Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 350/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
chromVAR 1.28.0 (landing page) Alicia Schep
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.28.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings chromVAR_1.28.0.tar.gz |
StartedAt: 2024-12-19 21:27:45 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 21:38:37 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 652.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: chromVAR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings chromVAR_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/chromVAR.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘chromVAR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘chromVAR’ version ‘1.28.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 for sufficient/correct file permissions ... OK * checking whether package ‘chromVAR’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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 loading without being on the library search path ... 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed deviationsCovariability 15.333 0.244 15.614 computeDeviations 5.281 0.094 5.376 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/chromVAR.Rcheck/00check.log’ for details.
chromVAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL chromVAR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘chromVAR’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwm_similarity.cpp -o pwm_similarity.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -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++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o chromVAR.so RcppExports.o pwm_similarity.o utils.o -llapack -L/home/biocbuild/bbs-3.20-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 21.773 1.214 22.972
chromVAR.Rcheck/chromVAR-Ex.timings
name | user | system | elapsed | |
addGCBias | 0.455 | 0.030 | 0.486 | |
annotationMatches | 0.011 | 0.001 | 0.012 | |
chromVAR_theme | 0.120 | 0.015 | 0.135 | |
computeDeviations | 5.281 | 0.094 | 5.376 | |
computeExpectations | 0.016 | 0.000 | 0.017 | |
computeVariability | 2.823 | 0.055 | 2.876 | |
counts | 0.006 | 0.000 | 0.005 | |
deviationScores | 0.004 | 0.000 | 0.004 | |
deviations | 0.003 | 0.001 | 0.004 | |
deviationsCovariability | 15.333 | 0.244 | 15.614 | |
deviationsTsne | 0.056 | 0.001 | 0.057 | |
differentialDeviations | 0.008 | 0.000 | 0.010 | |
differentialVariability | 0.019 | 0.000 | 0.019 | |
example_counts | 0.001 | 0.000 | 0.001 | |
filterPeaks | 0.168 | 0.001 | 0.169 | |
filterSamples | 0.036 | 0.003 | 0.038 | |
filterSamplesPlot | 0.085 | 0.004 | 0.090 | |
getAnnotations | 0.240 | 0.003 | 0.243 | |
getBackgroundPeaks | 0.458 | 0.101 | 0.558 | |
getCisGroups | 0.079 | 0.001 | 0.079 | |
getCounts | 1.796 | 0.056 | 1.850 | |
getFragmentsPerPeak | 0.005 | 0.001 | 0.006 | |
getFragmentsPerSample | 0.006 | 0.000 | 0.006 | |
getJasparMotifs | 4.206 | 0.042 | 4.249 | |
getPeaks | 0.082 | 0.016 | 0.097 | |
getPermutedData | 0.941 | 0.200 | 1.141 | |
getSampleCorrelation | 0.010 | 0.001 | 0.011 | |
getSampleDepths | 0.120 | 0.027 | 0.148 | |
getSampleDistance | 0.011 | 0.000 | 0.011 | |
getTotalFragments | 0.005 | 0.001 | 0.006 | |
makeBiasBins | 0.035 | 0.000 | 0.035 | |
makePermutedSets | 0.689 | 0.022 | 0.711 | |
matchKmers | 1.934 | 0.039 | 1.973 | |
mini_counts | 0.000 | 0.000 | 0.001 | |
mini_dev | 0.000 | 0.001 | 0.001 | |
mini_ix | 0.000 | 0.000 | 0.001 | |
plotVariability | 2.852 | 0.017 | 2.870 | |
pwmDistance | 4.457 | 0.042 | 4.499 | |
rbind-chromVARDeviations-method | 0.051 | 0.001 | 0.052 | |