Alicia Schep
| Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/chromVAR |
| git_branch: RELEASE_3_18 |
| git_last_commit: e2d61b0 |
| git_last_commit_date: 2023-10-24 11:00:14 -0400 (Tue, 24 Oct 2023) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:08 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 346/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| chromVAR 1.24.0 (landing page) Alicia Schep
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the chromVAR package: - 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: 1.24.0 |
| 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_1.24.0.tar.gz |
| StartedAt: 2024-04-17 09:01:17 -0400 (Wed, 17 Apr 2024) |
| EndedAt: 2024-04-17 09:09:16 -0400 (Wed, 17 Apr 2024) |
| EllapsedTime: 478.7 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_1.24.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/chromVAR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chromVAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chromVAR’ version ‘1.24.0’
* 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 15.0.0 (clang-1500.0.40.1)’
* 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 ... 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 ... 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 14.901 1.400 16.658
computeDeviations 7.379 0.111 7.571
pwmDistance 5.575 0.134 5.771
getJasparMotifs 5.532 0.135 5.739
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/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/4.3-arm64/Resources/library’ * installing *source* package ‘chromVAR’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwm_similarity.cpp -o pwm_similarity.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 65 ]
>
> proc.time()
user system elapsed
29.183 1.646 31.139
chromVAR.Rcheck/chromVAR-Ex.timings
| name | user | system | elapsed | |
| addGCBias | 2.073 | 0.069 | 2.246 | |
| annotationMatches | 0.014 | 0.002 | 0.017 | |
| chromVAR_theme | 0.124 | 0.013 | 0.144 | |
| computeDeviations | 7.379 | 0.111 | 7.571 | |
| computeExpectations | 0.023 | 0.001 | 0.025 | |
| computeVariability | 3.386 | 0.106 | 3.528 | |
| counts | 0.009 | 0.001 | 0.010 | |
| deviationScores | 0.005 | 0.001 | 0.006 | |
| deviations | 0.005 | 0.001 | 0.007 | |
| deviationsCovariability | 14.901 | 1.400 | 16.658 | |
| deviationsTsne | 0.076 | 0.004 | 0.079 | |
| differentialDeviations | 0.011 | 0.001 | 0.013 | |
| differentialVariability | 0.025 | 0.001 | 0.026 | |
| example_counts | 0.001 | 0.002 | 0.002 | |
| filterPeaks | 0.211 | 0.006 | 0.217 | |
| filterSamples | 0.056 | 0.003 | 0.058 | |
| filterSamplesPlot | 0.127 | 0.004 | 0.130 | |
| getAnnotations | 0.369 | 0.014 | 0.385 | |
| getBackgroundPeaks | 1.786 | 0.043 | 1.855 | |
| getCisGroups | 0.096 | 0.002 | 0.098 | |
| getCounts | 3.623 | 0.600 | 4.268 | |
| getFragmentsPerPeak | 0.009 | 0.001 | 0.010 | |
| getFragmentsPerSample | 0.008 | 0.000 | 0.009 | |
| getJasparMotifs | 5.532 | 0.135 | 5.739 | |
| getPeaks | 0.154 | 0.006 | 0.159 | |
| getPermutedData | 1.179 | 0.061 | 1.256 | |
| getSampleCorrelation | 0.015 | 0.002 | 0.018 | |
| getSampleDepths | 0.245 | 0.025 | 0.273 | |
| getSampleDistance | 0.014 | 0.001 | 0.015 | |
| getTotalFragments | 0.010 | 0.001 | 0.015 | |
| makeBiasBins | 0.045 | 0.001 | 0.046 | |
| makePermutedSets | 1.044 | 0.119 | 1.168 | |
| matchKmers | 1.227 | 0.133 | 1.380 | |
| mini_counts | 0.001 | 0.002 | 0.003 | |
| mini_dev | 0.000 | 0.002 | 0.002 | |
| mini_ix | 0.001 | 0.001 | 0.002 | |
| plotVariability | 3.490 | 0.027 | 3.557 | |
| pwmDistance | 5.575 | 0.134 | 5.771 | |
| rbind-chromVARDeviations-method | 0.064 | 0.002 | 0.066 | |