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This page was generated on 2021-10-15 15:06:31 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the chromVAR package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 309/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
chromVAR 1.14.0 (landing page) Alicia Schep
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: chromVAR |
Version: 1.14.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings chromVAR_1.14.0.tar.gz |
StartedAt: 2021-10-14 17:24:14 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 17:33:06 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 532.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: chromVAR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings chromVAR_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/chromVAR.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘chromVAR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘chromVAR’ version ‘1.14.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘chromVAR’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * 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 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 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed deviationsCovariability 28.895 1.001 30.027 plotVariability 27.060 0.101 27.181 computeVariability 25.957 0.077 26.046 getJasparMotifs 8.642 0.174 8.824 pwmDistance 7.019 0.151 7.179 getCounts 6.633 0.510 7.151 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/chromVAR.Rcheck/00check.log’ for details.
chromVAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL chromVAR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘chromVAR’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c pwm_similarity.cpp -o pwm_similarity.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o chromVAR.so RcppExports.o pwm_similarity.o utils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-chromVAR/00new/chromVAR/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** 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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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. 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 30.638 1.472 32.139
chromVAR.Rcheck/chromVAR-Ex.timings
name | user | system | elapsed | |
addGCBias | 1.161 | 0.080 | 1.241 | |
annotationMatches | 0.02 | 0.00 | 0.02 | |
chromVAR_theme | 0.025 | 0.000 | 0.026 | |
computeDeviations | 3.969 | 0.083 | 4.062 | |
computeExpectations | 0.055 | 0.001 | 0.057 | |
computeVariability | 25.957 | 0.077 | 26.046 | |
counts | 0.018 | 0.001 | 0.018 | |
deviationScores | 0.009 | 0.001 | 0.010 | |
deviations | 0.015 | 0.001 | 0.015 | |
deviationsCovariability | 28.895 | 1.001 | 30.027 | |
deviationsTsne | 0.107 | 0.002 | 0.109 | |
differentialDeviations | 0.026 | 0.001 | 0.027 | |
differentialVariability | 0.046 | 0.001 | 0.047 | |
example_counts | 0.001 | 0.001 | 0.002 | |
filterPeaks | 0.419 | 0.005 | 0.425 | |
filterSamples | 0.114 | 0.001 | 0.115 | |
filterSamplesPlot | 0.228 | 0.001 | 0.229 | |
getAnnotations | 0.612 | 0.013 | 0.626 | |
getBackgroundPeaks | 0.708 | 0.017 | 0.726 | |
getCisGroups | 0.513 | 0.011 | 0.524 | |
getCounts | 6.633 | 0.510 | 7.151 | |
getFragmentsPerPeak | 0.022 | 0.001 | 0.024 | |
getFragmentsPerSample | 0.021 | 0.001 | 0.022 | |
getJasparMotifs | 8.642 | 0.174 | 8.824 | |
getPeaks | 0.287 | 0.004 | 0.289 | |
getPermutedData | 1.567 | 0.035 | 1.602 | |
getSampleCorrelation | 0.030 | 0.001 | 0.032 | |
getSampleDepths | 0.165 | 0.002 | 0.167 | |
getSampleDistance | 0.029 | 0.001 | 0.029 | |
getTotalFragments | 0.022 | 0.000 | 0.022 | |
makeBiasBins | 0.123 | 0.001 | 0.123 | |
makePermutedSets | 1.681 | 0.083 | 1.765 | |
matchKmers | 1.736 | 0.078 | 1.815 | |
mini_counts | 0.000 | 0.001 | 0.002 | |
mini_dev | 0.001 | 0.001 | 0.002 | |
mini_ix | 0.000 | 0.000 | 0.001 | |
plotVariability | 27.060 | 0.101 | 27.181 | |
pwmDistance | 7.019 | 0.151 | 7.179 | |
rbind-chromVARDeviations-method | 0.136 | 0.001 | 0.138 | |