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CHECK report for affy on tokay1

This page was generated on 2020-10-29 12:24:28 -0400 (Thu, 29 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE affy PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 24/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affy 1.68.0
Rafael A. Irizarry
Snapshot Date: 2020-10-28 14:42:40 -0400 (Wed, 28 Oct 2020)
URL: https://git.bioconductor.org/packages/affy
Branch: RELEASE_3_12
Last Commit: 1664399
Last Changed Date: 2020-10-27 10:22:11 -0400 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: affy
Version: 1.68.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affy.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings affy_1.68.0.tar.gz
StartedAt: 2020-10-29 00:09:01 -0400 (Thu, 29 Oct 2020)
EndedAt: 2020-10-29 00:14:50 -0400 (Thu, 29 Oct 2020)
EllapsedTime: 348.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: affy.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affy.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings affy_1.68.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/affy.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.68.0'
* 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
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.
* 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 ... OK
* 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 use of PKG_*FLAGS in Makefiles ... 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-3.12-bioc/R/library/affy/libs/i386/affy.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/affy/libs/x64/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 (user + system) or elapsed time > 5s
                       user system elapsed
mas5                  24.19   0.11   24.31
MAplot                17.78   0.53   18.87
expresso              10.28   0.22   15.69
bgc                    5.85   0.20    6.53
read.affybatch         2.59   0.01    6.70
ProgressBarText-class  0.65   0.02   16.64
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
mas5                  29.08   0.06   29.14
MAplot                14.39   0.41   14.79
expresso              10.94   0.12   11.06
bgc                    5.25   0.17    5.42
fit.li.wong            5.13   0.06    5.19
ProgressBarText-class  0.82   0.01   16.81
* 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-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://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/affy_1.68.0.tar.gz && rm -rf affy.buildbin-libdir && mkdir affy.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affy.buildbin-libdir affy_1.68.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL affy_1.68.0.zip && rm affy_1.68.0.tar.gz affy_1.68.0.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  283k  100  283k    0     0  2249k      0 --:--:-- --:--:-- --:--:-- 2346k

install for i386

* installing *source* package 'affy' ...
** using staged installation

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


** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c chipbackground.c -o chipbackground.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getall_locations.c -o getall_locations.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mas5calls.c -o mas5calls.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma2.c -o rma2.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma_common.c -o rma_common.o
C:/rtools40/mingw32/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-3.12-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/affy.buildbin-libdir/00LOCK-affy/00new/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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

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

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


** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c chipbackground.c -o chipbackground.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getall_locations.c -o getall_locations.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mas5calls.c -o mas5calls.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma2.c -o rma2.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma_common.c -o rma_common.o
C:/rtools40/mingw64/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-3.12-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/affy.buildbin-libdir/affy/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affy' as affy_1.68.0.zip
* DONE (affy)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'affy' successfully unpacked and MD5 sums checked

Tests output


Example timings

affy.Rcheck/examples_i386/affy-Ex.timings

nameusersystemelapsed
AffyBatch-class3.370.363.73
AffyRNAdeg1.680.071.75
MAplot17.78 0.5318.87
ProbeSet-class0.550.010.56
ProgressBarText-class 0.65 0.0216.64
affy-options000
barplot.ProbeSet0.940.030.97
bgc5.850.206.53
cleancdfname000
expresso10.28 0.2215.69
expressoWidget000
fit.li.wong4.780.064.84
generateExprSet-methods0.360.020.38
generateExprVal-methods0.360.000.43
generateExprVal.method.avgdiff0.220.140.36
list.celfiles000
maffy.subset000
mas524.19 0.1124.31
mas5calls1.560.041.61
mva.pairs0.090.000.09
normalize-methods0.320.000.32
normalize.loess000
plot.ProbeSet0.010.000.01
plot.density0.580.020.60
plotLocation2.310.032.34
pmcorrect0.290.020.30
ppsetApply000
read.affybatch2.590.016.70
rma2.340.002.34
setAffyOptions000
xy2indices2.890.092.99

affy.Rcheck/examples_x64/affy-Ex.timings

nameusersystemelapsed
AffyBatch-class2.960.173.12
AffyRNAdeg2.140.032.17
MAplot14.39 0.4114.79
ProbeSet-class0.280.020.30
ProgressBarText-class 0.82 0.0116.81
affy-options000
barplot.ProbeSet0.630.020.64
bgc5.250.175.42
cleancdfname0.010.000.02
expresso10.94 0.1211.06
expressoWidget000
fit.li.wong5.130.065.19
generateExprSet-methods0.360.000.36
generateExprVal-methods0.390.020.41
generateExprVal.method.avgdiff0.320.030.36
list.celfiles000
maffy.subset0.020.000.01
mas529.08 0.0629.14
mas5calls1.620.021.64
mva.pairs0.110.000.11
normalize-methods0.330.030.36
normalize.loess0.020.000.02
plot.ProbeSet0.010.000.01
plot.density0.810.030.85
plotLocation2.710.082.78
pmcorrect0.510.010.53
ppsetApply000
read.affybatch3.330.073.39
rma3.080.033.11
setAffyOptions000
xy2indices3.370.123.50