Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-12 17:40 -0400 (Fri, 12 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4741 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 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 317/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cfdnakit 1.2.0 (landing page) Pitithat Puranachot
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the cfdnakit package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cfdnakit.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: cfdnakit |
Version: 1.2.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cfdnakit.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cfdnakit_1.2.0.tar.gz |
StartedAt: 2024-07-11 01:47:33 -0400 (Thu, 11 Jul 2024) |
EndedAt: 2024-07-11 01:55:08 -0400 (Thu, 11 Jul 2024) |
EllapsedTime: 454.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: cfdnakit.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cfdnakit.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cfdnakit_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/cfdnakit.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 12.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘cfdnakit/DESCRIPTION’ ... OK * this is package ‘cfdnakit’ version ‘1.2.0’ * 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 ‘cfdnakit’ 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed cfdnakit-package 28.953 1.336 33.914 call_cnv 22.438 0.217 25.275 plot_cnv_solution 21.780 0.305 23.796 plot_distance_matrix 21.412 0.282 23.129 get_solution_table 20.421 0.237 22.398 plot_transformed_sl 20.295 0.326 22.221 calculate_CES_score 19.466 0.326 21.964 get_zscore_profile 18.923 0.292 20.731 segmentByPSCB 18.877 0.276 20.736 plot_sl_ratio 14.982 0.135 16.096 create_PoN 12.587 0.323 14.384 read_bamfile 7.207 1.184 9.092 get_fragment_profile 4.638 0.032 5.225 * 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
cfdnakit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cfdnakit ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘cfdnakit’ ... ** using staged installation ** R ** 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 (cfdnakit)
cfdnakit.Rcheck/cfdnakit-Ex.timings
name | user | system | elapsed | |
calculate_CES_score | 19.466 | 0.326 | 21.964 | |
call_cnv | 22.438 | 0.217 | 25.275 | |
cfdnakit-package | 28.953 | 1.336 | 33.914 | |
create_PoN | 12.587 | 0.323 | 14.384 | |
extract_insert_size | 0.333 | 0.004 | 0.372 | |
get_fragment_profile | 4.638 | 0.032 | 5.225 | |
get_solution_table | 20.421 | 0.237 | 22.398 | |
get_zscore_profile | 18.923 | 0.292 | 20.731 | |
plot_cnv_solution | 21.780 | 0.305 | 23.796 | |
plot_distance_matrix | 21.412 | 0.282 | 23.129 | |
plot_fragment_dist | 1.008 | 0.011 | 1.052 | |
plot_sl_ratio | 14.982 | 0.135 | 16.096 | |
plot_transformed_sl | 20.295 | 0.326 | 22.221 | |
read_bamfile | 7.207 | 1.184 | 9.092 | |
segmentByPSCB | 18.877 | 0.276 | 20.736 | |
test_isize_KolmogorovSmirnov | 0.561 | 0.009 | 0.618 | |