Wolfgang Kopp
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/motifcounter |
| Branch: RELEASE_3_9 |
| Last Commit: ed124c3 |
| Last Changed Date: 2019-05-02 11:54:06 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:59:51 -0400 (Wed, 16 Oct 2019).
| Package 1040/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| motifcounter 1.8.0 Wolfgang Kopp
| malbec2 | Linux (Ubuntu 18.04.2 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: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2019-10-16 04:49:17 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:55:59 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 401.6 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_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/motifcounter.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.8.0’
* 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 13.243 0.232 13.476
* 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-3.9-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/3.6/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/3.6/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 version 3.6.1 (2019-07-05) -- "Action of the Toes"
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
259.888 4.086 264.126
motifcounter.Rcheck/motifcounter-Ex.timings
| name | user | system | elapsed | |
| clumpSizeDist | 0.506 | 0.015 | 0.527 | |
| combinatorialDist | 0.445 | 0.042 | 0.487 | |
| compoundPoissonDist | 0.379 | 0.064 | 0.443 | |
| computeClumpStartProb | 0.295 | 0.059 | 0.355 | |
| generateDNAString | 0.141 | 0.002 | 0.142 | |
| generateDNAStringSet | 0.127 | 0.002 | 0.129 | |
| hitStrand | 0.140 | 0.002 | 0.142 | |
| lenSequences | 0.129 | 0.004 | 0.133 | |
| markovModel | 0.270 | 0.034 | 0.303 | |
| motifAndBackgroundValid | 0.138 | 0.002 | 0.141 | |
| motifEnrichment | 3.850 | 0.045 | 3.896 | |
| motifHitProfile | 0.119 | 0.003 | 0.122 | |
| motifHits | 0.082 | 0.002 | 0.084 | |
| motifValid | 0.002 | 0.000 | 0.002 | |
| motifcounter-package | 1.102 | 0.024 | 1.126 | |
| motifcounterOptions | 0.000 | 0.000 | 0.001 | |
| normalizeMotif | 0.003 | 0.001 | 0.003 | |
| numMotifHits | 0.958 | 0.013 | 0.972 | |
| probOverlapHit | 0.269 | 0.013 | 0.282 | |
| readBackground | 0.141 | 0.004 | 0.146 | |
| revcompMotif | 0.003 | 0.000 | 0.003 | |
| scoreDist | 0.091 | 0.001 | 0.092 | |
| scoreDistBf | 0.137 | 0.001 | 0.138 | |
| scoreDistEmpirical | 3.132 | 0.052 | 3.185 | |
| scoreHistogram | 0.206 | 0.008 | 0.215 | |
| scoreHistogramSingleSeq | 0.080 | 0.007 | 0.087 | |
| scoreProfile | 0.625 | 0.005 | 0.629 | |
| scoreSequence | 0.123 | 0.004 | 0.127 | |
| scoreStrand | 0.134 | 0.003 | 0.137 | |
| scoreThreshold | 0.145 | 0.002 | 0.147 | |
| sigLevel | 0.001 | 0.000 | 0.000 | |
| simulateClumpSizeDist | 13.243 | 0.232 | 13.476 | |
| simulateNumHitsDist | 2.976 | 0.063 | 3.039 | |