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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HD2013SGI.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HD2013SGI_1.46.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/HD2013SGI.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘HD2013SGI/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HD2013SGI’ 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'
 NOTE
Depends: includes the non-default packages:
  'RColorBrewer', 'gplots', 'geneplotter', 'splots', 'limma', 'vcd',
  'LSD', 'EBImage'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘HD2013SGI’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 525.2Mb
  sub-directories of 1Mb or more:
    data  524.1Mb
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘EBImage’ ‘LSD’ ‘RColorBrewer’ ‘geneplotter’ ‘gplots’ ‘limma’
  ‘splots’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘humanReadableNames’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
HD2013SGIHeatmapHuman: no visible global function definition for ‘unit’
HD2013SGIHeatmapHuman: no visible global function definition for
  ‘pushViewport’
HD2013SGIHeatmapHuman: no visible global function definition for
  ‘viewport’
HD2013SGIHeatmapHuman: no visible global function definition for
  ‘grid.layout’
HD2013SGIHeatmapHuman: no visible global function definition for
  ‘grid.rect’
HD2013SGIHeatmapHuman: no visible global function definition for
  ‘grid.raster’
HD2013SGIHeatmapHuman: no visible global function definition for
  ‘popViewport’
HD2013SGIHeatmapHuman: no visible global function definition for
  ‘grid.text’
HD2013SGIHeatmapHuman: no visible global function definition for ‘gpar’
HD2013SGImaineffects: no visible binding for global variable ‘median’
HD2013SGImaineffects : <anonymous>: no visible binding for global
  variable ‘median’
HD2013SGImaineffects: no visible global function definition for
  ‘median’
HD2013SGIorderDim: no visible global function definition for ‘cor’
HD2013SGIorderDim: no visible global function definition for ‘hclust’
HD2013SGIorderDim: no visible global function definition for ‘as.dist’
HD2013SGIselectByStability: no visible global function definition for
  ‘lm’
HD2013SGIselectByStability : <anonymous>: no visible global function
  definition for ‘cor’
plotExampleInteractions: no visible binding for global variable ‘sd’
plotExampleInteractions: no visible global function definition for
  ‘par’
plotExampleInteractions: no visible global function definition for
  ‘barplot’
plotExampleInteractions: no visible global function definition for
  ‘abline’
plotExampleInteractions: no visible global function definition for
  ‘points’
plotExampleInteractions: no visible global function definition for
  ‘text’
plotExampleSingleGeneEffects: no visible global function definition for
  ‘mad’
plotExampleSingleGeneEffects: no visible global function definition for
  ‘par’
plotExampleSingleGeneEffects: no visible global function definition for
  ‘barplot’
plotExampleSingleGeneEffects: no visible global function definition for
  ‘abline’
plotExampleSingleGeneEffects: no visible global function definition for
  ‘points’
Undefined global functions or variables:
  abline as.dist barplot cor gpar grid.layout grid.raster grid.rect
  grid.text hclust lm mad median par points popViewport pushViewport sd
  text unit viewport
Consider adding
  importFrom("graphics", "abline", "barplot", "par", "points", "text")
  importFrom("stats", "as.dist", "cor", "hclust", "lm", "mad", "median",
             "sd")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) Interactions.Rd:5: Lost braces; missing escapes or markup?
     5 | \description{The genetic interaction data. Pairwise interaction scores (\code{piscore}) are presented in a 6-dimensional array with dimensions target genes x target siRNA designs x query genes x query siRNA designs x features x replicates. BH-corrected p-values ({padj}) are presented in a 5-dimensional array with dimensions target genes x target siRNA designs x query genes x query siRNA designs x features. An annotation of target and query genes and of phenotypes can be found in (\code{Anno}). \code{scale} is the standard deviation measure used for normalization. At first standard deviations were computed between replicates for each experiment and afterwards the median of standard deviations was computed.}
       |                                                                                                                                                                                                                                                                        ^
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
featuresPerWell 41.641  0.573  42.215
datamatrixfull   9.442  0.148   9.590
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-data-experiment/meat/HD2013SGI.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL HD2013SGI
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘HD2013SGI’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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 (HD2013SGI)