Multiple platform build/check report for BioC 3.8 - CHECK report for NormqPCR on tokay1

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NormqPCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings NormqPCR_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/NormqPCR.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'NormqPCR/DESCRIPTION' ... OK
* this is package 'NormqPCR' version '1.28.0'
* 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 whether package 'NormqPCR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpW4ygjE/R.INSTALLf809434e8f/NormqPCR/man/ComputeNRQs.Rd:14: file link 'qPCRBatch' in package 'ReadqPCR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpW4ygjE/R.INSTALLf809434e8f/NormqPCR/man/CqValues.Rd:23: file link 'CyclesSet' in package 'ReadqPCR' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/NormqPCR.Rcheck/00install.out' for details.
* 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 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CqValues,CyclesSet: no visible binding for global variable 'l5'
Undefined global functions or variables:
  l5
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
CqValues 39.95   0.15   40.89
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
CqValues 45.21   0.08   45.28
* 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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/NormqPCR.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/NormqPCR_1.28.0.tar.gz && rm -rf NormqPCR.buildbin-libdir && mkdir NormqPCR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NormqPCR.buildbin-libdir NormqPCR_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL NormqPCR_1.28.0.zip && rm NormqPCR_1.28.0.tar.gz NormqPCR_1.28.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  310k  100  310k    0     0  9265k      0 --:--:-- --:--:-- --:--:-- 10.4M

install for i386

* installing *source* package 'NormqPCR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'NormqPCR'
    finding HTML links ... done
    Bladder                                 html  
    BladderRepro                            html  
    Colon                                   html  
    ComputeNRQs                             html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpW4ygjE/R.INSTALLf809434e8f/NormqPCR/man/ComputeNRQs.Rd:14: file link 'qPCRBatch' in package 'ReadqPCR' does not exist and so has been treated as a topic
    CqValues                                html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpW4ygjE/R.INSTALLf809434e8f/NormqPCR/man/CqValues.Rd:23: file link 'CyclesSet' in package 'ReadqPCR' does not exist and so has been treated as a topic
    NormqPCR-package                        html  
    combineTechReps                         html  
    combineTechRepsSD                       html  
    deltaCt                                 html  
    deltaDeltaCt                            html  
    geNorm                                  html  
    geomMean                                html  
    makeAllNAs                              html  
    makeAllNewVal                           html  
    replaceAboveCutOff                      html  
    replaceNAs                              html  
    selectHKs                               html  
    stabMeasureM                            html  
    stabMeasureRho                          html  
** building package indices
** installing vignettes
   'NormqPCR.Rnw' 
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'NormqPCR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NormqPCR' as NormqPCR_1.28.0.zip
* DONE (NormqPCR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'NormqPCR' successfully unpacked and MD5 sums checked
In R CMD INSTALL

CHECK report for NormqPCR on tokay1

Summary

Command output

Installation output

Tests output

Example timings