Alicia Schep
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/chromVAR |
| Branch: RELEASE_3_10 |
| Last Commit: 7a74fdd |
| Last Changed Date: 2019-10-29 13:10:49 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:46:11 -0400 (Wed, 15 Apr 2020).
| Package 289/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| chromVAR 1.8.0 Alicia Schep
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: chromVAR |
| Version: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings chromVAR_1.8.0.tar.gz |
| StartedAt: 2020-04-15 01:11:23 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:18:41 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 437.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: chromVAR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings chromVAR_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/chromVAR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chromVAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chromVAR’ 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘chromVAR’ 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 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 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
deviationsCovariability 22.386 0.528 23.185
pwmDistance 7.822 0.128 8.031
getJasparMotifs 7.167 0.167 7.382
getCounts 4.950 0.363 5.366
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/chromVAR.Rcheck/00check.log’
for details.
chromVAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL chromVAR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘chromVAR’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c pwm_similarity.cpp -o pwm_similarity.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.o clang++ -std=gnu++11 -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 chromVAR.so RcppExports.o pwm_similarity.o utils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-chromVAR/00new/chromVAR/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘IRanges’ for request: ‘score’ when loading ‘TFBSTools’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘IRanges’ for request: ‘score’ when loading ‘TFBSTools’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location No methods found in package ‘IRanges’ for request: ‘score’ when loading ‘TFBSTools’ ** testing if installed package keeps a record of temporary installation path * DONE (chromVAR)
chromVAR.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(chromVAR)
No methods found in package 'IRanges' for request: 'score' when loading 'TFBSTools'
> BiocParallel::register(BiocParallel::SerialParam())
> test_check("chromVAR")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 65 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
26.016 1.428 27.696
chromVAR.Rcheck/chromVAR-Ex.timings
| name | user | system | elapsed | |
| addGCBias | 1.748 | 0.036 | 1.800 | |
| annotationMatches | 0.020 | 0.003 | 0.024 | |
| chromVAR_theme | 0.028 | 0.003 | 0.031 | |
| computeDeviations | 3.669 | 0.101 | 3.810 | |
| computeExpectations | 0.040 | 0.004 | 0.045 | |
| computeVariability | 4.586 | 0.285 | 4.910 | |
| counts | 0.010 | 0.001 | 0.010 | |
| deviationScores | 0.011 | 0.000 | 0.012 | |
| deviations | 0.011 | 0.000 | 0.012 | |
| deviationsCovariability | 22.386 | 0.528 | 23.185 | |
| deviationsTsne | 0.110 | 0.002 | 0.113 | |
| differentialDeviations | 0.022 | 0.001 | 0.024 | |
| differentialVariability | 0.035 | 0.001 | 0.037 | |
| example_counts | 0.001 | 0.001 | 0.002 | |
| filterPeaks | 0.336 | 0.015 | 0.356 | |
| filterSamples | 0.067 | 0.008 | 0.074 | |
| filterSamplesPlot | 0.190 | 0.009 | 0.199 | |
| getAnnotations | 0.560 | 0.009 | 0.581 | |
| getBackgroundPeaks | 0.869 | 0.125 | 1.007 | |
| getCisGroups | 0.087 | 0.001 | 0.089 | |
| getCounts | 4.950 | 0.363 | 5.366 | |
| getFragmentsPerPeak | 0.013 | 0.000 | 0.013 | |
| getFragmentsPerSample | 0.016 | 0.001 | 0.018 | |
| getJasparMotifs | 7.167 | 0.167 | 7.382 | |
| getPeaks | 0.133 | 0.001 | 0.138 | |
| getPermutedData | 1.589 | 0.128 | 1.727 | |
| getSampleCorrelation | 0.021 | 0.001 | 0.023 | |
| getSampleDepths | 0.137 | 0.001 | 0.139 | |
| getSampleDistance | 0.023 | 0.000 | 0.024 | |
| getTotalFragments | 0.015 | 0.001 | 0.016 | |
| makeBiasBins | 0.068 | 0.001 | 0.069 | |
| makePermutedSets | 1.309 | 0.047 | 1.369 | |
| matchKmers | 1.667 | 0.069 | 1.753 | |
| mini_counts | 0.001 | 0.001 | 0.002 | |
| mini_dev | 0.001 | 0.001 | 0.003 | |
| mini_ix | 0.002 | 0.001 | 0.005 | |
| plotVariability | 4.506 | 0.041 | 4.593 | |
| pwmDistance | 7.822 | 0.128 | 8.031 | |
| rbind-chromVARDeviations-method | 0.077 | 0.001 | 0.077 | |