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This page was generated on 2024-05-03 11:38:12 -0400 (Fri, 03 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4660
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4391
merida1macOS 12.7.4 Montereyx86_644.4.0 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 309/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cfdnakit 1.3.0  (landing page)
Pitithat Puranachot
Snapshot Date: 2024-05-01 14:05:06 -0400 (Wed, 01 May 2024)
git_url: https://git.bioconductor.org/packages/cfdnakit
git_branch: devel
git_last_commit: 02ed35d
git_last_commit_date: 2024-04-30 11:50:10 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is only available as a source package that needs compilation
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for cfdnakit on merida1


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: 1.3.0
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

Command output

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### 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
###
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* 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


Installation output

cfdnakit.Rcheck/00install.out

##############################################################################
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###
### 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)

Tests output


Example timings

cfdnakit.Rcheck/cfdnakit-Ex.timings

nameusersystemelapsed
calculate_CES_score19.665 0.29523.429
call_cnv22.518 0.23426.092
cfdnakit-package28.635 1.24034.805
create_PoN12.707 0.31615.246
extract_insert_size0.3230.0040.381
get_fragment_profile4.6590.0395.471
get_solution_table20.663 0.25123.982
get_zscore_profile18.768 0.29922.170
plot_cnv_solution21.728 0.28624.461
plot_distance_matrix21.531 0.27724.291
plot_fragment_dist0.9600.0111.112
plot_sl_ratio15.103 0.12416.577
plot_transformed_sl20.702 0.33523.439
read_bamfile7.1251.1889.379
segmentByPSCB18.984 0.26121.456
test_isize_KolmogorovSmirnov0.5430.0080.608