Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:42 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 358/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CleanUpRNAseq 0.99.14 (landing page) Haibo Liu
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the CleanUpRNAseq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CleanUpRNAseq.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: CleanUpRNAseq |
Version: 0.99.14 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CleanUpRNAseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CleanUpRNAseq_0.99.14.tar.gz |
StartedAt: 2024-08-20 20:30:29 -0400 (Tue, 20 Aug 2024) |
EndedAt: 2024-08-20 20:49:17 -0400 (Tue, 20 Aug 2024) |
EllapsedTime: 1127.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CleanUpRNAseq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CleanUpRNAseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CleanUpRNAseq_0.99.14.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CleanUpRNAseq.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CleanUpRNAseq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CleanUpRNAseq’ version ‘0.99.14’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.19/bioc/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.19/data/annotation/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.19/data/annotation/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.19/data/experiment/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.19/data/experiment/src/contrib/PACKAGES' 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 ‘CleanUpRNAseq’ can be installed ... OK * 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 ... OK * 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed summarize_reads 0.987 0.213 181.894 get_saf 1.004 0.068 181.074 salmon_tximport 0.829 0.115 180.871 * 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: OK
CleanUpRNAseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CleanUpRNAseq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘CleanUpRNAseq’ ... ** using staged installation ** R ** data ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CleanUpRNAseq)
CleanUpRNAseq.Rcheck/CleanUpRNAseq-Ex.timings
name | user | system | elapsed | |
calc_gene_gc | 0.003 | 0.001 | 0.004 | |
calc_region_gc | 0.377 | 0.026 | 0.405 | |
correct_GC | 1.039 | 0.016 | 1.059 | |
correct_IR | 0.160 | 0.008 | 0.167 | |
correct_global | 0.029 | 0.004 | 0.034 | |
correct_stranded | 0.028 | 0.003 | 0.032 | |
create_summarizedcounts | 0.002 | 0.000 | 0.003 | |
get_region_stat | 0.031 | 0.003 | 0.035 | |
get_saf | 1.004 | 0.068 | 181.074 | |
plot_assignment_stat | 0.311 | 0.039 | 0.350 | |
plot_expr_distr | 1.880 | 0.049 | 1.932 | |
plot_gene_content | 0.190 | 0.005 | 0.195 | |
plot_pca_heatmap | 1.842 | 0.025 | 1.868 | |
plot_read_distr | 0.311 | 0.005 | 0.317 | |
plot_sample_corr | 1.046 | 0.153 | 1.202 | |
salmon_tximport | 0.829 | 0.115 | 180.871 | |
style_BSgenome | 0.164 | 0.013 | 0.177 | |
summarize_reads | 0.987 | 0.213 | 181.894 | |