Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-18 12:03:57 -0400 (Mon, 18 Oct 2021).

CHECK results for affy on riesling1

To the developers/maintainers of the affy package:
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raw results

Package 23/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affy 1.71.0  (landing page)
Rafael A. Irizarry
Snapshot Date: 2021-10-17 14:50:03 -0400 (Sun, 17 Oct 2021)
git_url: https://git.bioconductor.org/packages/affy
git_branch: master
git_last_commit: 0e374ba
git_last_commit_date: 2021-05-19 11:32:58 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: affy
Version: 1.71.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affy.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings affy_1.71.0.tar.gz
StartedAt: 2021-10-17 23:48:04 -0400 (Sun, 17 Oct 2021)
EndedAt: 2021-10-17 23:53:07 -0400 (Sun, 17 Oct 2021)
EllapsedTime: 303.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: affy.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affy.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings affy_1.71.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/affy.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.71.0'
* 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 'D:/biocbuild/bbs-3.14-bioc/R/library/affy/libs/i386/affy.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbuild/bbs-3.14-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                  16.78   0.12   16.90
MAplot                13.97   0.58   14.61
expresso               8.05   0.08    8.13
bgc                    4.96   0.17    5.14
ProgressBarText-class  0.73   0.05   16.28
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
mas5                  13.22   0.08   13.30
MAplot                12.00   0.54   12.64
expresso               7.25   0.05    7.29
ProgressBarText-class  0.80   0.02   16.35
* 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
  'D:/biocbuild/bbs-3.14-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://155.52.207.166/BBS/3.14/bioc/src/contrib/affy_1.71.0.tar.gz && rm -rf affy.buildbin-libdir && mkdir affy.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affy.buildbin-libdir affy_1.71.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL affy_1.71.0.zip && rm affy_1.71.0.tar.gz affy_1.71.0.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
 13  285k   13 40437    0     0   259k      0  0:00:01 --:--:--  0:00:01  258k
100  285k  100  285k    0     0  1251k      0 --:--:-- --:--:-- --:--:-- 1246k

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-3.14-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/biocbuild/bbs-3.14-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-3.14-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/biocbuild/bbs-3.14-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-3.14-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/biocbuild/bbs-3.14-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-3.14-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/biocbuild/bbs-3.14-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-3.14-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/biocbuild/bbs-3.14-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-3.14-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.14-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-3.14-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/biocbuild/bbs-3.14-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-3.14-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/biocbuild/bbs-3.14-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-3.14-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/biocbuild/bbs-3.14-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-3.14-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/biocbuild/bbs-3.14-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-3.14-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DHAVE_ZLIB -I'D:/biocbuild/bbs-3.14-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-3.14-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/affy.buildbin-libdir/affy/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affy' as affy_1.71.0.zip
* DONE (affy)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'affy' successfully unpacked and MD5 sums checked

Tests output


Example timings

affy.Rcheck/examples_i386/affy-Ex.timings

nameusersystemelapsed
AffyBatch-class2.940.143.08
AffyRNAdeg1.750.081.83
MAplot13.97 0.5814.61
ProbeSet-class0.300.010.31
ProgressBarText-class 0.73 0.0516.28
affy-options000
barplot.ProbeSet0.610.020.62
bgc4.960.175.14
cleancdfname000
expresso8.050.088.13
expressoWidget000
fit.li.wong3.500.063.57
generateExprSet-methods0.260.000.26
generateExprVal-methods0.280.010.30
generateExprVal.method.avgdiff0.410.020.42
list.celfiles000
maffy.subset0.020.000.02
mas516.78 0.1216.90
mas5calls0.870.070.94
mva.pairs0.060.000.06
normalize-methods0.210.000.21
normalize.loess000
plot.ProbeSet0.010.000.01
plot.density0.720.040.77
plotLocation1.600.101.69
pmcorrect0.150.040.20
ppsetApply000
read.affybatch2.220.132.37
rma1.780.001.78
setAffyOptions000
xy2indices1.890.172.07

affy.Rcheck/examples_x64/affy-Ex.timings

nameusersystemelapsed
AffyBatch-class3.220.163.37
AffyRNAdeg1.370.111.48
MAplot12.00 0.5412.64
ProbeSet-class0.300.020.31
ProgressBarText-class 0.80 0.0216.35
affy-options000
barplot.ProbeSet0.480.000.48
bgc4.380.204.60
cleancdfname000
expresso7.250.057.29
expressoWidget0.010.000.02
fit.li.wong2.940.063.00
generateExprSet-methods0.200.010.22
generateExprVal-methods0.210.000.20
generateExprVal.method.avgdiff0.110.020.13
list.celfiles000
maffy.subset0.010.000.01
mas513.22 0.0813.30
mas5calls1.050.001.05
mva.pairs0.090.000.09
normalize-methods0.130.010.14
normalize.loess000
plot.ProbeSet0.020.000.01
plot.density0.610.050.66
plotLocation1.250.111.36
pmcorrect0.160.020.17
ppsetApply000
read.affybatch1.780.031.82
rma1.530.031.56
setAffyOptions000
xy2indices1.580.111.69