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This page was generated on 2022-01-14 13:05:58 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for affy on tokay2


To the developers/maintainers of the affy package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/affy.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 23/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affy 1.72.0  (landing page)
Rafael A. Irizarry
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/affy
git_branch: RELEASE_3_14
git_last_commit: 3750b4e
git_last_commit_date: 2021-10-26 11:45:47 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: affy
Version: 1.72.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affy.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings affy_1.72.0.tar.gz
StartedAt: 2022-01-13 15:15:03 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 15:19:40 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 277.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: affy.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affy.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings affy_1.72.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/affy.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.72.0'
* 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-3.14-bioc/R/library/affy/libs/i386/affy.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/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                  20.51   0.09   20.61
MAplot                14.00   0.39   14.65
expresso               9.20   0.15    9.34
bgc                    6.84   0.13    6.97
read.affybatch         4.14   0.08    5.84
ProgressBarText-class  0.97   0.03   16.98
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
mas5                  22.08   0.05   22.14
MAplot                14.28   0.62   14.92
expresso              10.41   0.06   10.47
AffyBatch-class        5.60   0.16    5.75
bgc                    5.08   0.14    5.23
ProgressBarText-class  0.94   0.02   16.95
* 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-3.14-bioc/meat/affy.Rcheck/00check.log'
for details.



Installation output

affy.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/affy_1.72.0.tar.gz && rm -rf affy.buildbin-libdir && mkdir affy.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affy.buildbin-libdir affy_1.72.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL affy_1.72.0.zip && rm affy_1.72.0.tar.gz affy_1.72.0.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
 79  285k   79  226k    0     0  1246k      0 --:--:-- --:--:-- --:--:-- 1244k
100  285k  100  285k    0     0  1379k      0 --:--:-- --:--:-- --:--:-- 1378k

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-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/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"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/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"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/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"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/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"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/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 -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/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"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/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"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/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"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/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"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/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"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/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 -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/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_1.72.0.zip
* DONE (affy)
* installing to library 'C:/Users/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-class3.890.224.11
AffyRNAdeg1.500.141.64
MAplot14.00 0.3914.65
ProbeSet-class0.260.070.33
ProgressBarText-class 0.97 0.0316.98
affy-options000
barplot.ProbeSet0.710.010.72
bgc6.840.136.97
cleancdfname000
expresso9.200.159.34
expressoWidget000
fit.li.wong3.640.044.38
generateExprSet-methods0.630.050.67
generateExprVal-methods0.420.050.84
generateExprVal.method.avgdiff0.640.060.71
list.celfiles000
maffy.subset0.020.000.01
mas520.51 0.0920.61
mas5calls1.250.081.33
mva.pairs0.080.000.08
normalize-methods0.260.000.27
normalize.loess000
plot.ProbeSet0.030.000.03
plot.density0.890.060.96
plotLocation2.460.062.51
pmcorrect0.280.030.32
ppsetApply000
read.affybatch4.140.085.84
rma2.400.022.42
setAffyOptions000
xy2indices3.080.043.13

affy.Rcheck/examples_x64/affy-Ex.timings

nameusersystemelapsed
AffyBatch-class5.600.165.75
AffyRNAdeg1.810.081.89
MAplot14.28 0.6214.92
ProbeSet-class0.340.030.38
ProgressBarText-class 0.94 0.0216.95
affy-options000
barplot.ProbeSet0.620.020.64
bgc5.080.145.23
cleancdfname0.000.010.02
expresso10.41 0.0610.47
expressoWidget000
fit.li.wong4.360.084.44
generateExprSet-methods0.320.020.34
generateExprVal-methods0.270.030.30
generateExprVal.method.avgdiff0.160.010.17
list.celfiles000
maffy.subset0.010.000.01
mas522.08 0.0522.14
mas5calls1.520.051.57
mva.pairs0.090.010.11
normalize-methods0.390.000.39
normalize.loess0.010.000.02
plot.ProbeSet0.010.000.02
plot.density1.030.041.06
plotLocation2.500.062.56
pmcorrect0.270.010.29
ppsetApply000
read.affybatch2.730.082.81
rma2.190.002.19
setAffyOptions000
xy2indices2.660.172.82