Wolfgang Kopp
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/motifcounter |
| Branch: master |
| Last Commit: 55781fb |
| Last Changed Date: 2019-10-29 13:42:17 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:47:35 -0500 (Thu, 16 Jan 2020).
| Package 1083/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| motifcounter 1.11.0 Wolfgang Kopp
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: motifcounter |
| Version: 1.11.0 |
| 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_1.11.0.tar.gz |
| StartedAt: 2020-01-16 06:42:24 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 06:49:34 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 430.2 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_1.11.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/motifcounter.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.11.0’
* 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 15.586 0.315 15.902
* 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-3.11-bioc/meat/motifcounter.Rcheck/00check.log’
for details.
motifcounter.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL motifcounter
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘motifcounter’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/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)
motifcounter.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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: 841 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
>
> proc.time()
user system elapsed
266.414 4.584 271.042
motifcounter.Rcheck/motifcounter-Ex.timings
| name | user | system | elapsed | |
| clumpSizeDist | 0.514 | 0.012 | 0.531 | |
| combinatorialDist | 0.414 | 0.014 | 0.429 | |
| compoundPoissonDist | 0.312 | 0.047 | 0.359 | |
| computeClumpStartProb | 0.303 | 0.058 | 0.361 | |
| generateDNAString | 0.156 | 0.003 | 0.159 | |
| generateDNAStringSet | 0.229 | 0.004 | 0.232 | |
| hitStrand | 0.159 | 0.005 | 0.164 | |
| lenSequences | 0.183 | 0.032 | 0.215 | |
| markovModel | 0.254 | 0.042 | 0.297 | |
| motifAndBackgroundValid | 0.162 | 0.013 | 0.175 | |
| motifEnrichment | 3.783 | 0.036 | 3.818 | |
| motifHitProfile | 0.148 | 0.004 | 0.152 | |
| motifHits | 0.150 | 0.003 | 0.154 | |
| motifValid | 0.003 | 0.000 | 0.004 | |
| motifcounter-package | 1.422 | 0.040 | 1.461 | |
| motifcounterOptions | 0.001 | 0.000 | 0.001 | |
| normalizeMotif | 0.002 | 0.001 | 0.003 | |
| numMotifHits | 1.091 | 0.022 | 1.118 | |
| probOverlapHit | 0.233 | 0.015 | 0.248 | |
| readBackground | 0.135 | 0.001 | 0.136 | |
| revcompMotif | 0.003 | 0.000 | 0.004 | |
| scoreDist | 0.160 | 0.002 | 0.163 | |
| scoreDistBf | 0.158 | 0.001 | 0.159 | |
| scoreDistEmpirical | 4.459 | 0.071 | 4.531 | |
| scoreHistogram | 0.399 | 0.015 | 0.416 | |
| scoreHistogramSingleSeq | 0.165 | 0.012 | 0.177 | |
| scoreProfile | 0.772 | 0.005 | 0.777 | |
| scoreSequence | 0.144 | 0.005 | 0.148 | |
| scoreStrand | 0.143 | 0.003 | 0.146 | |
| scoreThreshold | 0.128 | 0.001 | 0.130 | |
| sigLevel | 0 | 0 | 0 | |
| simulateClumpSizeDist | 15.586 | 0.315 | 15.902 | |
| simulateNumHitsDist | 3.397 | 0.087 | 3.489 | |