Alicia Schep
| Snapshot Date: 2024-05-30 18:28:32 -0400 (Thu, 30 May 2024) |
| git_url: https://git.bioconductor.org/packages/chromVAR |
| git_branch: RELEASE_3_19 |
| git_last_commit: 8150876 |
| git_last_commit_date: 2024-04-30 11:01:15 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-31 17:02:52 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 350/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| chromVAR 1.26.0 (landing page) Alicia Schep
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the chromVAR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chromVAR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: chromVAR |
| Version: 1.26.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings chromVAR_1.26.0.tar.gz |
| StartedAt: 2024-05-31 02:14:28 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 02:22:20 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 472.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: chromVAR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings chromVAR_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/chromVAR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘chromVAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chromVAR’ version ‘1.26.0’
* 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
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub records with missing/empty fields:
Record: 1 Field(s): COPYRIGHT HOLDER
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 loading without being on the library search path ... 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 ... NOTE
left_right_to_grglist: no visible global function definition for
‘GenomicRangesList’
Undefined global functions or variables:
GenomicRangesList
* 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 LazyData ... 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
deviationsCovariability 17.151 0.756 17.937
computeDeviations 5.489 0.196 5.685
pwmDistance 4.897 0.119 5.018
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.19-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-3.19-bioc/R/bin/R CMD INSTALL chromVAR
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘chromVAR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-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 of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const unsigned int’} [-Wsign-compare]
12 | for( int j=0; j < X.n_rows; j++ ) {
| ~~^~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o chromVAR.so RcppExports.o pwm_similarity.o utils.o -llapack -L/home/biocbuild/bbs-3.19-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-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 version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 65 ]
>
> proc.time()
user system elapsed
21.730 1.040 22.764
chromVAR.Rcheck/chromVAR-Ex.timings
| name | user | system | elapsed | |
| addGCBias | 1.403 | 0.024 | 1.426 | |
| annotationMatches | 0.008 | 0.004 | 0.012 | |
| chromVAR_theme | 0.101 | 0.016 | 0.117 | |
| computeDeviations | 5.489 | 0.196 | 5.685 | |
| computeExpectations | 0.016 | 0.000 | 0.017 | |
| computeVariability | 2.849 | 0.135 | 2.985 | |
| counts | 0.006 | 0.000 | 0.007 | |
| deviationScores | 0.004 | 0.000 | 0.005 | |
| deviations | 0.004 | 0.000 | 0.005 | |
| deviationsCovariability | 17.151 | 0.756 | 17.937 | |
| deviationsTsne | 0.054 | 0.002 | 0.057 | |
| differentialDeviations | 0.010 | 0.001 | 0.010 | |
| differentialVariability | 0.021 | 0.000 | 0.021 | |
| example_counts | 0.000 | 0.000 | 0.001 | |
| filterPeaks | 0.170 | 0.003 | 0.174 | |
| filterSamples | 0.035 | 0.001 | 0.035 | |
| filterSamplesPlot | 0.087 | 0.004 | 0.091 | |
| getAnnotations | 0.257 | 0.004 | 0.260 | |
| getBackgroundPeaks | 0.454 | 0.091 | 0.546 | |
| getCisGroups | 0.083 | 0.001 | 0.083 | |
| getCounts | 1.905 | 0.052 | 1.972 | |
| getFragmentsPerPeak | 0.002 | 0.004 | 0.006 | |
| getFragmentsPerSample | 0.006 | 0.000 | 0.006 | |
| getJasparMotifs | 4.720 | 0.119 | 4.845 | |
| getPeaks | 0.095 | 0.005 | 0.096 | |
| getPermutedData | 0.925 | 0.235 | 1.161 | |
| getSampleCorrelation | 0.012 | 0.001 | 0.012 | |
| getSampleDepths | 0.09 | 0.02 | 0.11 | |
| getSampleDistance | 0.012 | 0.000 | 0.012 | |
| getTotalFragments | 0.007 | 0.000 | 0.007 | |
| makeBiasBins | 0.038 | 0.000 | 0.038 | |
| makePermutedSets | 0.786 | 0.096 | 0.883 | |
| matchKmers | 0.874 | 0.144 | 1.018 | |
| mini_counts | 0.001 | 0.000 | 0.000 | |
| mini_dev | 0.001 | 0.000 | 0.001 | |
| mini_ix | 0.001 | 0.000 | 0.001 | |
| plotVariability | 2.954 | 0.056 | 3.010 | |
| pwmDistance | 4.897 | 0.119 | 5.018 | |
| rbind-chromVARDeviations-method | 0.049 | 0.000 | 0.050 | |