Back to Multiple platform build/check report for BioC 3.15
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-01-27 11:10:23 -0500 (Thu, 27 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for contiBAIT on merida1


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 391/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
contiBAIT 1.23.1  (landing page)
Kieran O'Neill
Snapshot Date: 2022-01-26 13:55:18 -0500 (Wed, 26 Jan 2022)
git_url: https://git.bioconductor.org/packages/contiBAIT
git_branch: master
git_last_commit: 1a66f2b
git_last_commit_date: 2021-11-20 03:56:57 -0500 (Sat, 20 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'Rsamtools' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: contiBAIT
Version: 1.23.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:contiBAIT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings contiBAIT_1.23.1.tar.gz
StartedAt: 2022-01-26 23:42:42 -0500 (Wed, 26 Jan 2022)
EndedAt: 2022-01-26 23:51:19 -0500 (Wed, 26 Jan 2022)
EllapsedTime: 516.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: contiBAIT.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:contiBAIT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings contiBAIT_1.23.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/contiBAIT.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.23.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
contiBAIT            9.281  1.667  10.856
findSimilarLibraries 6.069  2.407   8.367
strandSeqFreqTable   6.493  0.070   6.570
* 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
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/contiBAIT.Rcheck/00check.log’
for details.



Installation output

contiBAIT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL contiBAIT
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘contiBAIT’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c buildLinkageGroups.cpp -o buildLinkageGroups.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c computeSim.cpp -o computeSim.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c orderContigsGreedy.cpp -o orderContigsGreedy.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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/4.2/Resources/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
ContigOrdering0.0020.0000.002
LibraryGroupList0.0150.0010.016
LinkageGroupList0.0010.0000.001
StrandFreqMatrix0.0470.0090.057
StrandReadMatrix0.0200.0030.023
StrandStateMatrix0.0030.0000.003
barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method0.7030.0770.780
clusterContigs-StrandStateMatrix-method0.0350.0060.041
contiBAIT 9.281 1.66710.856
findSimilarLibraries6.0692.4078.367
ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method3.4520.3153.772
makeBoxPlot0.0410.0060.047
makeChrTable1.1040.0131.119
orderAllLinkageGroups2.0260.0552.084
plotContigOrder0.4240.0150.440
plotLGDistances-LinkageGroupList-StrandStateMatrix-method0.1720.0080.183
plotWCdistribution-StrandFreqMatrix-method0.1060.0060.112
preprocessStrandTable-StrandFreqMatrix-method0.3180.0060.324
reorientAndMergeLGs0.1570.0060.163
strandSeqFreqTable6.4930.0706.570
thoroughBed0.0630.0040.067
writeBed0.0000.0010.001