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CHECK report for contiBAIT on merida2

This page was generated on 2019-04-09 13:32:45 -0400 (Tue, 09 Apr 2019).

Package 334/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
contiBAIT 1.11.1
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)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

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

Command output

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### Running command:
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###   /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
###
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* 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.



Installation output

contiBAIT.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL contiBAIT
###
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* 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)

Tests output


Example timings

contiBAIT.Rcheck/contiBAIT-Ex.timings

nameusersystemelapsed
BAIT0.0000.0010.000
ContigOrdering0.0020.0000.001
LibraryGroupList0.0100.0010.011
LinkageGroupList0.0010.0000.001
StrandFreqMatrix0.0320.0070.039
StrandReadMatrix0.0110.0020.013
StrandStateMatrix0.0030.0000.003
barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method0.5130.0270.541
clusterContigs-StrandStateMatrix-method0.0250.0010.027
contiBAIT4.2950.1024.473
findSimilarLibraries0.3010.0260.329
ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method1.9440.0301.981
makeBoxPlot0.0300.0040.034
makeChrTable0.7910.0030.797
orderAllLinkageGroups2.0910.0312.126
plotContigOrder0.2910.0030.295
plotLGDistances-LinkageGroupList-StrandStateMatrix-method0.1360.0060.144
plotWCdistribution-StrandFreqMatrix-method0.0750.0040.079
preprocessStrandTable-StrandFreqMatrix-method0.2440.0040.249
reorientAndMergeLGs0.0950.0030.098
strandSeqFreqTable3.6570.0323.713
thoroughBed0.0390.0030.042
writeBed0.0000.0000.001