##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:hgu2beta7.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings hgu2beta7_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/hgu2beta7.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* 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 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘hgu2beta7/DESCRIPTION’ ... OK
* this is package ‘hgu2beta7’ version ‘1.44.0’
* 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 ‘hgu2beta7’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Subdirectory ‘data’ contains no data sets.
* 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 ... NOTE
hgu2beta7: no visible binding for global variable ‘hgu2beta7QC’
Undefined global functions or variables:
  hgu2beta7QC
* checking Rd files ... NOTE
checkRd: (-1) hgu2beta7REFSEQ.Rd:15: Escaped LaTeX specials: \_
checkRd: (-1) hgu2beta7REFSEQ.Rd:17: Escaped LaTeX specials: \_
checkRd: (-1) hgu2beta7REFSEQ.Rd:19: Escaped LaTeX specials: \_
checkRd: (-1) hgu2beta7REFSEQ.Rd:21: Escaped LaTeX specials: \_
checkRd: (-1) hgu2beta7REFSEQ.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) hgu2beta7REFSEQ.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) hgu2beta7REFSEQ.Rd:28: 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 ... WARNING
'library' or 'require' call not declared from: ‘annotate’
* checking contents of ‘data’ directory ... WARNING
Files not of a type allowed in a ‘data’ directory:
  ‘Rdata.rdb’ ‘Rdata.rds’ ‘Rdata.rdx’
Please use e.g. ‘inst/extdata’ for non-R data files

* checking data for non-ASCII characters ... OK
* checking LazyData ... WARNING
  LazyData DB of 6.9 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-data-experiment/meat/hgu2beta7.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL hgu2beta7
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘hgu2beta7’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (hgu2beta7)