Kieran O'Neill
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/contiBAIT |
| Branch: master |
| Last Commit: af65175 |
| Last Changed Date: 2019-01-04 13:26:30 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:32:45 -0400 (Tue, 09 Apr 2019).
| Package 334/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| contiBAIT 1.11.1 Kieran O'Neill
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| Package: contiBAIT |
| Version: 1.11.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:contiBAIT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings contiBAIT_1.11.1.tar.gz |
| StartedAt: 2019-04-09 00:07:50 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 00:13:17 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 326.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: contiBAIT.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:contiBAIT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings contiBAIT_1.11.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/contiBAIT.Rcheck’ * using R Under development (unstable) (2018-11-27 r75683) * using platform: x86_64-apple-darwin15.6.0 (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 ‘1.11.1’ * 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 ... 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 ... 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 ... 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 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 compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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-3.9-bioc/meat/contiBAIT.Rcheck/00check.log’ for details.
contiBAIT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL contiBAIT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘contiBAIT’ ... ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c buildLinkageGroups.cpp -o buildLinkageGroups.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c computeSim.cpp -o computeSim.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c orderContigsGreedy.cpp -o orderContigsGreedy.o clang++ -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 contiBAIT.so buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/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 * DONE (contiBAIT)
contiBAIT.Rcheck/contiBAIT-Ex.timings
| name | user | system | elapsed | |
| BAIT | 0.000 | 0.001 | 0.000 | |
| ContigOrdering | 0.002 | 0.000 | 0.001 | |
| LibraryGroupList | 0.010 | 0.001 | 0.011 | |
| LinkageGroupList | 0.001 | 0.000 | 0.001 | |
| StrandFreqMatrix | 0.032 | 0.007 | 0.039 | |
| StrandReadMatrix | 0.011 | 0.002 | 0.013 | |
| StrandStateMatrix | 0.003 | 0.000 | 0.003 | |
| barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method | 0.513 | 0.027 | 0.541 | |
| clusterContigs-StrandStateMatrix-method | 0.025 | 0.001 | 0.027 | |
| contiBAIT | 4.295 | 0.102 | 4.473 | |
| findSimilarLibraries | 0.301 | 0.026 | 0.329 | |
| ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method | 1.944 | 0.030 | 1.981 | |
| makeBoxPlot | 0.030 | 0.004 | 0.034 | |
| makeChrTable | 0.791 | 0.003 | 0.797 | |
| orderAllLinkageGroups | 2.091 | 0.031 | 2.126 | |
| plotContigOrder | 0.291 | 0.003 | 0.295 | |
| plotLGDistances-LinkageGroupList-StrandStateMatrix-method | 0.136 | 0.006 | 0.144 | |
| plotWCdistribution-StrandFreqMatrix-method | 0.075 | 0.004 | 0.079 | |
| preprocessStrandTable-StrandFreqMatrix-method | 0.244 | 0.004 | 0.249 | |
| reorientAndMergeLGs | 0.095 | 0.003 | 0.098 | |
| strandSeqFreqTable | 3.657 | 0.032 | 3.713 | |
| thoroughBed | 0.039 | 0.003 | 0.042 | |
| writeBed | 0.000 | 0.000 | 0.001 | |