Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:38:58 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 313/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cfdnakit 1.1.0 (landing page) Pitithat Puranachot
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.1.0 |
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_1.1.0.tar.gz |
StartedAt: 2024-03-02 01:30:41 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 01:38:11 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 450.3 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_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/cfdnakit.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 ‘cfdnakit/DESCRIPTION’ ... OK * this is package ‘cfdnakit’ version ‘1.1.0’ * 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 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 ... 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 26.933 1.357 32.688 call_cnv 21.389 0.257 25.273 plot_cnv_solution 20.833 0.349 24.483 plot_distance_matrix 20.405 0.353 23.889 plot_transformed_sl 19.651 0.382 23.057 get_solution_table 19.414 0.283 22.628 calculate_CES_score 18.627 0.318 21.816 segmentByPSCB 17.940 0.303 20.700 get_zscore_profile 17.846 0.336 20.961 plot_sl_ratio 14.438 0.174 16.672 create_PoN 11.996 0.353 13.768 read_bamfile 6.706 1.140 8.931 get_fragment_profile 4.606 0.049 5.321 * 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 | 18.627 | 0.318 | 21.816 | |
call_cnv | 21.389 | 0.257 | 25.273 | |
cfdnakit-package | 26.933 | 1.357 | 32.688 | |
create_PoN | 11.996 | 0.353 | 13.768 | |
extract_insert_size | 0.315 | 0.005 | 0.376 | |
get_fragment_profile | 4.606 | 0.049 | 5.321 | |
get_solution_table | 19.414 | 0.283 | 22.628 | |
get_zscore_profile | 17.846 | 0.336 | 20.961 | |
plot_cnv_solution | 20.833 | 0.349 | 24.483 | |
plot_distance_matrix | 20.405 | 0.353 | 23.889 | |
plot_fragment_dist | 0.923 | 0.015 | 1.079 | |
plot_sl_ratio | 14.438 | 0.174 | 16.672 | |
plot_transformed_sl | 19.651 | 0.382 | 23.057 | |
read_bamfile | 6.706 | 1.140 | 8.931 | |
segmentByPSCB | 17.940 | 0.303 | 20.700 | |
test_isize_KolmogorovSmirnov | 0.530 | 0.010 | 0.621 | |