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This page was generated on 2023-10-16 11:35:32 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 1281/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Motif2Site 1.4.0  (landing page)
Peyman Zarrineh
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/Motif2Site
git_branch: RELEASE_3_17
git_last_commit: 6d3a455
git_last_commit_date: 2023-04-25 11:36:00 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 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
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for Motif2Site on nebbiolo1


To the developers/maintainers of the Motif2Site package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Motif2Site.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: Motif2Site
Version: 1.4.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Motif2Site.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings Motif2Site_1.4.0.tar.gz
StartedAt: 2023-10-15 23:01:03 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 23:14:01 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 777.6 seconds
RetCode: 0
Status:   OK  
CheckDir: Motif2Site.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Motif2Site.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings Motif2Site_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Motif2Site.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Motif2Site/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Motif2Site’ version ‘1.4.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .gitignoreommit
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Motif2Site’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                         user system elapsed
recenterBindingSitesAcrossExperiments 130.515  0.949 131.464
Motif2Site                            122.819  2.882 125.707
pairwisDifferential                   123.844  1.720 125.569
DetectBindingSitesBed                  67.187  1.975  72.413
DetectBindingSitesMotif                54.894  1.197  56.102
compareMotifs2UserProvidedRegions      15.023  0.464  15.488
compareBedFiless2UserProvidedRegions    6.063  0.221   6.285
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Motif2Site.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/Motif2Site.Rcheck/00check.log’
for details.



Installation output

Motif2Site.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Motif2Site
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘Motif2Site’ ...
** 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 (Motif2Site)

Tests output


Example timings

Motif2Site.Rcheck/Motif2Site-Ex.timings

nameusersystemelapsed
Bed2Granges2.7100.1082.818
DetectBindingSitesBed67.187 1.97572.413
DetectBindingSitesMotif54.894 1.19756.102
Motif2Site122.819 2.882125.707
compareBedFiless2UserProvidedRegions6.0630.2216.285
compareMotifs2UserProvidedRegions15.023 0.46415.488
data0.7710.0000.772
pairwisDifferential123.844 1.720125.569
recenterBindingSitesAcrossExperiments130.515 0.949131.464