##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:ReportingTools.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings ReportingTools_2.47.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/ReportingTools.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ReportingTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ReportingTools’ version ‘2.47.0’
* 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 ‘ReportingTools’ 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 ... NOTE
.GeneSetCollection.to.data.frame: no visible binding for global
  variable 'description'
.GeneSetCollection.to.html: no visible binding for global variable
  'description'
.GeneSetCollection.to.html2: no visible binding for global variable
  'description'
.PFAMhyperG.to.html: no visible binding for global variable 'keytype'
.PFAMhyperG.to.html: no visible binding for global variable 'columns'
.make.gene.plots: no visible global function definition for 'exprs'
.marrayLM.to.data.frame: no visible global function definition for
  'featureNames'
.marrayLM.to.data.frame: no visible global function definition for
  'fData'
.marrayLM.to.html: no visible global function definition for
  'featureNames'
.marrayLM.to.html: no visible global function definition for 'fData'
check.ids: no visible binding for global variable 'org.Hs.eg.db'
check.ids: no visible global function definition for 'keys'
custHeaderPanel : <anonymous>: no visible binding for global variable
  'tags'
custHeaderPanel : <anonymous>: no visible global function definition
  for 'HTML'
custHeaderPanel: no visible global function definition for 'tagList'
custHeaderPanel: no visible global function definition for 'tag'
custHeaderPanel: no visible global function definition for 'div'
custHeaderPanel: no visible global function definition for 'h1'
publish,trellis-HTMLReport: no visible binding for global variable
  'htmlRep'
toReportDF,DESeqDataSet: no visible global function definition for
  'mcols'
Undefined global functions or variables:
  HTML columns description div exprs fData featureNames h1 htmlRep keys
  keytype mcols org.Hs.eg.db tag tagList tags
* checking Rd files ... WARNING
BaseReportType-class.Rd: Sections \title, and \name must exist and be unique in Rd files
CSVFile-class.Rd: Sections \title, and \name must exist and be unique in Rd files
CSVFile.Rd: Sections \title, and \name must exist and be unique in Rd files
HTMLReportRef-class.rd: Sections \title, and \name must exist and be unique in Rd files
Link.Rd: Sections \title, and \name must exist and be unique in Rd files
ReportHandlers-class.Rd: Sections \title, and \name must exist and be unique in Rd files
addReportColumns-methods.Rd: Sections \title, and \name must exist and be unique in Rd files
custHeaderPanel.Rd: Sections \title, and \name must exist and be unique in Rd files
filename-methods.Rd: Sections \title, and \name must exist and be unique in Rd files
finish-methods.Rd: Sections \title, and \name must exist and be unique in Rd files
mockRnaSeqData.Rd: Sections \title, and \name must exist and be unique in Rd files
objectToHTML-methods.Rd: Sections \title, and \name must exist and be unique in Rd files
Error writing to connection:  No space left on device
readReport.Rd: Sections \title, and \name must exist and be unique in Rd files
reporting.theme.Rd: Sections \title, and \name must exist and be unique in Rd files
reporting.theme.alternate.Rd: Sections \title, and \name must exist and be unique in Rd files
toReportDF-methods.Rd: Sections \title, and \name must exist and be unique in Rd files
validConnection.Rd: Sections \title, and \name must exist and be unique in Rd files
problems found in ‘BaseReportType-class.Rd’, ‘CSVFile-class.Rd’, ‘CSVFile.Rd’, ‘HTMLReportRef-class.rd’, ‘Link.Rd’, ‘ReportHandlers-class.Rd’, ‘addReportColumns-methods.Rd’, ‘custHeaderPanel.Rd’, ‘filename-methods.Rd’, ‘finish-methods.Rd’, ‘mockRnaSeqData.Rd’, ‘objectToHTML-methods.Rd’, ‘publish-methods.Rd’, ‘readReport.Rd’, ‘reporting.theme.Rd’, ‘reporting.theme.alternate.Rd’, ‘toReportDF-methods.Rd’, ‘validConnection.Rd’
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  publish-methods.Rd: DESeqDataSet-class, results, DESeq,
    DESeqResults-class
  reporting.theme.Rd: standard.theme
  reporting.theme.alternate.Rd: standard.theme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
  Error in load(p, envir = env) : error reading from connection
  Calls: <Anonymous> ... suppressPackageStartupMessages -> withCallingHandlers -> load
  Execution halted
* checking files in ‘vignettes’ ...Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Error: inferior call failed
Execution halted

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL ReportingTools
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘ReportingTools’ ...
** this is package ‘ReportingTools’ version ‘2.47.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'objectToHTML' with signature 'object="ggbio"': no definition for class "ggbio"
** 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 (ReportingTools)