Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-03 11:38:12 -0400 (Fri, 03 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4660 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4391 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4422 |
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 309/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cfdnakit 1.3.0 (landing page) Pitithat Puranachot
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | 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 | see weekly results here | ||||||||||||
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: 1.3.0 |
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_1.3.0.tar.gz |
StartedAt: 2024-05-02 01:33:29 -0400 (Thu, 02 May 2024) |
EndedAt: 2024-05-02 01:41:24 -0400 (Thu, 02 May 2024) |
EllapsedTime: 474.5 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_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/cfdnakit.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘cfdnakit/DESCRIPTION’ ... OK * this is package ‘cfdnakit’ version ‘1.3.0’ * 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 28.635 1.240 34.805 call_cnv 22.518 0.234 26.092 plot_cnv_solution 21.728 0.286 24.461 plot_distance_matrix 21.531 0.277 24.291 plot_transformed_sl 20.702 0.335 23.439 get_solution_table 20.663 0.251 23.982 calculate_CES_score 19.665 0.295 23.429 segmentByPSCB 18.984 0.261 21.456 get_zscore_profile 18.768 0.299 22.170 plot_sl_ratio 15.103 0.124 16.577 create_PoN 12.707 0.316 15.246 read_bamfile 7.125 1.188 9.379 get_fragment_profile 4.659 0.039 5.471 * 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 | 19.665 | 0.295 | 23.429 | |
call_cnv | 22.518 | 0.234 | 26.092 | |
cfdnakit-package | 28.635 | 1.240 | 34.805 | |
create_PoN | 12.707 | 0.316 | 15.246 | |
extract_insert_size | 0.323 | 0.004 | 0.381 | |
get_fragment_profile | 4.659 | 0.039 | 5.471 | |
get_solution_table | 20.663 | 0.251 | 23.982 | |
get_zscore_profile | 18.768 | 0.299 | 22.170 | |
plot_cnv_solution | 21.728 | 0.286 | 24.461 | |
plot_distance_matrix | 21.531 | 0.277 | 24.291 | |
plot_fragment_dist | 0.960 | 0.011 | 1.112 | |
plot_sl_ratio | 15.103 | 0.124 | 16.577 | |
plot_transformed_sl | 20.702 | 0.335 | 23.439 | |
read_bamfile | 7.125 | 1.188 | 9.379 | |
segmentByPSCB | 18.984 | 0.261 | 21.456 | |
test_isize_KolmogorovSmirnov | 0.543 | 0.008 | 0.608 | |