Alicia Schep
| Snapshot Date: 2025-11-20 15:01 -0500 (Thu, 20 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/chromVAR |
| git_branch: RELEASE_3_22 |
| git_last_commit: c67de98 |
| git_last_commit_date: 2025-10-29 10:41:16 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-24 12:04 -0500 (Mon, 24 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4873 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4654 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4600 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 363/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| chromVAR 1.32.0 (landing page) Alicia Schep
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.32.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings chromVAR_1.32.0.tar.gz |
| StartedAt: 2025-11-21 02:46:00 -0500 (Fri, 21 Nov 2025) |
| EndedAt: 2025-11-21 02:58:19 -0500 (Fri, 21 Nov 2025) |
| EllapsedTime: 739.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: chromVAR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings chromVAR_1.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/chromVAR.Rcheck’
* using R version 4.5.2 Patched (2025-11-05 r88990)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chromVAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chromVAR’ version ‘1.32.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 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 27.740 1.147 29.336
getJasparMotifs 11.500 0.240 11.966
pwmDistance 11.357 0.257 13.178
getCounts 8.591 1.245 9.836
plotVariability 9.641 0.063 9.979
computeVariability 8.704 0.301 9.104
computeDeviations 5.870 0.131 6.128
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/chromVAR.Rcheck/00check.log’
for details.
chromVAR.Rcheck/00install.out
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###
### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL chromVAR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘chromVAR’ ...
** this is package ‘chromVAR’ version ‘1.32.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
#pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwm_similarity.cpp -o pwm_similarity.o
In file included from pwm_similarity.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
#pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o
In file included from utils.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
#pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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
44.743 3.060 56.417
chromVAR.Rcheck/chromVAR-Ex.timings
| name | user | system | elapsed | |
| addGCBias | 1.186 | 0.078 | 1.287 | |
| annotationMatches | 0.027 | 0.004 | 0.031 | |
| chromVAR_theme | 0.508 | 0.011 | 0.521 | |
| computeDeviations | 5.870 | 0.131 | 6.128 | |
| computeExpectations | 0.056 | 0.008 | 0.069 | |
| computeVariability | 8.704 | 0.301 | 9.104 | |
| counts | 0.016 | 0.002 | 0.017 | |
| deviationScores | 0.011 | 0.001 | 0.014 | |
| deviations | 0.011 | 0.002 | 0.012 | |
| deviationsCovariability | 27.740 | 1.147 | 29.336 | |
| deviationsTsne | 0.108 | 0.005 | 0.112 | |
| differentialDeviations | 0.020 | 0.002 | 0.023 | |
| differentialVariability | 0.045 | 0.002 | 0.047 | |
| example_counts | 0.001 | 0.002 | 0.003 | |
| filterPeaks | 0.431 | 0.004 | 0.438 | |
| filterSamples | 0.086 | 0.001 | 0.088 | |
| filterSamplesPlot | 0.521 | 0.005 | 0.529 | |
| getAnnotations | 0.592 | 0.021 | 0.615 | |
| getBackgroundPeaks | 0.817 | 0.044 | 0.867 | |
| getCisGroups | 0.206 | 0.002 | 0.209 | |
| getCounts | 8.591 | 1.245 | 9.836 | |
| getFragmentsPerPeak | 0.016 | 0.001 | 0.018 | |
| getFragmentsPerSample | 0.016 | 0.002 | 0.018 | |
| getJasparMotifs | 11.500 | 0.240 | 11.966 | |
| getPeaks | 0.298 | 0.008 | 0.307 | |
| getPermutedData | 2.859 | 0.057 | 2.979 | |
| getSampleCorrelation | 0.027 | 0.002 | 0.029 | |
| getSampleDepths | 0.200 | 0.005 | 0.205 | |
| getSampleDistance | 0.028 | 0.001 | 0.030 | |
| getTotalFragments | 0.017 | 0.001 | 0.018 | |
| makeBiasBins | 0.105 | 0.002 | 0.108 | |
| makePermutedSets | 1.855 | 0.152 | 2.037 | |
| matchKmers | 3.244 | 0.185 | 3.951 | |
| mini_counts | 0.001 | 0.001 | 0.003 | |
| mini_dev | 0.002 | 0.002 | 0.003 | |
| mini_ix | 0.001 | 0.002 | 0.004 | |
| plotVariability | 9.641 | 0.063 | 9.979 | |
| pwmDistance | 11.357 | 0.257 | 13.178 | |
| rbind-chromVARDeviations-method | 0.120 | 0.002 | 0.140 | |