Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:43 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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 1800/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RnaSeqSampleSize 2.14.0 (landing page) Shilin Zhao Developer
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the RnaSeqSampleSize 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: RnaSeqSampleSize |
Version: 2.14.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RnaSeqSampleSize.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RnaSeqSampleSize_2.14.0.tar.gz |
StartedAt: 2024-05-07 00:26:56 -0400 (Tue, 07 May 2024) |
EndedAt: 2024-05-07 00:29:15 -0400 (Tue, 07 May 2024) |
EllapsedTime: 138.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RnaSeqSampleSize.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RnaSeqSampleSize.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RnaSeqSampleSize_2.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/RnaSeqSampleSize.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-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 Ventura 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RnaSeqSampleSize/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RnaSeqSampleSize’ version ‘2.14.0’ * package encoding: UTF-8 * 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 ‘RnaSeqSampleSize’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 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 analyze_dataset: no visible binding for global variable ‘logFC’ analyze_dataset: no visible binding for global variable ‘DispersionInTreatmentVsControl’ analyze_dataset: no visible binding for global variable ‘DispersionInControlOnly’ plot_gene_counts_range: no visible binding for global variable ‘name’ plot_gene_counts_range: no visible binding for global variable ‘value’ plot_mappedReads_percent: no visible binding for global variable ‘Reads’ plot_mappedReads_percent: no visible binding for global variable ‘Category’ plot_mappedReads_percent: no visible binding for global variable ‘Tissue’ plot_mappedReads_percent: no visible binding for global variable ‘MappedReadsPercent’ Undefined global functions or variables: Category DispersionInControlOnly DispersionInTreatmentVsControl logFC MappedReadsPercent name Reads Tissue value * checking Rd files ... NOTE checkRd: (-1) plot_power_curve.Rd:42: Lost braces; missing escapes or markup? 42 | \item{las}{Numeric in {0,1,2,3}; the style of axis labels.} | ^ * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/RnaSeqSampleSize.Rcheck/00check.log’ for details.
RnaSeqSampleSize.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RnaSeqSampleSize ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘RnaSeqSampleSize’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RnaSeqSampleSize.c -o RnaSeqSampleSize.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bd0.c -o bd0.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cumsumBorder.cpp -o cumsumBorder.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stirlerr.c -o stirlerr.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o RnaSeqSampleSize.so RcppExports.o RnaSeqSampleSize.o bd0.o cumsumBorder.o stirlerr.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-RnaSeqSampleSize/00new/RnaSeqSampleSize/libs ** R ** 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 (RnaSeqSampleSize)
RnaSeqSampleSize.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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(RnaSeqSampleSize) Loading required package: ggplot2 Loading required package: RnaSeqSampleSizeData Loading required package: edgeR Loading required package: limma Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) > > test_check("RnaSeqSampleSize") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ] > > proc.time() user system elapsed 6.647 0.228 6.873
RnaSeqSampleSize.Rcheck/RnaSeqSampleSize-Ex.timings
name | user | system | elapsed | |
analyze_dataset | 0 | 0 | 0 | |
convertIdOneToOne | 0.722 | 0.029 | 3.833 | |
est_count_dispersion | 0.052 | 0.001 | 0.054 | |
est_power | 0.629 | 0.023 | 0.653 | |
est_power_curve | 3.322 | 0.188 | 3.511 | |
est_power_distribution | 1.867 | 0.076 | 1.947 | |
optimize_parameter | 2.077 | 0.200 | 2.277 | |
plot_gene_counts_range | 0 | 0 | 0 | |
plot_mappedReads_percent | 0 | 0 | 0 | |
plot_power_curve | 0.084 | 0.014 | 0.098 | |
sample_size | 0.137 | 0.020 | 0.157 | |
sample_size_distribution | 2.498 | 0.219 | 2.720 | |