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 12:13:19 -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: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings chromVAR_1.8.0.tar.gz |
| StartedAt: 2020-04-15 05:10:34 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:17:48 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 433.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: chromVAR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings chromVAR_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/chromVAR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.8.0’
* 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 24.988 0.332 25.843
getJasparMotifs 7.224 0.084 7.336
pwmDistance 7.000 0.056 7.065
* 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-3.10-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-3.10-bioc/R/bin/R CMD INSTALL chromVAR
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘chromVAR’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/lib -L/usr/local/lib -o chromVAR.so RcppExports.o pwm_similarity.o utils.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/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-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)
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
24.656 1.108 25.890
chromVAR.Rcheck/chromVAR-Ex.timings
| name | user | system | elapsed | |
| addGCBias | 1.992 | 0.016 | 2.015 | |
| annotationMatches | 0.020 | 0.000 | 0.022 | |
| chromVAR_theme | 0.020 | 0.008 | 0.028 | |
| computeDeviations | 4.284 | 0.492 | 4.836 | |
| computeExpectations | 0.036 | 0.004 | 0.040 | |
| computeVariability | 4.408 | 0.172 | 4.593 | |
| counts | 0.016 | 0.000 | 0.014 | |
| deviationScores | 0.012 | 0.000 | 0.010 | |
| deviations | 0.004 | 0.004 | 0.010 | |
| deviationsCovariability | 24.988 | 0.332 | 25.843 | |
| deviationsTsne | 0.076 | 0.004 | 0.080 | |
| differentialDeviations | 0.020 | 0.000 | 0.019 | |
| differentialVariability | 0.032 | 0.000 | 0.030 | |
| example_counts | 0.000 | 0.000 | 0.001 | |
| filterPeaks | 0.284 | 0.000 | 0.284 | |
| filterSamples | 0.076 | 0.000 | 0.073 | |
| filterSamplesPlot | 0.164 | 0.000 | 0.164 | |
| getAnnotations | 0.492 | 0.000 | 0.494 | |
| getBackgroundPeaks | 1.040 | 0.080 | 1.121 | |
| getCisGroups | 0.072 | 0.000 | 0.072 | |
| getCounts | 4.500 | 0.120 | 4.705 | |
| getFragmentsPerPeak | 0.016 | 0.000 | 0.014 | |
| getFragmentsPerSample | 0.016 | 0.000 | 0.014 | |
| getJasparMotifs | 7.224 | 0.084 | 7.336 | |
| getPeaks | 0.132 | 0.000 | 0.133 | |
| getPermutedData | 1.692 | 0.144 | 1.839 | |
| getSampleCorrelation | 0.016 | 0.000 | 0.014 | |
| getSampleDepths | 0.084 | 0.020 | 0.104 | |
| getSampleDistance | 0.020 | 0.000 | 0.021 | |
| getTotalFragments | 0.016 | 0.000 | 0.016 | |
| makeBiasBins | 0.064 | 0.000 | 0.065 | |
| makePermutedSets | 1.036 | 0.008 | 1.047 | |
| matchKmers | 1.612 | 0.020 | 1.639 | |
| mini_counts | 0.000 | 0.004 | 0.001 | |
| mini_dev | 0.000 | 0.000 | 0.001 | |
| mini_ix | 0.004 | 0.000 | 0.002 | |
| plotVariability | 3.732 | 0.020 | 3.759 | |
| pwmDistance | 7.000 | 0.056 | 7.065 | |
| rbind-chromVARDeviations-method | 0.08 | 0.00 | 0.08 | |