Package: qpcrNorm

Version: 1.38.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qpcrNorm.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings qpcrNorm_1.38.0.tar.gz

StartedAt: 2018-10-17 04:09:46 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 04:10:50 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 63.7 seconds

RetCode: 0

Status:  OK

CheckDir: qpcrNorm.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qpcrNorm.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings qpcrNorm_1.38.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/qpcrNorm.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'qpcrNorm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'qpcrNorm' version '1.38.0'
* 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 whether package 'qpcrNorm' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'affy' 'limma'
  Please remove these calls from your code.
Package in Depends field not imported from: 'Biobase'
  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
calcCV : <anonymous>: no visible global function definition for 'sd'
normQpcrRankInvariant: no visible global function definition for
  'median'
normQpcrRankInvariant: no visible binding for global variable 'median'
plotVarMean: no visible binding for global variable 'var'
plotVarMean: no visible global function definition for 'plot'
plotVarMean: no visible global function definition for 'abline'
plotVarMean: no visible global function definition for 'lines'
plotVarMean: no visible global function definition for 'lowess'
readQpcr: no visible global function definition for 'read.table'
writeQpcr: no visible global function definition for 'write.table'
Undefined global functions or variables:
  abline lines lowess median plot read.table sd var write.table
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "lowess", "median", "sd", "var")
  importFrom("utils", "read.table", "write.table")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/qpcrNorm.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/qpcrNorm_1.38.0.tar.gz && rm -rf qpcrNorm.buildbin-libdir && mkdir qpcrNorm.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qpcrNorm.buildbin-libdir qpcrNorm_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL qpcrNorm_1.38.0.zip && rm qpcrNorm_1.38.0.tar.gz qpcrNorm_1.38.0.zip
###
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install for i386

* installing *source* package 'qpcrNorm' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'qpcrNorm'
    finding HTML links ... done
    calcCV                                  html  
    ctQc                                    html  
    matrixByPlate                           html  
    normQpcrHouseKeepingGenes               html  
    normQpcrQuantile                        html  
    normQpcrRankInvariant                   html  
    plotVarMean                             html  
    qpcrBatch-class                         html  
    qpcrBatch.object                        html  
    readQpcr                                html  
    readQpcrBatch                           html  
    writeQpcr                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'qpcrNorm' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qpcrNorm' as qpcrNorm_1.38.0.zip
* DONE (qpcrNorm)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'qpcrNorm' successfully unpacked and MD5 sums checked
In R CMD INSTALL