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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SCAN.UPC.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SCAN.UPC_2.48.0.tar.gz
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/SCAN.UPC.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 ‘SCAN.UPC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SCAN.UPC’ version ‘2.48.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Biobase', 'oligo', 'Biostrings', 'GEOquery', 'affy', 'affyio',
  'foreach', 'sva'
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 ‘SCAN.UPC’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* 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
BatchAdjust: no visible global function definition for ‘varLabels’
BatchAdjust: no visible global function definition for ‘exprs<-’
BatchAdjust: no visible global function definition for ‘pData’
BatchAdjustFromFile: no visible global function definition for
  ‘sampleNames’
BatchAdjustFromFile: no visible global function definition for ‘pData’
BatchAdjustFromFile: no visible global function definition for
  ‘varLabels’
BatchAdjustFromFile: no visible global function definition for
  ‘pData<-’
InstallBrainArrayPackage: no visible global function definition for
  ‘download.file’
InstallBrainArrayPackage: no visible global function definition for
  ‘install.packages’
ProcessGtfSubset: no visible global function definition for ‘IRanges’
RS_BC: no visible global function definition for ‘median’
RS_BC: no visible global function definition for ‘dlnorm’
RS_BC: no visible global function definition for ‘rlnorm’
UPC_Generic_ExpressionSet: no visible global function definition for
  ‘pData’
UPC_Generic_ExpressionSet: no visible global function definition for
  ‘featureData’
UPC_Generic_ExpressionSet: no visible global function definition for
  ‘DNAStringSet’
UPC_Generic_ExpressionSet: no visible global function definition for
  ‘exprs<-’
UPC_RNASeq: no visible global function definition for ‘runif’
UPC_RNASeq: no visible global function definition for ‘sampleNames<-’
UPC_RNASeq: no visible global function definition for ‘featureNames<-’
UPC_nb: no visible global function definition for ‘dnbinom’
UPC_nn: no visible global function definition for ‘median’
UPC_nn: no visible global function definition for ‘var’
UPC_nn: no visible global function definition for ‘dnorm’
UPC_nn: no visible global function definition for ‘rnorm’
UPC_nn_bayes: no visible global function definition for ‘median’
UPC_nn_bayes: no visible global function definition for ‘var’
assign_bin: no visible global function definition for ‘rnorm’
channelNormalize: no visible global function definition for ‘var’
downloadBeadChipFromGEO: no visible global function definition for
  ‘untar’
downloadFromGEO: no visible global function definition for ‘untar’
iglNormalize: no visible global function definition for ‘loess’
madNormalize: no visible global function definition for ‘median’
processCelFiles: no visible global function definition for ‘%dopar%’
processCelFiles: no visible global function definition for
  ‘sampleNames<-’
processCelFiles: no visible global function definition for
  ‘featureNames<-’
processTwoColor: no visible global function definition for
  ‘sampleNames<-’
processTwoColor: no visible global function definition for
  ‘featureNames<-’
readAgilentData: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  %dopar% DNAStringSet IRanges dlnorm dnbinom dnorm download.file
  exprs<- featureData featureNames<- install.packages loess median
  pData pData<- read.delim rlnorm rnorm runif sampleNames sampleNames<-
  untar var varLabels
Consider adding
  importFrom("stats", "dlnorm", "dnbinom", "dnorm", "loess", "median",
             "rlnorm", "rnorm", "runif", "var")
  importFrom("utils", "download.file", "install.packages", "read.delim",
             "untar")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 3 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/SCAN.UPC.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL SCAN.UPC
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* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘SCAN.UPC’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load and register a 'foreach' adaptor
        Example - Using 'multicore' for 2 cores:
             library(doMC)
             registerDoMC(2)
================================================================================
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load and register a 'foreach' adaptor
        Example - Using 'multicore' for 2 cores:
             library(doMC)
             registerDoMC(2)
================================================================================
** testing if installed package can be loaded from final location
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load and register a 'foreach' adaptor
        Example - Using 'multicore' for 2 cores:
             library(doMC)
             registerDoMC(2)
================================================================================
** testing if installed package keeps a record of temporary installation path
* DONE (SCAN.UPC)