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This page was generated on 2024-03-18 11:38:35 -0400 (Mon, 18 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-06 r86056) -- "Unsuffered Consequences" 4685
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-06 r86056 ucrt) -- "Unsuffered Consequences" 4423
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-04 r86048) -- "Unsuffered Consequences" 4450
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-06 r86056) -- "Unsuffered Consequences" 4361
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 75/2257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotationTools 1.77.0  (landing page)
Alexandre Kuhn
Snapshot Date: 2024-03-17 14:00:14 -0400 (Sun, 17 Mar 2024)
git_url: https://git.bioconductor.org/packages/annotationTools
git_branch: devel
git_last_commit: f51f75a
git_last_commit_date: 2023-10-24 09:38:01 -0400 (Tue, 24 Oct 2023)
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  

CHECK results for annotationTools on lconway


To the developers/maintainers of the annotationTools package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/annotationTools.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: annotationTools
Version: 1.77.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:annotationTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings annotationTools_1.77.0.tar.gz
StartedAt: 2024-03-17 18:48:47 -0400 (Sun, 17 Mar 2024)
EndedAt: 2024-03-17 18:49:23 -0400 (Sun, 17 Mar 2024)
EllapsedTime: 36.6 seconds
RetCode: 0
Status:   OK  
CheckDir: annotationTools.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:annotationTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings annotationTools_1.77.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/annotationTools.Rcheck’
* using R Under development (unstable) (2024-03-04 r86048)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotationTools/DESCRIPTION’ ... OK
* this is package ‘annotationTools’ version ‘1.77.0’
* 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 ‘annotationTools’ 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 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 ... NOTE
checkRd: (-1) annot_HGU133A.Rd:4: Escaped LaTeX specials: \_
checkRd: (-1) getGENEID.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) getGENEONTOLOGY.Rd:21: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) getGENESYMBOL.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) getGENETITLE.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) getHOMOLOG.Rd:37: Escaped LaTeX specials: \_ \_
checkRd: (-1) getOrthologousProbesets.Rd:18: Escaped LaTeX specials: \_ \_
checkRd: (-1) getOrthologousProbesets.Rd:22: Escaped LaTeX specials: \_ \_
checkRd: (-1) getOrthologousProbesets.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) getOrthologousProbesets.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) getPROBESET.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) table_human.Rd:4: Escaped LaTeX specials: \_
checkRd: (-1) table_mouse.Rd:4: Escaped LaTeX specials: \_
* 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 data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/annotationTools.Rcheck/00check.log’
for details.



Installation output

annotationTools.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL annotationTools
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘annotationTools’ ...
** using staged installation
** R
** data
** 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 (annotationTools)

Tests output


Example timings

annotationTools.Rcheck/annotationTools-Ex.timings

nameusersystemelapsed
compactList000
getANNOTATION0.0020.0010.003
getGENEID0.0080.0020.011
getGENEONTOLOGY0.0110.0030.014
getGENESYMBOL0.0050.0010.006
getGENETITLE0.0080.0010.010
getHOMOLOG0.0110.0040.016
getMULTIANNOTATION0.0010.0010.003
getOrthologousProbesets0.0360.0070.044
getPROBESET0.0090.0030.011
listToCharacterVector0.0000.0010.000
ps2ps0.0000.0010.001