR |
Version: 1.27.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chromVAR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings chromVAR_1.27.0.tar.gz |
StartedAt: 2024-08-20 23:22:34 -0400 (Tue, 20 Aug 2024) |
EndedAt: 2024-08-20 23:30:45 -0400 (Tue, 20 Aug 2024) |
EllapsedTime: 490.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: chromVAR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chromVAR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings chromVAR_1.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/chromVAR.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'chromVAR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'chromVAR' version '1.27.0' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'chromVAR' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub records with missing/empty fields: Record: 1 Field(s): COPYRIGHT HOLDER * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 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 ... NOTE left_right_to_grglist: no visible global function definition for 'GenomicRangesList' Undefined global functions or variables: GenomicRangesList * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * 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 compiled code ... NOTE Note: information on .o files for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/chromVAR/libs/x64/chromVAR.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed deviationsCovariability 20.39 0.91 22.13 getJasparMotifs 7.96 0.28 8.24 getCounts 4.89 2.24 7.64 pwmDistance 6.43 0.25 6.69 plotVariability 5.49 0.01 5.50 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/chromVAR.Rcheck/00check.log' for details.
chromVAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL chromVAR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'chromVAR' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' using C++11 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwm_similarity.cpp -o pwm_similarity.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o utils.cpp: In function 'Rcpp::NumericVector row_sds(arma::mat&, bool)': utils.cpp:12:21: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 12 | for( int j=0; j < X.n_rows; j++ ) { | ~~^~~~~~~~~~ g++ -shared -s -static-libgcc -o chromVAR.dll tmp.def RcppExports.o pwm_similarity.o utils.o -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-chromVAR/00new/chromVAR/libs/x64 ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (chromVAR)
chromVAR.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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. 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. > library(testthat) > library(chromVAR) > BiocParallel::register(BiocParallel::SerialParam()) > test_check("chromVAR") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 65 ] > > proc.time() user system elapsed 26.60 3.67 30.79
chromVAR.Rcheck/chromVAR-Ex.timings
name | user | system | elapsed | |
addGCBias | 1.88 | 0.05 | 1.95 | |
annotationMatches | 0.01 | 0.00 | 0.01 | |
chromVAR_theme | 0.11 | 0.00 | 0.11 | |
computeDeviations | 3.95 | 0.20 | 4.15 | |
computeExpectations | 0.03 | 0.00 | 0.04 | |
computeVariability | 4.16 | 0.14 | 4.29 | |
counts | 0.01 | 0.00 | 0.02 | |
deviationScores | 0 | 0 | 0 | |
deviations | 0.02 | 0.00 | 0.01 | |
deviationsCovariability | 20.39 | 0.91 | 22.13 | |
deviationsTsne | 0.11 | 0.02 | 0.12 | |
differentialDeviations | 0.01 | 0.00 | 0.02 | |
differentialVariability | 0.02 | 0.00 | 0.02 | |
example_counts | 0 | 0 | 0 | |
filterPeaks | 0.17 | 0.01 | 0.18 | |
filterSamples | 0.03 | 0.00 | 0.03 | |
filterSamplesPlot | 0.10 | 0.00 | 0.09 | |
getAnnotations | 0.36 | 0.06 | 0.44 | |
getBackgroundPeaks | 2.54 | 0.06 | 2.61 | |
getCisGroups | 0.10 | 0.00 | 0.09 | |
getCounts | 4.89 | 2.24 | 7.64 | |
getFragmentsPerPeak | 0.02 | 0.00 | 0.02 | |
getFragmentsPerSample | 0.01 | 0.00 | 0.01 | |
getJasparMotifs | 7.96 | 0.28 | 8.24 | |
getPeaks | 0.14 | 0.03 | 0.19 | |
getPermutedData | 2.69 | 0.23 | 2.92 | |
getSampleCorrelation | 0.01 | 0.00 | 0.01 | |
getSampleDepths | 0.10 | 0.02 | 0.11 | |
getSampleDistance | 0.01 | 0.01 | 0.03 | |
getTotalFragments | 0.02 | 0.00 | 0.02 | |
makeBiasBins | 0.04 | 0.00 | 0.05 | |
makePermutedSets | 1.24 | 0.21 | 1.48 | |
matchKmers | 1.31 | 0.25 | 1.56 | |
mini_counts | 0.00 | 0.01 | 0.02 | |
mini_dev | 0 | 0 | 0 | |
mini_ix | 0.00 | 0.02 | 0.01 | |
plotVariability | 5.49 | 0.01 | 5.50 | |
pwmDistance | 6.43 | 0.25 | 6.69 | |
rbind-chromVARDeviations-method | 0.07 | 0.00 | 0.06 | |