Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:38 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the contiBAIT package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/contiBAIT.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 383/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
contiBAIT 1.20.0 (landing page) Kieran O'Neill
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: contiBAIT |
Version: 1.20.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:contiBAIT.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings contiBAIT_1.20.0.tar.gz |
StartedAt: 2021-10-14 09:23:01 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:27:54 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 292.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: contiBAIT.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:contiBAIT.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings contiBAIT_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/contiBAIT.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘contiBAIT/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘contiBAIT’ version ‘1.20.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘contiBAIT’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: extdata 3.4Mb * 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 ... NOTE ideogramPlot.func: no visible binding for global variable ‘w’ ideogramPlot.func: no visible binding for global variable ‘w2’ makeChrTable: no visible global function definition for ‘queryHits’ makeChrTable: no visible global function definition for ‘subjectHits’ orderContigsGreedy: no visible global function definition for ‘makeCluster’ orderContigsGreedy: no visible global function definition for ‘clusterCall’ orderContigsGreedy: no visible global function definition for ‘stopCluster’ strandSeqFreqTable: no visible global function definition for ‘queryHits’ strandSeqFreqTable: no visible global function definition for ‘subjectHits’ ideogramPlot,StrandReadMatrix-StrandReadMatrix-ChrTable: no visible binding for global variable ‘w’ ideogramPlot,StrandReadMatrix-StrandReadMatrix-ChrTable: no visible binding for global variable ‘w2’ Undefined global functions or variables: clusterCall makeCluster queryHits stopCluster subjectHits w w2 * 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 ... WARNING Documented arguments not in \usage in documentation object 'plotLGDistances,LinkageGroupList,StrandStateMatrix-method': ‘...’ 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 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 contiBAIT 5.52 0.137 5.678 * 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: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/contiBAIT.Rcheck/00check.log’ for details.
contiBAIT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL contiBAIT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘contiBAIT’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c buildLinkageGroups.cpp -o buildLinkageGroups.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c computeSim.cpp -o computeSim.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c orderContigsGreedy.cpp -o orderContigsGreedy.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o contiBAIT.so buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-contiBAIT/00new/contiBAIT/libs ** R ** data ** 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 (contiBAIT)
contiBAIT.Rcheck/contiBAIT-Ex.timings
name | user | system | elapsed | |
BAIT | 0.001 | 0.000 | 0.000 | |
ContigOrdering | 0.001 | 0.000 | 0.001 | |
LibraryGroupList | 0.007 | 0.000 | 0.008 | |
LinkageGroupList | 0.001 | 0.000 | 0.001 | |
StrandFreqMatrix | 0.020 | 0.004 | 0.024 | |
StrandReadMatrix | 0.012 | 0.000 | 0.012 | |
StrandStateMatrix | 0.002 | 0.000 | 0.002 | |
barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method | 0.324 | 0.035 | 0.360 | |
clusterContigs-StrandStateMatrix-method | 0.020 | 0.005 | 0.024 | |
contiBAIT | 5.520 | 0.137 | 5.678 | |
findSimilarLibraries | 4.853 | 0.041 | 4.907 | |
ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method | 1.448 | 0.028 | 1.477 | |
makeBoxPlot | 0.034 | 0.000 | 0.033 | |
makeChrTable | 0.87 | 0.02 | 0.89 | |
orderAllLinkageGroups | 0.846 | 0.036 | 0.883 | |
plotContigOrder | 0.212 | 0.000 | 0.212 | |
plotLGDistances-LinkageGroupList-StrandStateMatrix-method | 0.079 | 0.012 | 0.092 | |
plotWCdistribution-StrandFreqMatrix-method | 0.050 | 0.004 | 0.055 | |
preprocessStrandTable-StrandFreqMatrix-method | 0.154 | 0.000 | 0.154 | |
reorientAndMergeLGs | 0.074 | 0.000 | 0.074 | |
strandSeqFreqTable | 3.610 | 0.036 | 3.647 | |
thoroughBed | 0.042 | 0.000 | 0.041 | |
writeBed | 0 | 0 | 0 | |