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This page was generated on 2025-10-03 12:03 -0400 (Fri, 03 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4845
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4632
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4577
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 322/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cfdnakit 1.7.0  (landing page)
Pitithat Puranachot
Snapshot Date: 2025-10-02 13:45 -0400 (Thu, 02 Oct 2025)
git_url: https://git.bioconductor.org/packages/cfdnakit
git_branch: devel
git_last_commit: 76e9f40
git_last_commit_date: 2025-04-15 13:17:21 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for cfdnakit on nebbiolo2

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.

raw results


Summary

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: 2025-10-02 22:07:19 -0400 (Thu, 02 Oct 2025)
EndedAt: 2025-10-02 22:11:57 -0400 (Thu, 02 Oct 2025)
EllapsedTime: 278.4 seconds
RetCode: 0
Status:   OK  
CheckDir: cfdnakit.Rcheck
Warnings: 0

Command output

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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     21.979  0.207  22.187
plot_distance_matrix 15.089  0.044  15.135
plot_cnv_solution    14.933  0.135  15.069
call_cnv             14.912  0.078  14.992
plot_transformed_sl  14.500  0.015  14.515
get_solution_table   14.265  0.119  14.384
calculate_CES_score  13.598  0.121  13.720
segmentByPSCB        13.430  0.014  13.444
get_zscore_profile   13.225  0.056  13.281
create_PoN            6.558  0.025   6.584
plot_sl_ratio         6.312  0.008   6.320
* 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.


Installation output

cfdnakit.Rcheck/00install.out

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###
### 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)

Tests output


Example timings

cfdnakit.Rcheck/cfdnakit-Ex.timings

nameusersystemelapsed
calculate_CES_score13.598 0.12113.720
call_cnv14.912 0.07814.992
cfdnakit-package21.979 0.20722.187
create_PoN6.5580.0256.584
extract_insert_size0.1480.0010.150
get_fragment_profile2.7040.0002.704
get_solution_table14.265 0.11914.384
get_zscore_profile13.225 0.05613.281
plot_cnv_solution14.933 0.13515.069
plot_distance_matrix15.089 0.04415.135
plot_fragment_dist0.5860.0000.586
plot_sl_ratio6.3120.0086.320
plot_transformed_sl14.500 0.01514.515
read_bamfile2.8590.0402.900
segmentByPSCB13.430 0.01413.444
test_isize_KolmogorovSmirnov0.2560.0010.257