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This page was generated on 2021-12-01 17:17:22 -0500 (Wed, 01 Dec 2021).

CHECK results for contiBAIT on nebbiolo2

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.

raw results

Package 391/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
contiBAIT 1.22.0  (landing page)
Kieran O'Neill
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
git_url: https://git.bioconductor.org/packages/contiBAIT
git_branch: RELEASE_3_14
git_last_commit: 7642d19
git_last_commit_date: 2021-10-26 12:25:24 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: contiBAIT
Version: 1.22.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:contiBAIT.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings contiBAIT_1.22.0.tar.gz
StartedAt: 2021-11-30 08:39:10 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 08:44:26 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 315.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: contiBAIT.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:contiBAIT.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings contiBAIT_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/contiBAIT.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.22.0’
* 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  6.3Mb
  sub-directories of 1Mb or more:
    extdata   3.4Mb
    libs      1.7Mb
* 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
findSimilarLibraries 6.474  1.575   7.712
contiBAIT            6.495  1.283   7.411
* 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-3.14-bioc/meat/contiBAIT.Rcheck/00check.log’
for details.



Installation output

contiBAIT.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL contiBAIT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘contiBAIT’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/lib -L/usr/local/lib -o contiBAIT.so buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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
ContigOrdering0.0020.0000.001
LibraryGroupList0.0110.0000.011
LinkageGroupList0.0010.0000.001
StrandFreqMatrix1.3560.0401.397
StrandReadMatrix0.0130.0000.013
StrandStateMatrix0.0020.0000.002
barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method0.3710.0070.379
clusterContigs-StrandStateMatrix-method0.0260.0010.026
contiBAIT6.4951.2837.411
findSimilarLibraries6.4741.5757.712
ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method1.6460.1921.765
makeBoxPlot0.0270.0040.030
makeChrTable0.8770.0040.881
orderAllLinkageGroups0.9800.0281.009
plotContigOrder0.2270.0040.231
plotLGDistances-LinkageGroupList-StrandStateMatrix-method0.1050.0040.109
plotWCdistribution-StrandFreqMatrix-method0.0520.0120.065
preprocessStrandTable-StrandFreqMatrix-method0.1540.0400.194
reorientAndMergeLGs0.0910.0000.091
strandSeqFreqTable4.2980.0084.307
thoroughBed0.0510.0000.050
writeBed000