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CHECK report for contiBAIT on malbec1

This page was generated on 2021-05-05 12:09:37 -0400 (Wed, 05 May 2021).

To the developers/maintainers of the contiBAIT package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 369/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
contiBAIT 1.18.0  (landing page)
Kieran O'Neill
Snapshot Date: 2021-05-04 14:50:13 -0400 (Tue, 04 May 2021)
URL: https://git.bioconductor.org/packages/contiBAIT
Branch: RELEASE_3_12
Last Commit: d50ef02
Last Changed Date: 2020-10-27 11:11:14 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: contiBAIT
Version: 1.18.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:contiBAIT.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings contiBAIT_1.18.0.tar.gz
StartedAt: 2021-05-05 00:24:20 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 00:31:00 -0400 (Wed, 05 May 2021)
EllapsedTime: 400.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: contiBAIT.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:contiBAIT.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings contiBAIT_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/contiBAIT.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.18.0’
* 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  5.8Mb
  sub-directories of 1Mb or more:
    extdata   3.4Mb
    libs      1.2Mb
* 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            7.868  0.308   8.337
findSimilarLibraries 5.268  1.072   6.367
strandSeqFreqTable   5.124  0.012   5.147
* 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-3.12-bioc/meat/contiBAIT.Rcheck/00check.log’
for details.



Installation output

contiBAIT.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL contiBAIT
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘contiBAIT’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c buildLinkageGroups.cpp -o buildLinkageGroups.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c computeSim.cpp -o computeSim.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c orderContigsGreedy.cpp -o orderContigsGreedy.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o contiBAIT.so buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-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)

Tests output


Example timings

contiBAIT.Rcheck/contiBAIT-Ex.timings

nameusersystemelapsed
BAIT000
ContigOrdering0.0040.0000.002
LibraryGroupList0.0080.0000.009
LinkageGroupList000
StrandFreqMatrix0.0280.0000.026
StrandReadMatrix0.0120.0000.013
StrandStateMatrix0.0040.0000.003
barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method0.4600.0040.466
clusterContigs-StrandStateMatrix-method0.0240.0000.024
contiBAIT7.8680.3088.337
findSimilarLibraries5.2681.0726.367
ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method2.0520.0602.115
makeBoxPlot0.0280.0080.036
makeChrTable1.3720.0041.377
orderAllLinkageGroups1.4720.0121.495
plotContigOrder0.3400.0000.341
plotLGDistances-LinkageGroupList-StrandStateMatrix-method0.1080.0000.108
plotWCdistribution-StrandFreqMatrix-method0.0560.0000.059
preprocessStrandTable-StrandFreqMatrix-method0.1640.0000.167
reorientAndMergeLGs0.0880.0040.089
strandSeqFreqTable5.1240.0125.147
thoroughBed0.0600.0000.057
writeBed0.0000.0000.001