Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-08-21 11:42 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 408/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoCiteStats 1.80.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2025-08-18 13:40 -0400 (Mon, 18 Aug 2025)
git_url: https://git.bioconductor.org/packages/CoCiteStats
git_branch: RELEASE_3_21
git_last_commit: 7dbecb0
git_last_commit_date: 2025-04-15 09:35:42 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for CoCiteStats on kunpeng2

To the developers/maintainers of the CoCiteStats package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CoCiteStats.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: CoCiteStats
Version: 1.80.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:CoCiteStats.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CoCiteStats_1.80.0.tar.gz
StartedAt: 2025-08-19 07:11:30 -0000 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 07:16:24 -0000 (Tue, 19 Aug 2025)
EllapsedTime: 294.2 seconds
RetCode: 0
Status:   OK  
CheckDir: CoCiteStats.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:CoCiteStats.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CoCiteStats_1.80.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CoCiteStats.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoCiteStats/DESCRIPTION’ ... OK
* this is package ‘CoCiteStats’ version ‘1.80.0’
* 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 ‘CoCiteStats’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... NOTE
Package in Depends field not imported from: ‘org.Hs.eg.db’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
gene.geneslist.sig: no visible global function definition for ‘Lkeys’
gene.geneslist.sig: no visible binding for global variable
  ‘org.Hs.egPMID’
paperLen: no visible global function definition for ‘toTable’
paperLen: no visible binding for global variable ‘org.Hs.egPMID’
paperLen: no visible global function definition for ‘nhit’
paperLen: no visible global function definition for ‘revmap’
Undefined global functions or variables:
  Lkeys nhit org.Hs.egPMID revmap toTable
* checking Rd files ... NOTE
prepare_Rd: gene.geneslist.statistic.Rd:19-21: Dropping empty section \details
* 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 examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
gene.geneslist.sig       40.079  0.627  40.809
actorAdjTable            28.597  3.657  32.403
gene.geneslist.statistic 23.654  0.248  23.959
gene.gene.statistic      21.653  1.166  22.874
twTStats                 22.065  0.135  22.255
twowayTable              21.960  0.120  22.130
paperLen                 20.335  0.156  20.532
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/CoCiteStats.Rcheck/00check.log’
for details.


Installation output

CoCiteStats.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL CoCiteStats
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘CoCiteStats’ ...
** this is package ‘CoCiteStats’ version ‘1.80.0’
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (CoCiteStats)

Tests output


Example timings

CoCiteStats.Rcheck/CoCiteStats-Ex.timings

nameusersystemelapsed
actorAdjTable28.597 3.65732.403
gene.gene.statistic21.653 1.16622.874
gene.geneslist.sig40.079 0.62740.809
gene.geneslist.statistic23.654 0.24823.959
paperLen20.335 0.15620.532
twTStats22.065 0.13522.255
twowayTable21.96 0.1222.13