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CHECK report for affy on riesling1

This page was generated on 2020-10-28 13:27:29 -0400 (Wed, 28 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: 2020-10-27 13:12:07 -0400 (Tue, 27 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 YES, new version is higher than 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 YES, new version is higher than in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ WARNINGS ] OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK YES, new version is higher than in internal repository

Summary

Package: affy
Version: 1.68.0
Command: D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affy.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings affy_1.68.0.tar.gz
StartedAt: 2020-10-27 20:01:07 -0400 (Tue, 27 Oct 2020)
EndedAt: 2020-10-27 20:06:06 -0400 (Tue, 27 Oct 2020)
EllapsedTime: 299.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: affy.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affy.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings affy_1.68.0.tar.gz
###
##############################################################################
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* using log directory 'D:/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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* 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 'D:/biocbuild/bbs-3.12-bioc/R/library/affy/libs/i386/affy.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/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                  13.89   0.08   13.97
MAplot                10.79   0.50   11.31
expresso               8.69   0.16    8.84
bgc                    4.99   0.35    5.34
ProgressBarText-class  0.53   0.04   16.54
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
mas5                  12.81   0.05   12.86
MAplot                10.33   0.39   10.73
expresso               7.04   0.10    7.13
ProgressBarText-class  0.52   0.03   16.53
* 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
  'D:/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 http://172.29.0.3/BBS/3.12/bioc/src/contrib/affy_1.68.0.tar.gz && rm -rf affy.buildbin-libdir && mkdir affy.buildbin-libdir && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affy.buildbin-libdir affy_1.68.0.tar.gz && D:\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
###
##############################################################################
##############################################################################


  % 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  4237k      0 --:--:-- --:--:-- --:--:-- 4237k

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"D:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/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"D:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/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"D:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/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"D:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/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"D:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/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 -LD:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.12-bioc/R/bin/i386 -lR
installing to D:/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"D:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/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"D:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/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"D:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/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"D:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/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"D:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/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 -LD:/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.12-bioc/R/bin/x64 -lR
installing to D:/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 'D:/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-class2.000.062.06
AffyRNAdeg0.970.020.98
MAplot10.79 0.5011.31
ProbeSet-class0.360.050.41
ProgressBarText-class 0.53 0.0416.54
affy-options000
barplot.ProbeSet0.430.040.50
bgc4.990.355.34
cleancdfname0.000.020.02
expresso8.690.168.84
expressoWidget000
fit.li.wong3.420.093.53
generateExprSet-methods0.400.000.41
generateExprVal-methods0.350.020.37
generateExprVal.method.avgdiff0.180.060.25
list.celfiles000
maffy.subset0.010.000.01
mas513.89 0.0813.97
mas5calls1.230.031.27
mva.pairs0.090.000.09
normalize-methods0.20.00.2
normalize.loess0.020.000.02
plot.ProbeSet0.000.000.01
plot.density0.580.010.59
plotLocation1.820.081.91
pmcorrect0.180.030.21
ppsetApply000
read.affybatch1.710.021.75
rma1.690.011.70
setAffyOptions000
xy2indices2.050.132.17

affy.Rcheck/examples_x64/affy-Ex.timings

nameusersystemelapsed
AffyBatch-class2.110.112.22
AffyRNAdeg1.200.051.25
MAplot10.33 0.3910.73
ProbeSet-class0.180.030.22
ProgressBarText-class 0.52 0.0316.53
affy-options000
barplot.ProbeSet0.420.020.54
bgc3.690.063.77
cleancdfname0.010.000.01
expresso7.040.107.13
expressoWidget000
fit.li.wong2.900.073.00
generateExprSet-methods0.220.000.22
generateExprVal-methods0.220.000.22
generateExprVal.method.avgdiff0.120.000.13
list.celfiles000
maffy.subset0.020.000.01
mas512.81 0.0512.86
mas5calls0.780.030.81
mva.pairs0.070.000.06
normalize-methods0.150.000.15
normalize.loess000
plot.ProbeSet0.020.000.01
plot.density0.530.030.58
plotLocation1.190.111.31
pmcorrect0.200.020.22
ppsetApply000
read.affybatch1.520.011.53
rma1.590.041.62
setAffyOptions000
xy2indices1.560.071.64