Alicia Schep
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/chromVAR |
| git_branch: RELEASE_3_20 |
| git_last_commit: 0f0fb6e |
| git_last_commit_date: 2024-10-29 10:22:54 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 350/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| chromVAR 1.28.0 (landing page) Alicia Schep
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: 1.28.0 |
| 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_1.28.0.tar.gz |
| StartedAt: 2024-12-20 01:07:21 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 01:20:52 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 810.5 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_1.28.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/chromVAR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* 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 ‘1.28.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.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 30.990 1.285 34.500
pwmDistance 12.338 0.265 13.419
getJasparMotifs 12.152 0.271 13.337
computeVariability 9.141 0.181 9.745
plotVariability 9.010 0.047 9.612
getCounts 7.831 1.213 9.572
computeDeviations 7.872 0.115 8.319
* 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-3.20-bioc/meat/chromVAR.Rcheck/00check.log’
for details.
chromVAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL chromVAR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘chromVAR’ ... ** 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.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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 clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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 clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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 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-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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
48.342 3.225 55.780
chromVAR.Rcheck/chromVAR-Ex.timings
| name | user | system | elapsed | |
| addGCBias | 1.215 | 0.117 | 1.415 | |
| annotationMatches | 0.026 | 0.005 | 0.034 | |
| chromVAR_theme | 0.302 | 0.035 | 0.357 | |
| computeDeviations | 7.872 | 0.115 | 8.319 | |
| computeExpectations | 0.048 | 0.001 | 0.052 | |
| computeVariability | 9.141 | 0.181 | 9.745 | |
| counts | 0.015 | 0.002 | 0.017 | |
| deviationScores | 0.012 | 0.001 | 0.014 | |
| deviations | 0.011 | 0.002 | 0.013 | |
| deviationsCovariability | 30.990 | 1.285 | 34.500 | |
| deviationsTsne | 0.113 | 0.006 | 0.125 | |
| differentialDeviations | 0.021 | 0.002 | 0.026 | |
| differentialVariability | 0.048 | 0.002 | 0.050 | |
| example_counts | 0.001 | 0.002 | 0.004 | |
| filterPeaks | 0.461 | 0.003 | 0.489 | |
| filterSamples | 0.087 | 0.002 | 0.094 | |
| filterSamplesPlot | 0.225 | 0.002 | 0.241 | |
| getAnnotations | 0.690 | 0.021 | 0.756 | |
| getBackgroundPeaks | 0.874 | 0.041 | 0.960 | |
| getCisGroups | 0.216 | 0.003 | 0.224 | |
| getCounts | 7.831 | 1.213 | 9.572 | |
| getFragmentsPerPeak | 0.016 | 0.002 | 0.019 | |
| getFragmentsPerSample | 0.014 | 0.002 | 0.018 | |
| getJasparMotifs | 12.152 | 0.271 | 13.337 | |
| getPeaks | 0.313 | 0.010 | 0.342 | |
| getPermutedData | 1.809 | 0.027 | 1.964 | |
| getSampleCorrelation | 0.029 | 0.002 | 0.035 | |
| getSampleDepths | 0.293 | 0.018 | 0.321 | |
| getSampleDistance | 0.029 | 0.001 | 0.035 | |
| getTotalFragments | 0.016 | 0.002 | 0.018 | |
| makeBiasBins | 0.104 | 0.002 | 0.110 | |
| makePermutedSets | 1.966 | 0.158 | 2.273 | |
| matchKmers | 3.460 | 0.171 | 3.885 | |
| mini_counts | 0.002 | 0.003 | 0.005 | |
| mini_dev | 0.001 | 0.002 | 0.004 | |
| mini_ix | 0.002 | 0.002 | 0.005 | |
| plotVariability | 9.010 | 0.047 | 9.612 | |
| pwmDistance | 12.338 | 0.265 | 13.419 | |
| rbind-chromVARDeviations-method | 0.149 | 0.002 | 0.153 | |