Alicia Schep
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/chromVAR |
| Branch: RELEASE_3_8 |
| Last Commit: e185549 |
| Last Changed Date: 2019-01-04 13:14:02 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:53:05 -0400 (Tue, 16 Apr 2019).
| Package 261/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| chromVAR 1.4.1 Alicia Schep
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: chromVAR |
| Version: 1.4.1 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings chromVAR_1.4.1.tar.gz |
| StartedAt: 2019-04-15 22:54:58 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:01:07 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 369.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: chromVAR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings chromVAR_1.4.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/chromVAR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.1’
* 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 24.072 0.308 28.664
pwmDistance 8.128 0.072 8.318
getJasparMotifs 7.540 0.060 7.767
* 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
‘/home/biocbuild/bbs-3.8-bioc/meat/chromVAR.Rcheck/00check.log’
for details.
chromVAR.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL chromVAR
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘chromVAR’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c pwm_similarity.cpp -o pwm_similarity.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o
utils.cpp: In function ‘Rcpp::NumericVector row_sds(arma::mat&, bool)’:
utils.cpp:12:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( int j=0; j < X.n_rows; j++ ) {
^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o chromVAR.so RcppExports.o pwm_similarity.o utils.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/chromVAR/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (chromVAR)
chromVAR.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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)
> BiocParallel::register(BiocParallel::SerialParam())
> test_check("chromVAR")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 65 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
22.920 0.888 23.932
chromVAR.Rcheck/chromVAR-Ex.timings
| name | user | system | elapsed | |
| addGCBias | 0.952 | 0.024 | 0.978 | |
| annotationMatches | 0.016 | 0.000 | 0.019 | |
| chromVAR_theme | 0.028 | 0.000 | 0.029 | |
| computeDeviations | 3.112 | 0.308 | 3.447 | |
| computeExpectations | 0.028 | 0.004 | 0.035 | |
| computeVariability | 4.236 | 0.084 | 4.326 | |
| counts | 0.012 | 0.000 | 0.009 | |
| deviationScores | 0.004 | 0.000 | 0.006 | |
| deviations | 0.008 | 0.000 | 0.006 | |
| deviationsCovariability | 24.072 | 0.308 | 28.664 | |
| deviationsTsne | 0.064 | 0.000 | 0.065 | |
| differentialDeviations | 0.012 | 0.000 | 0.011 | |
| differentialVariability | 0.024 | 0.000 | 0.025 | |
| example_counts | 0.004 | 0.000 | 0.001 | |
| filterPeaks | 0.180 | 0.008 | 0.188 | |
| filterSamples | 0.056 | 0.004 | 0.059 | |
| filterSamplesPlot | 0.100 | 0.000 | 0.101 | |
| getAnnotations | 0.304 | 0.008 | 0.311 | |
| getBackgroundPeaks | 0.596 | 0.060 | 0.657 | |
| getCisGroups | 0.052 | 0.004 | 0.054 | |
| getCounts | 3.896 | 0.084 | 4.012 | |
| getFragmentsPerPeak | 0.016 | 0.000 | 0.013 | |
| getFragmentsPerSample | 0.012 | 0.000 | 0.014 | |
| getJasparMotifs | 7.540 | 0.060 | 7.767 | |
| getPeaks | 0.104 | 0.004 | 0.106 | |
| getPermutedData | 2.104 | 0.196 | 2.305 | |
| getSampleCorrelation | 0.020 | 0.000 | 0.019 | |
| getSampleDepths | 0.144 | 0.012 | 0.155 | |
| getSampleDistance | 0.02 | 0.00 | 0.02 | |
| getTotalFragments | 0.016 | 0.000 | 0.014 | |
| makeBiasBins | 0.060 | 0.000 | 0.059 | |
| makePermutedSets | 1.112 | 0.020 | 1.149 | |
| matchKmers | 1.580 | 0.016 | 1.598 | |
| mini_counts | 0.000 | 0.000 | 0.001 | |
| mini_dev | 0.000 | 0.000 | 0.001 | |
| mini_ix | 0.000 | 0.000 | 0.001 | |
| plotVariability | 4.116 | 0.016 | 4.191 | |
| pwmDistance | 8.128 | 0.072 | 8.318 | |
| rbind-chromVARDeviations-method | 0.072 | 0.000 | 0.072 | |