Multiple platform build/check report for BioC 3.6 - CHECK report for gcrma on tokay1

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### Running command:
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###   rm -rf gcrma.buildbin-libdir gcrma.Rcheck && mkdir gcrma.buildbin-libdir gcrma.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gcrma.buildbin-libdir gcrma_2.50.0.tar.gz >gcrma.Rcheck\00install.out 2>&1 && cp gcrma.Rcheck\00install.out gcrma-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=gcrma.buildbin-libdir --install="check:gcrma-install.out" --force-multiarch --no-vignettes --timings gcrma_2.50.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/gcrma.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gcrma/DESCRIPTION' ... OK
* this is package 'gcrma' version '2.50.0'
* 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 'gcrma' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'affy' 'splines'
A package should be listed in only one of these fields.
* 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 ... NOTE
Foreign function call to a different package:
  .Call("rma_c_complete", ..., PACKAGE = "affy")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
compute.affinities: no visible binding for global variable
  'affinity.spline.coefs'
compute.affinities.nomm: no visible binding for global variable
  'affinity.spline.coefs'
compute.affinities2: no visible binding for global variable
  'affinity.spline.coefs'
Undefined global functions or variables:
  affinity.spline.coefs
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/gcrma.buildbin-libdir/gcrma/libs/i386/gcrma.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
bg.adjust.gcrma 21.57   0.44    22.0
gcrma           19.39   0.41    19.8
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
bg.adjust.gcrma 25.59   0.39   25.98
gcrma           22.30   0.55   22.85
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/gcrma.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'gcrma' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c baseProfile.c -o baseProfile.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c computeAffinities.c -o computeAffinities.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c postmean.c -o postmean.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o gcrma.dll tmp.def baseProfile.o computeAffinities.o postmean.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/gcrma.buildbin-libdir/gcrma/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'gcrma'
    finding HTML links ... done
    affinity.spline.coefs                   html  
    bg.adjust.affinities                    html  
    bg.adjust.gcrma                         html  
    bg.parameters.ns                        html  
    compute.affinities                      html  
    fast.bkg                                html  
    gcrma                                   html  
    gcrma.engine                            html  
    gcrma.engine2                           html  
    getCDF                                  html  
    justGCRMA                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'gcrma' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c baseProfile.c -o baseProfile.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c computeAffinities.c -o computeAffinities.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c postmean.c -o postmean.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o gcrma.dll tmp.def baseProfile.o computeAffinities.o postmean.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/gcrma.buildbin-libdir/gcrma/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gcrma' as gcrma_2.50.0.zip
* DONE (gcrma)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for gcrma on tokay1

Summary

Command output

Installation output

Tests output

Example timings