##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SpikeInSubset.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SpikeInSubset_1.47.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/SpikeInSubset.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘SpikeInSubset/DESCRIPTION’ ... OK
* this is package ‘SpikeInSubset’ version ‘1.47.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘SpikeInSubset’ can be installed ... WARNING
Found the following significant warnings:
  Warning: xhyb.Rd:2: docType ‘instance’ is unrecognized
See ‘/home/biocbuild/bbs-3.21-data-experiment/meat/SpikeInSubset.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
  installed size is 18.6Mb
  sub-directories of 1Mb or more:
    data  18.5Mb
* 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 ... 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
Packages in Depends field not imported from:
  ‘Biobase’ ‘affy’
  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 ... WARNING
prepare_Rd: xhyb.Rd:2: docType ‘instance’ is unrecognized
* checking Rd metadata ... OK
* checking Rd cross-references ...Warning: xhyb.Rd:2: docType ‘instance’ is unrecognized
 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                           old_size new_size compress
  hgu133a.spikein.xhyb.rda     12Kb      2Kb     gzip
  mas133.rda                  2.2Mb    989Kb       xz
  mas95.rda                   1.3Mb    572Kb       xz
  rma133.rda                  2.2Mb    897Kb       xz
  rma95.rda                   1.3Mb    522Kb       xz
  spikein133.rda              7.3Mb    4.3Mb       xz
  spikein95.rda               6.1Mb    3.6Mb       xz
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-data-experiment/meat/SpikeInSubset.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL SpikeInSubset
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘SpikeInSubset’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
Warning: xhyb.Rd:2: docType ‘instance’ is unrecognized
*** 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 (SpikeInSubset)