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### Running command:
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###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MAQCsubsetILM.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MAQCsubsetILM_1.40.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-data-experiment/meat/MAQCsubsetILM.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘MAQCsubsetILM/DESCRIPTION’ ... OK
* this is package ‘MAQCsubsetILM’ version ‘1.40.0’
* 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 ‘MAQCsubsetILM’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'MAQCsubsetILM' is deprecated and will be removed from
See ‘/home/biocbuild/bbs-3.18-data-experiment/meat/MAQCsubsetILM.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 ... 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 startup messages can be suppressed ... NOTE
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘lumi’
  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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) refA.Rd:9: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) refB.Rd:9: 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 ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘MAQCsubsetILM.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-data-experiment/meat/MAQCsubsetILM.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL MAQCsubsetILM
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘MAQCsubsetILM’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
Warning: Package 'MAQCsubsetILM' is deprecated and will be removed from
  Bioconductor version 3.19
** testing if installed package can be loaded from final location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
Warning: Package 'MAQCsubsetILM' is deprecated and will be removed from
  Bioconductor version 3.19
** testing if installed package keeps a record of temporary installation path
* DONE (MAQCsubsetILM)