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

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### Running command:
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###   rm -rf simpleaffy.buildbin-libdir simpleaffy.Rcheck && mkdir simpleaffy.buildbin-libdir simpleaffy.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=simpleaffy.buildbin-libdir simpleaffy_2.54.0.tar.gz >simpleaffy.Rcheck\00install.out 2>&1 && cp simpleaffy.Rcheck\00install.out simpleaffy-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=simpleaffy.buildbin-libdir --install="check:simpleaffy-install.out" --force-multiarch --no-vignettes --timings simpleaffy_2.54.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/simpleaffy.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 'simpleaffy/DESCRIPTION' ... OK
* this is package 'simpleaffy' version '2.54.0'
* 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 'simpleaffy' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'utils' 'grDevices' 'graphics' 'stats' 'BiocGenerics' 'Biobase' 'affy' 'genefilter' 'gcrma'
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 ... OK
* checking R code for possible problems ... NOTE
hmap.eset : <anonymous>: no visible global function definition for
  'var'
hmap.pc : <anonymous>: no visible global function definition for 'var'
qc.affy: no visible binding for global variable 'var'
standard.pearson: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor var
Consider adding
  importFrom("stats", "cor", "var")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'PairComp,ANY,ANY,ANY'
  generic '[<-' and siglist 'PairComp,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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/simpleaffy.buildbin-libdir/simpleaffy/libs/i386/simpleaffy.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
** 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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/simpleaffy.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'simpleaffy' ...
** 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 simpleaffy.c -o simpleaffy.o
simpleaffy.c: In function 'bgmas':
simpleaffy.c:440:30: warning: passing argument 1 of 'REprintf' from incompatible pointer type
     if(gn >= ngrid) REprintf(stderr,"Really ouch! %d %d\n",gn,ends[gn]);
                              ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/R.h:88:0,
                 from simpleaffy.c:5:
C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/R_ext/Print.h:43:6: note: expected 'const char *' but argument is of type 'struct FILE *'
 void REprintf(const char *, ...);
      ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o simpleaffy.dll tmp.def simpleaffy.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/simpleaffy.buildbin-libdir/simpleaffy/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'simpleaffy'
    finding HTML links ... done
    PairComp-class                          html  
    QCStats-class                           html  
    all.present                             html  
    all.present.in.group                    html  
    bg.correct.sa                           html  
    call.exprs                              html  
    detection.p.val                         html  
    get.annotation                          html  
    get.array.indices                       html  
    get.array.subset                        html  
    get.array.subset.affy                   html  
    get.fold.change.and.t.test              html  
    hmap.colors                             html  
    hmap.eset                               html  
    hmap.pc                                 html  
    journalpng                              html  
    justMAS                                 html  
    pairwise.comparison                     html  
    pairwise.filter                         html  
    plot.pairwise.comparison                html  
    plot.qc.stats                           html  
    qc                                      html  
    qc.affy                                 html  
    qc.get.alpha1                           html  
    qc.get.array                            html  
    qc.get.probes                           html  
    qc.get.ratios                           html  
    qc.get.spikes                           html  
    qc.have.params                          html  
    qc.ok                                   html  
    qc.read.file                            html  
    qc.stats                                html  
    read.affy                               html  
    read.affy.mixed                         html  
    setQCEnvironment                        html  
    simpleaffy-deprecated                   html  
    standard.pearson                        html  
    trad.scatter.plot                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'simpleaffy' ...
** 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 simpleaffy.c -o simpleaffy.o
simpleaffy.c: In function 'bgmas':
simpleaffy.c:440:30: warning: passing argument 1 of 'REprintf' from incompatible pointer type
     if(gn >= ngrid) REprintf(stderr,"Really ouch! %d %d\n",gn,ends[gn]);
                              ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/R.h:88:0,
                 from simpleaffy.c:5:
C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/R_ext/Print.h:43:6: note: expected 'const char *' but argument is of type 'struct FILE *'
 void REprintf(const char *, ...);
      ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o simpleaffy.dll tmp.def simpleaffy.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/simpleaffy.buildbin-libdir/simpleaffy/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'simpleaffy' as simpleaffy_2.54.0.zip
* DONE (simpleaffy)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for simpleaffy on tokay1

Summary

Command output

Installation output

Tests output

Example timings