| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-25 12:03 -0400 (Sat, 25 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 327/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cfdnakit 1.7.0 (landing page) Pitithat Puranachot
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | NA | NA | ||||||||||
|
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: 1.7.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:cfdnakit.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings cfdnakit_1.7.0.tar.gz |
| StartedAt: 2025-10-24 22:04:13 -0400 (Fri, 24 Oct 2025) |
| EndedAt: 2025-10-24 22:08:47 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 274.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cfdnakit.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:cfdnakit.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings cfdnakit_1.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/cfdnakit.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘cfdnakit/DESCRIPTION’ ... OK
* this is package ‘cfdnakit’ version ‘1.7.0’
* 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'pipe.Rd':
‘[magrittr:pipe]{%>%}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 21.682 0.249 21.933
call_cnv 15.024 0.083 15.108
plot_cnv_solution 14.834 0.037 14.872
plot_transformed_sl 14.433 0.022 14.456
get_solution_table 14.225 0.140 14.366
plot_distance_matrix 14.263 0.013 14.278
calculate_CES_score 13.842 0.147 13.992
get_zscore_profile 13.503 0.058 13.562
segmentByPSCB 13.422 0.020 13.442
create_PoN 6.528 0.047 6.575
plot_sl_ratio 6.183 0.004 6.186
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.22-bioc/meat/cfdnakit.Rcheck/00check.log’
for details.
cfdnakit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL cfdnakit ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘cfdnakit’ ... ** this is package ‘cfdnakit’ version ‘1.7.0’ ** 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 | 13.842 | 0.147 | 13.992 | |
| call_cnv | 15.024 | 0.083 | 15.108 | |
| cfdnakit-package | 21.682 | 0.249 | 21.933 | |
| create_PoN | 6.528 | 0.047 | 6.575 | |
| extract_insert_size | 0.16 | 0.00 | 0.16 | |
| get_fragment_profile | 2.677 | 0.015 | 2.692 | |
| get_solution_table | 14.225 | 0.140 | 14.366 | |
| get_zscore_profile | 13.503 | 0.058 | 13.562 | |
| plot_cnv_solution | 14.834 | 0.037 | 14.872 | |
| plot_distance_matrix | 14.263 | 0.013 | 14.278 | |
| plot_fragment_dist | 0.558 | 0.002 | 0.560 | |
| plot_sl_ratio | 6.183 | 0.004 | 6.186 | |
| plot_transformed_sl | 14.433 | 0.022 | 14.456 | |
| read_bamfile | 2.842 | 0.034 | 2.876 | |
| segmentByPSCB | 13.422 | 0.020 | 13.442 | |
| test_isize_KolmogorovSmirnov | 0.251 | 0.001 | 0.252 | |