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CHECK report for affy on tokay2

This page was generated on 2018-10-17 08:31:49 -0400 (Wed, 17 Oct 2018).

Package 17/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affy 1.58.0
Rafael A. Irizarry
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/affy
Branch: RELEASE_3_7
Last Commit: 4698231
Last Changed Date: 2018-04-30 10:34:55 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: affy
Version: 1.58.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affy.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings affy_1.58.0.tar.gz
StartedAt: 2018-10-17 00:25:43 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 00:30:21 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 278.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: affy.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affy.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings affy_1.58.0.tar.gz
###
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##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/affy.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 'affy/DESCRIPTION' ... OK
* this is package 'affy' version '1.58.0'
* 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 'affy' can be installed ... OK
* 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 ... NOTE
'library' or 'require' call to 'tkWidgets' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  'stats:::C_loess_raw' 'stats:::C_lowesp' 'stats:::C_lowesw'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'bg.correct'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function calls to a base package:
  .C(stats:::C_loess_raw, ...)
  .Fortran(stats:::C_lowesp, ...)
  .Fortran(stats:::C_lowesw, ...)
Packages should not make .C/.Call/.External/.Fortran calls to a base
package. They are not part of the API, for use only by R itself and
subject to change without notice.
* checking R code for possible problems ... NOTE
AllButCelsForReadAffy: no visible global function definition for
  'fileBrowser'
AllButCelsForReadAffy: no visible global function definition for
  'hasSuffix'
expressoWidget: no visible global function definition for 'tclVar'
expressoWidget : quit: no visible global function definition for
  'tkdestroy'
expressoWidget : end: no visible global function definition for
  'tclvalue'
expressoWidget: no visible global function definition for 'tktoplevel'
expressoWidget: no visible global function definition for 'tkdestroy'
expressoWidget: no visible global function definition for 'tktitle<-'
expressoWidget: no visible global function definition for 'tkpack'
expressoWidget: no visible global function definition for 'tklabel'
expressoWidget: no visible global function definition for 'tkframe'
expressoWidget: no visible global function definition for
  'dropdownList'
expressoWidget: no visible global function definition for 'tclvalue'
expressoWidget: no visible global function definition for 'tkgrid'
expressoWidget: no visible global function definition for
  'tkgrid.configure'
expressoWidget: no visible global function definition for 'tkbutton'
expressoWidget: no visible global function definition for
  'tkwait.window'
Undefined global functions or variables:
  dropdownList fileBrowser hasSuffix tclVar tclvalue tkbutton tkdestroy
  tkframe tkgrid tkgrid.configure tklabel tkpack tktitle<- tktoplevel
  tkwait.window
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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-3.7-bioc/R/library/affy/libs/i386/affy.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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mas5                  22.11   0.07   22.17
MAplot                17.01   0.66   17.82
expresso              12.39   0.09   12.49
read.affybatch         3.61   0.07    5.28
ProgressBarText-class  0.68   0.03   16.68
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mas5                  27.13   0.12   27.25
MAplot                17.05   0.53   17.59
expresso              13.08   0.13   13.21
ProgressBarText-class  0.92   0.01   16.92
* 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-3.7-bioc/meat/affy.Rcheck/00check.log'
for details.



Installation output

affy.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/affy_1.58.0.tar.gz && rm -rf affy.buildbin-libdir && mkdir affy.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affy.buildbin-libdir affy_1.58.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL affy_1.58.0.zip && rm affy_1.58.0.tar.gz affy_1.58.0.zip
###
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  % 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  289k  100  289k    0     0  4786k      0 --:--:-- --:--:-- --:--:-- 5459k

install for i386

* installing *source* package 'affy' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c chipbackground.c -o chipbackground.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c getall_locations.c -o getall_locations.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c mas5calls.c -o mas5calls.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c rma2.c -o rma2.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c rma_common.c -o rma_common.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o affy.dll tmp.def chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/affy.buildbin-libdir/affy/libs/i386
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'affy'
    finding HTML links ... done
    AffyBatch-class                         html  
    finding level-2 HTML links ... done

    AffyRNAdeg                              html  
    MAplot                                  html  
    ProbeSet-class                          html  
    ProgressBarText-class                   html  
    SpikeIn                                 html  
    affy-deprecated                         html  
    affy-options                            html  
    affy.scalevalue.exprSet                 html  
    barplot.ProbeSet                        html  
    bg.adjust                               html  
    bgc                                     html  
    cdfFromBioC                             html  
    cdfenv.example                          html  
    cleancdfname                            html  
    debug.affy123                           html  
    expresso                                html  
    expressoWidget                          html  
    fit.li.wong                             html  
    generateExprSet-methods                 html  
    generateExprVal-methods                 html  
    generateExprVal.method.avgdiff          html  
    generateExprVal.method.playerout        html  
    hlog                                    html  
    justrma                                 html  
    list.celfiles                           html  
    maffy.subset                            html  
    mas5                                    html  
    mas5calls                               html  
    merge.AffyBatch                         html  
    mva.pairs                               html  
    normalize-methods                       html  
    normalize.constant                      html  
    normalize.contrast                      html  
    normalize.invariantset                  html  
    normalize.loess                         html  
    normalize.qspline                       html  
    normalize.quantiles                     html  
    normalize.quantiles.robust              html  
    pairs.AffyBatch                         html  
    plot.ProbeSet                           html  
    plot.density                            html  
    plotLocation                            html  
    pmcorrect                               html  
    ppsetApply                              html  
    probeMatch-methods                      html  
    probeNames-methods                      html  
    read.affybatch                          html  
    read.probematrix                        html  
    rma                                     html  
    setAffyOptions                          html  
    summary                                 html  
    tukey.biweight                          html  
    whatcdf                                 html  
    xy2indices                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'affy' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c chipbackground.c -o chipbackground.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c getall_locations.c -o getall_locations.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c mas5calls.c -o mas5calls.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c rma2.c -o rma2.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c rma_common.c -o rma_common.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o affy.dll tmp.def chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/affy.buildbin-libdir/affy/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affy' as affy_1.58.0.zip
* DONE (affy)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'affy' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

affy.Rcheck/examples_i386/affy-Ex.timings

nameusersystemelapsed
AffyBatch-class3.900.254.16
AffyRNAdeg1.860.061.92
MAplot17.01 0.6617.82
ProbeSet-class0.440.000.44
ProgressBarText-class 0.68 0.0316.68
affy-options000
barplot.ProbeSet0.490.010.50
bgc3.390.053.44
cleancdfname000
expresso12.39 0.0912.49
expressoWidget000
fit.li.wong0.420.020.43
generateExprSet-methods0.470.030.50
generateExprVal-methods0.370.020.46
generateExprVal.method.avgdiff0.320.030.34
list.celfiles000
maffy.subset000
mas522.11 0.0722.17
mas5calls1.310.061.38
mva.pairs0.080.010.09
normalize-methods0.30.00.3
normalize.loess000
plot.ProbeSet0.030.000.03
plot.density0.840.070.91
plotLocation2.580.032.61
pmcorrect0.390.000.39
ppsetApply000
read.affybatch3.610.075.28
rma2.460.032.49
setAffyOptions000
xy2indices2.670.012.69

affy.Rcheck/examples_x64/affy-Ex.timings

nameusersystemelapsed
AffyBatch-class3.540.083.61
AffyRNAdeg2.490.082.56
MAplot17.05 0.5317.59
ProbeSet-class0.340.000.35
ProgressBarText-class 0.92 0.0116.92
affy-options000
barplot.ProbeSet0.370.020.42
bgc2.630.122.75
cleancdfname0.010.000.01
expresso13.08 0.1313.21
expressoWidget000
fit.li.wong0.220.030.25
generateExprSet-methods0.550.000.54
generateExprVal-methods0.440.000.44
generateExprVal.method.avgdiff0.210.000.22
list.celfiles0.020.000.01
maffy.subset000
mas527.13 0.1227.25
mas5calls1.310.041.35
mva.pairs0.090.000.09
normalize-methods0.220.010.24
normalize.loess0.020.000.01
plot.ProbeSet0.030.020.05
plot.density0.500.060.56
plotLocation2.370.142.52
pmcorrect0.280.000.28
ppsetApply0.020.000.01
read.affybatch2.530.122.66
rma2.360.022.38
setAffyOptions000
xy2indices2.720.132.84