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CHECK report for contiBAIT on malbec2

This page was generated on 2018-10-17 08:28:31 -0400 (Wed, 17 Oct 2018).

Package 301/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
contiBAIT 1.8.0
Kieran O'Neill
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/contiBAIT
Branch: RELEASE_3_7
Last Commit: 4d793ab
Last Changed Date: 2018-04-30 10:35:40 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: contiBAIT
Version: 1.8.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:contiBAIT.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings contiBAIT_1.8.0.tar.gz
StartedAt: 2018-10-15 23:28:35 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 23:32:17 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 222.1 seconds
RetCode: 0
Status:  OK 
CheckDir: contiBAIT.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:contiBAIT.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings contiBAIT_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/contiBAIT.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.8.0’
* 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  5.5Mb
  sub-directories of 1Mb or more:
    extdata   3.4Mb
    libs      1.1Mb
* 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 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/contiBAIT.Rcheck/00check.log’
for details.



Installation output

contiBAIT.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL contiBAIT
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘contiBAIT’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c buildLinkageGroups.cpp -o buildLinkageGroups.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c computeSim.cpp -o computeSim.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c orderContigsGreedy.cpp -o orderContigsGreedy.o
g++ -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o contiBAIT.so buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/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
BAIT000
ContigOrdering0.0040.0000.001
LibraryGroupList0.0080.0000.008
LinkageGroupList0.0000.0000.001
StrandFreqMatrix0.0240.0040.027
StrandReadMatrix0.0120.0000.012
StrandStateMatrix0.0000.0000.003
barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method0.5560.0200.574
clusterContigs-StrandStateMatrix-method0.0160.0040.021
contiBAIT3.8880.1484.187
findSimilarLibraries0.2200.1560.402
ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method1.8520.0721.923
makeBoxPlot0.0200.0040.024
makeChrTable0.5440.0000.543
orderAllLinkageGroups0.9680.0120.978
plotContigOrder0.2520.0040.255
plotLGDistances-LinkageGroupList-StrandStateMatrix-method0.1120.0000.113
plotWCdistribution-StrandFreqMatrix-method0.0520.0000.053
preprocessStrandTable-StrandFreqMatrix-method0.160.000.16
reorientAndMergeLGs0.0840.0000.081
strandSeqFreqTable2.9400.0042.945
thoroughBed0.0280.0000.027
writeBed000