Alicia Schep
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/chromVAR |
| Branch: master |
| Last Commit: fbbba6b |
| Last Changed Date: 2018-11-30 00:02:42 -0400 (Fri, 30 Nov 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:49:19 -0400 (Tue, 09 Apr 2019).
| Package 270/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| chromVAR 1.5.0 Alicia Schep
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: chromVAR |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings chromVAR_1.5.0.tar.gz |
| StartedAt: 2019-04-08 23:27:22 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:33:56 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 394.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: chromVAR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings chromVAR_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/chromVAR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.5.0’
* 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 25.028 0.260 25.553
pwmDistance 7.317 0.087 7.585
getJasparMotifs 5.818 0.080 5.897
* 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-3.9-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-3.9-bioc/R/bin/R CMD INSTALL chromVAR
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘chromVAR’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -L/usr/local/lib -o chromVAR.so RcppExports.o pwm_similarity.o utils.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-chromVAR/00new/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 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 (chromVAR)
chromVAR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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
24.486 1.025 26.079
chromVAR.Rcheck/chromVAR-Ex.timings
| name | user | system | elapsed | |
| addGCBias | 0.691 | 0.004 | 0.694 | |
| annotationMatches | 0.011 | 0.000 | 0.011 | |
| chromVAR_theme | 0.018 | 0.000 | 0.017 | |
| computeDeviations | 3.179 | 0.267 | 3.443 | |
| computeExpectations | 0.032 | 0.000 | 0.032 | |
| computeVariability | 4.689 | 0.108 | 4.812 | |
| counts | 0.014 | 0.000 | 0.014 | |
| deviationScores | 0.011 | 0.000 | 0.011 | |
| deviations | 0.011 | 0.000 | 0.010 | |
| deviationsCovariability | 25.028 | 0.260 | 25.553 | |
| deviationsTsne | 0.086 | 0.000 | 0.086 | |
| differentialDeviations | 0.015 | 0.000 | 0.015 | |
| differentialVariability | 0.033 | 0.000 | 0.034 | |
| example_counts | 0.002 | 0.000 | 0.002 | |
| filterPeaks | 0.254 | 0.000 | 0.253 | |
| filterSamples | 0.079 | 0.004 | 0.083 | |
| filterSamplesPlot | 0.147 | 0.000 | 0.147 | |
| getAnnotations | 0.479 | 0.012 | 0.491 | |
| getBackgroundPeaks | 0.972 | 0.112 | 1.085 | |
| getCisGroups | 0.067 | 0.000 | 0.067 | |
| getCounts | 3.262 | 0.111 | 3.395 | |
| getFragmentsPerPeak | 0.014 | 0.000 | 0.014 | |
| getFragmentsPerSample | 0.014 | 0.000 | 0.014 | |
| getJasparMotifs | 5.818 | 0.080 | 5.897 | |
| getPeaks | 0.104 | 0.000 | 0.105 | |
| getPermutedData | 3.093 | 0.196 | 3.331 | |
| getSampleCorrelation | 0.019 | 0.000 | 0.019 | |
| getSampleDepths | 0.131 | 0.016 | 0.152 | |
| getSampleDistance | 0.019 | 0.000 | 0.019 | |
| getTotalFragments | 0.014 | 0.000 | 0.014 | |
| makeBiasBins | 0.055 | 0.000 | 0.056 | |
| makePermutedSets | 1.142 | 0.016 | 1.374 | |
| matchKmers | 1.434 | 0.039 | 1.540 | |
| mini_counts | 0.002 | 0.000 | 0.002 | |
| mini_dev | 0.001 | 0.000 | 0.001 | |
| mini_ix | 0.001 | 0.000 | 0.001 | |
| plotVariability | 4.288 | 0.040 | 4.335 | |
| pwmDistance | 7.317 | 0.087 | 7.585 | |
| rbind-chromVARDeviations-method | 0.064 | 0.000 | 0.065 | |