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This page was generated on 2024-02-21 11:36:27 -0500 (Wed, 21 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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 1954/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SigsPack 1.16.0  (landing page)
Franziska Schumann
Snapshot Date: 2024-02-20 14:05:06 -0500 (Tue, 20 Feb 2024)
git_url: https://git.bioconductor.org/packages/SigsPack
git_branch: RELEASE_3_18
git_last_commit: bbf5709
git_last_commit_date: 2023-10-24 11:15:49 -0500 (Tue, 24 Oct 2023)
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  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for SigsPack on nebbiolo2


To the developers/maintainers of the SigsPack package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SigsPack.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: SigsPack
Version: 1.16.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:SigsPack.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings SigsPack_1.16.0.tar.gz
StartedAt: 2024-02-21 02:38:56 -0500 (Wed, 21 Feb 2024)
EndedAt: 2024-02-21 02:42:25 -0500 (Wed, 21 Feb 2024)
EllapsedTime: 208.9 seconds
RetCode: 0
Status:   OK  
CheckDir: SigsPack.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:SigsPack.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings SigsPack_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SigsPack.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘SigsPack/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SigsPack’ version ‘1.16.0’
* 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 ‘SigsPack’ 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 R 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
get_context_freq 46.818  5.924  52.746
normalize        32.430  4.276  36.706
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘SigsPack.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

SigsPack.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL SigsPack
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘SigsPack’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (SigsPack)

Tests output


Example timings

SigsPack.Rcheck/SigsPack-Ex.timings

nameusersystemelapsed
bootstrap_mut_catalogues0.0450.0040.049
create_mut_catalogues0.3470.0120.359
decomposeQP0.0070.0000.007
get_context_freq46.818 5.92452.746
normalize32.430 4.27636.706
plot_bootstrapped_exposure0.4560.0600.515
signature_exposure0.0220.0110.034
summarize_exposures0.4590.0250.483
vcf2mut_cat000