Wolfgang Kopp
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/motifcounter |
| Branch: RELEASE_3_7 |
| Last Commit: fbf03de |
| Last Changed Date: 2018-04-30 10:35:45 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:57:58 -0400 (Wed, 17 Oct 2018).
| Package 939/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| motifcounter 1.4.0 Wolfgang Kopp
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: motifcounter |
| Version: 1.4.0 |
| 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_1.4.0.tar.gz |
| StartedAt: 2018-10-16 22:45:02 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 22:51:05 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 362.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: motifcounter.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/motifcounter.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.4.0’
* 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
simulateClumpSizeDist 41.569 0.298 42.166
* 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-3.7-bioc/meat/motifcounter.Rcheck/00check.log’
for details.
motifcounter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL motifcounter ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘motifcounter’ ... ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c Rbackground.c -o Rbackground.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c Rcombinatorial.c -o Rcombinatorial.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c Rcompoundpoisson.c -o Rcompoundpoisson.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c Rminmaxscore.c -o Rminmaxscore.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c Roption.c -o Roption.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c Roverlap.c -o Roverlap.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c Rscore1d.c -o Rscore1d.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c Rsequence.c -o Rsequence.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c Rsimulate.c -o Rsimulate.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c background.c -o background.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c combinatorial.c -o combinatorial.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c compoundpoisson.c -o compoundpoisson.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c markovchain.c -o markovchain.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c markovchain_single.c -o markovchain_single.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c matrix.c -o matrix.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c mdist_register.c -o mdist_register.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c minmaxscore.c -o minmaxscore.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c overlap.c -o overlap.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c score1d.c -o score1d.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c score2d.c -o score2d.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c scorefunctions.c -o scorefunctions.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c sequence.c -o sequence.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fPIC -Wall -g -O2 -c simulate.c -o simulate.o clang -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 -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/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 * DONE (motifcounter)
motifcounter.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 831 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
222.903 1.957 226.369
motifcounter.Rcheck/motifcounter-Ex.timings
| name | user | system | elapsed | |
| clumpSizeDist | 0.225 | 0.015 | 0.243 | |
| combinatorialDist | 0.364 | 0.019 | 0.386 | |
| compoundPoissonDist | 0.281 | 0.026 | 0.307 | |
| computeClumpStartProb | 0.198 | 0.018 | 0.216 | |
| generateDNAString | 0.099 | 0.000 | 0.099 | |
| generateDNAStringSet | 0.163 | 0.001 | 0.165 | |
| lenSequences | 0.115 | 0.003 | 0.119 | |
| markovModel | 0.165 | 0.004 | 0.170 | |
| motifAndBackgroundValid | 0.093 | 0.001 | 0.097 | |
| motifEnrichment | 4.104 | 0.052 | 4.182 | |
| motifHitProfile | 0.153 | 0.005 | 0.159 | |
| motifHits | 0.127 | 0.003 | 0.131 | |
| motifValid | 0.004 | 0.000 | 0.004 | |
| motifcounter-package | 1.205 | 0.011 | 1.223 | |
| motifcounterOptions | 0.001 | 0.000 | 0.002 | |
| normalizeMotif | 0.003 | 0.000 | 0.004 | |
| numMotifHits | 1.158 | 0.015 | 1.187 | |
| probOverlapHit | 0.220 | 0.006 | 0.229 | |
| readBackground | 0.099 | 0.001 | 0.100 | |
| revcompMotif | 0.004 | 0.001 | 0.003 | |
| scoreDist | 0.112 | 0.001 | 0.114 | |
| scoreDistBf | 0.118 | 0.003 | 0.121 | |
| scoreDistEmpirical | 3.501 | 0.017 | 3.534 | |
| scoreHistogram | 0.254 | 0.006 | 0.261 | |
| scoreHistogramSingleSeq | 0.116 | 0.004 | 0.121 | |
| scoreProfile | 0.563 | 0.002 | 0.570 | |
| scoreSequence | 0.093 | 0.001 | 0.097 | |
| scoreStrand | 0.099 | 0.001 | 0.100 | |
| scoreThreshold | 0.078 | 0.000 | 0.085 | |
| sigLevel | 0.001 | 0.000 | 0.001 | |
| simulateClumpSizeDist | 41.569 | 0.298 | 42.166 | |
| simulateNumHitsDist | 2.867 | 0.052 | 2.943 | |