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This page was generated on 2024-05-04 11:40:21 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 317/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cfdnakit 1.2.0  (landing page)
Pitithat Puranachot
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/cfdnakit
git_branch: RELEASE_3_19
git_last_commit: c461945
git_last_commit_date: 2024-04-30 11:50:10 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for cfdnakit on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: cfdnakit
Version: 1.2.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:cfdnakit.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings cfdnakit_1.2.0.tar.gz
StartedAt: 2024-05-04 05:50:18 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 05:54:52 -0000 (Sat, 04 May 2024)
EllapsedTime: 273.5 seconds
RetCode: 0
Status:   OK  
CheckDir: cfdnakit.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:cfdnakit.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings cfdnakit_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/cfdnakit.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cfdnakit/DESCRIPTION’ ... OK
* this is package ‘cfdnakit’ version ‘1.2.0’
* 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     17.367  0.332  17.738
call_cnv             16.787  0.107  16.926
plot_cnv_solution    16.215  0.120  16.364
plot_distance_matrix 15.915  0.048  15.991
plot_transformed_sl  15.749  0.060  15.837
calculate_CES_score  15.522  0.172  15.730
get_solution_table   15.383  0.119  15.529
segmentByPSCB        14.929  0.024  14.981
get_zscore_profile   14.790  0.060  14.877
create_PoN           10.328  0.043  10.393
plot_sl_ratio        10.113  0.040  10.170
* 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:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL cfdnakit
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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)

Tests output


Example timings

cfdnakit.Rcheck/cfdnakit-Ex.timings

nameusersystemelapsed
calculate_CES_score15.522 0.17215.730
call_cnv16.787 0.10716.926
cfdnakit-package17.367 0.33217.738
create_PoN10.328 0.04310.393
extract_insert_size0.1860.0000.187
get_fragment_profile4.8010.0004.808
get_solution_table15.383 0.11915.529
get_zscore_profile14.790 0.06014.877
plot_cnv_solution16.215 0.12016.364
plot_distance_matrix15.915 0.04815.991
plot_fragment_dist0.5500.0000.551
plot_sl_ratio10.113 0.04010.170
plot_transformed_sl15.749 0.06015.837
read_bamfile4.0130.0474.071
segmentByPSCB14.929 0.02414.981
test_isize_KolmogorovSmirnov0.3110.0040.316