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CHECK report for motifcounter on merida1

This page was generated on 2021-05-06 12:35:47 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the motifcounter package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1143/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifcounter 1.14.0  (landing page)
Wolfgang Kopp
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/motifcounter
Branch: RELEASE_3_12
Last Commit: 021b279
Last Changed Date: 2020-10-27 11:22:37 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: motifcounter
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings motifcounter_1.14.0.tar.gz
StartedAt: 2021-05-06 03:53:49 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:57:56 -0400 (Thu, 06 May 2021)
EllapsedTime: 246.8 seconds
RetCode: 0
Status:   OK  
CheckDir: motifcounter.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings motifcounter_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/motifcounter.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifcounter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifcounter’ version ‘1.14.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .zenodo.json
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 ‘motifcounter’ 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 ... OK
* 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 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
simulateClumpSizeDist 14.887  0.316  15.226
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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-3.12-bioc/meat/motifcounter.Rcheck/00check.log’
for details.



Installation output

motifcounter.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘motifcounter’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c Rbackground.c -o Rbackground.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c Rcombinatorial.c -o Rcombinatorial.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c Rcompoundpoisson.c -o Rcompoundpoisson.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c Rminmaxscore.c -o Rminmaxscore.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c Roption.c -o Roption.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c Roverlap.c -o Roverlap.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c Rscore1d.c -o Rscore1d.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c Rsequence.c -o Rsequence.o
Rsequence.c:143:21: warning: unused variable 'noscores' [-Wunused-variable]
    int mins, maxs, noscores;
                    ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c Rsimulate.c -o Rsimulate.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c background.c -o background.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c combinatorial.c -o combinatorial.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c compoundpoisson.c -o compoundpoisson.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c markovchain.c -o markovchain.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c markovchain_single.c -o markovchain_single.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c matrix.c -o matrix.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c mdist_register.c -o mdist_register.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c minmaxscore.c -o minmaxscore.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c overlap.c -o overlap.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c score1d.c -o score1d.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c score2d.c -o score2d.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c scorefunctions.c -o scorefunctions.o
scorefunctions.c:84:22: warning: unused variable 'cindex' [-Wunused-variable]
    int j, i, index, cindex, ds;
                     ^
scorefunctions.c:119:17: warning: unused variable 'cindex' [-Wunused-variable]
  int s, index, cindex;
                ^
scorefunctions.c:159:19: warning: unused variable 'cindex' [-Wunused-variable]
    int s, index, cindex;
                  ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c sequence.c -o sequence.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c simulate.c -o simulate.o
clang -mmacosx-version-min=10.13 -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 motifcounter.so Rbackground.o Rcombinatorial.o Rcompoundpoisson.o Rminmaxscore.o Roption.o Roverlap.o Rscore1d.o Rsequence.o Rsimulate.o background.o combinatorial.o compoundpoisson.o markovchain.o markovchain_single.o matrix.o mdist_register.o minmaxscore.o overlap.o score1d.o score2d.o scorefunctions.o sequence.o simulate.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-motifcounter/00new/motifcounter/libs
** R
** 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 (motifcounter)

Tests output

motifcounter.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(motifcounter)
> 
> test_check("motifcounter")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 841 ]
> 
> proc.time()
   user  system elapsed 
129.401   1.408 130.962 

Example timings

motifcounter.Rcheck/motifcounter-Ex.timings

nameusersystemelapsed
clumpSizeDist0.3680.0070.416
combinatorialDist0.2880.0080.297
compoundPoissonDist0.2160.0150.230
computeClumpStartProb0.1720.0200.191
generateDNAString0.1120.0010.112
generateDNAStringSet0.1680.0020.171
hitStrand0.1070.0020.110
lenSequences0.0960.0120.108
markovModel0.1500.0160.166
motifAndBackgroundValid0.1050.0050.111
motifEnrichment3.3130.0183.335
motifHitProfile0.1080.0040.112
motifHits0.1200.0040.125
motifValid0.0020.0000.003
motifcounter-package0.8520.0140.866
motifcounterOptions0.0000.0010.001
normalizeMotif0.0020.0000.002
numMotifHits0.6450.0080.653
probOverlapHit0.1880.0040.192
readBackground0.1120.0010.113
revcompMotif0.0020.0000.002
scoreDist0.1090.0020.111
scoreDistBf0.1360.0020.138
scoreDistEmpirical3.0310.0323.067
scoreHistogram0.2900.0100.302
scoreHistogramSingleSeq0.0850.0060.091
scoreProfile0.5090.0040.513
scoreSequence0.1060.0040.110
scoreStrand0.1160.0020.118
scoreThreshold0.1020.0020.104
sigLevel000
simulateClumpSizeDist14.887 0.31615.226
simulateNumHitsDist2.5720.0382.614