Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-30 12:34:25 -0400 (Thu, 30 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" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
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 309/2233 | 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 | 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: 1.3.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:cfdnakit.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings cfdnakit_1.3.0.tar.gz |
StartedAt: 2024-05-29 18:26:08 -0400 (Wed, 29 May 2024) |
EndedAt: 2024-05-29 18:29:49 -0400 (Wed, 29 May 2024) |
EllapsedTime: 221.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: cfdnakit.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:cfdnakit.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings cfdnakit_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/cfdnakit.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 loading without being on the library search path ... 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 11.856 0.180 12.044 call_cnv 10.748 0.188 10.936 plot_distance_matrix 10.768 0.116 10.884 plot_cnv_solution 10.593 0.044 10.637 plot_transformed_sl 10.471 0.039 10.512 get_solution_table 9.968 0.080 10.048 calculate_CES_score 9.828 0.172 10.001 get_zscore_profile 9.227 0.096 9.323 segmentByPSCB 9.274 0.049 9.322 create_PoN 6.888 0.132 7.020 plot_sl_ratio 5.889 0.008 5.898 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
cfdnakit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL cfdnakit ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 | 9.828 | 0.172 | 10.001 | |
call_cnv | 10.748 | 0.188 | 10.936 | |
cfdnakit-package | 11.856 | 0.180 | 12.044 | |
create_PoN | 6.888 | 0.132 | 7.020 | |
extract_insert_size | 0.172 | 0.000 | 0.172 | |
get_fragment_profile | 2.817 | 0.004 | 2.821 | |
get_solution_table | 9.968 | 0.080 | 10.048 | |
get_zscore_profile | 9.227 | 0.096 | 9.323 | |
plot_cnv_solution | 10.593 | 0.044 | 10.637 | |
plot_distance_matrix | 10.768 | 0.116 | 10.884 | |
plot_fragment_dist | 0.451 | 0.000 | 0.451 | |
plot_sl_ratio | 5.889 | 0.008 | 5.898 | |
plot_transformed_sl | 10.471 | 0.039 | 10.512 | |
read_bamfile | 2.902 | 0.031 | 2.933 | |
segmentByPSCB | 9.274 | 0.049 | 9.322 | |
test_isize_KolmogorovSmirnov | 0.260 | 0.004 | 0.264 | |