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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:dyebiasexamples.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings dyebiasexamples_1.46.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/dyebiasexamples.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘dyebiasexamples/DESCRIPTION’ ... OK
* this is package ‘dyebiasexamples’ version ‘1.46.0’
* 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 ‘dyebiasexamples’ can be installed ... WARNING
Found the following significant warnings:
  Warning: dyebias.geo2marray.Rd:10-17: Section \synopsis is unrecognized and will be dropped
  Warning: dyebias.umcu.proper.estimators.Rd:11-13: Section \synopsis is unrecognized and will be dropped
See ‘/home/biocbuild/bbs-3.20-data-experiment/meat/dyebiasexamples.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 40.3Mb
  sub-directories of 1Mb or more:
    data        5.3Mb
    extradata  34.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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:
  ‘GEOquery’ ‘marray’
  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 ... NOTE
.extract.measurements: no visible global function definition for
  ‘GSMList’
.extract.measurements : <anonymous>: no visible global function
  definition for ‘Table’
.extract.meta: no visible global function definition for ‘GSMList’
.extract.meta : <anonymous>: no visible global function definition for
  ‘Meta’
.gsmlist2targetinfo: no visible global function definition for
  ‘GSMList’
.gsmlist2targetinfo: no visible global function definition for ‘Meta’
.have.umcu.version: no visible global function definition for
  ‘package.version’
dyebias.geo2marray: no visible global function definition for ‘GSMList’
dyebias.geo2marray : <anonymous>: no visible global function definition
  for ‘Meta’
dyebias.geo2marray: no visible global function definition for ‘Meta’
dyebias.geo2marray: no visible global function definition for ‘GPLList’
dyebias.geo2marray: no visible global function definition for ‘Table’
dyebias.geo2marray: no visible global function definition for
  ‘read.marrayLayout’
dyebias.geo2marray: no visible global function definition for
  ‘Accession’
dyebias.geo2marray: no visible global function definition for
  ‘maControls<-’
dyebias.geo2marray: no visible global function definition for ‘new’
dyebias.geo2marray: no visible global function definition for
  ‘maLabels<-’
dyebias.geo2marray: no visible global function definition for
  ‘maInfo<-’
dyebias.geo2marray: no visible global function definition for ‘maRf’
dyebias.geo2marray: no visible global function definition for ‘maRb<-’
dyebias.geo2marray: no visible global function definition for ‘maGb<-’
dyebias.geo2marray: no visible global function definition for
  ‘maTargets<-’
dyebias.geo2marray: no visible global function definition for
  ‘maLayout<-’
dyebias.geo2marray: no visible global function definition for
  ‘maGnames<-’
Undefined global functions or variables:
  Accession GPLList GSMList Meta Table maControls<- maGb<- maGnames<-
  maInfo<- maLabels<- maLayout<- maRb<- maRf maTargets<- new
  package.version read.marrayLayout
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... WARNING
prepare_Rd: dyebias.geo2marray.Rd:10-17: Section \synopsis is unrecognized and will be dropped
prepare_Rd: dyebias.umcu.proper.estimators.Rd:11-13: Section \synopsis is unrecognized and will be dropped
* 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 ... WARNING
Files not of a type allowed in a ‘data’ directory:
  ‘README’
Please use e.g. ‘inst/extdata’ for non-R data files

* 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
  data.norm.rda    2.1Mb    1.5Mb       xz
  data.raw.rda     3.2Mb    2.2Mb       xz
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘ChangeLog’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
* checking package vignettes ... NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... OK
* DONE

Status: 5 WARNINGs, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-data-experiment/meat/dyebiasexamples.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL dyebiasexamples
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘dyebiasexamples’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: dyebias.geo2marray.Rd:10-17: Section \synopsis is unrecognized and will be dropped
Warning: dyebias.umcu.proper.estimators.Rd:11-13: Section \synopsis is unrecognized and will be dropped
*** 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 (dyebiasexamples)