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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:annotationTools.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings annotationTools_1.80.0.tar.gz
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/annotationTools.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘annotationTools/DESCRIPTION’ ... OK
* this is package ‘annotationTools’ 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 ‘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 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/annotationTools.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL annotationTools
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* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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)