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BioC 2.12: CHECK report for beadarray on moscato2

This page was generated on 2013-10-09 09:38:15 -0700 (Wed, 09 Oct 2013).

Package 59/671HostnameOS / ArchBUILDCHECKBUILD BIN
beadarray 2.10.0
Mark Dunning
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/beadarray
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: beadarray
Version: 2.10.0
Command: rm -rf beadarray.buildbin-libdir && mkdir beadarray.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=beadarray.buildbin-libdir beadarray_2.10.0.tar.gz >beadarray-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=beadarray.buildbin-libdir --install="check:beadarray-install.out" --force-multiarch --no-vignettes --timings beadarray_2.10.0.tar.gz && mv beadarray.buildbin-libdir/* beadarray.Rcheck/ && rmdir beadarray.buildbin-libdir
StartedAt: 2013-10-09 01:05:20 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:27:04 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 1304.5 seconds
RetCode: 0
Status:  OK  
CheckDir: beadarray.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/beadarray.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'beadarray/DESCRIPTION' ... OK
* this is package 'beadarray' version '2.10.0'
* 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 'beadarray' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    2.6Mb
* checking package 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call with 'PACKAGE' argument in a different package:
  .Call("roundLocsFileValues", ..., PACKAGE = "BeadDataPackR")
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* checking R code for possible problems ... NOTE
expressionQCPipeline: warning in ggsave(im, file = fname.im, width = 4,
  height = 1): partial argument match of 'file' to 'filename'
makeControlProfile: warning in packageDescription(annoPkg, field =
  "Version"): partial argument match of 'field' to 'fields'
plotMAXY: warning in close.screen(all = TRUE): partial argument match
  of 'all' to 'all.screens'
summarize: warning in packageDescription(annoPkg, field = "Version"):
  partial argument match of 'field' to 'fields'
combinedControlPlot: no visible binding for global variable 'Control'
combinedControlPlot: no visible binding for global variable 'Negative'
combinedControlPlot: no visible binding for global variable 'ID'
combinedControlPlot: no visible binding for global variable
  'Log2Intensity'
combinedControlPlot: no visible binding for global variable
  'ControlType'
combinedControlPlot: no visible binding for global variable 'Masked'
getPlatformSigs: no visible global function definition for
  'lumiHumanIDMapping_dbconn'
getPlatformSigs: no visible global function definition for
  'lumiMouseIDMapping_dbconn'
getPlatformSigs: no visible global function definition for
  'lumiRatIDMapping_dbconn'
imageplot: no visible binding for global variable 'Var1'
imageplot: no visible binding for global variable 'Var2'
imageplot: no visible binding for global variable 'value'
* 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 C/C++/Fortran sources/headers ... OK
* checking line endings 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 'E:/biocbld/bbs-2.12-bioc/meat/beadarray.buildbin-libdir/beadarray/libs/i386/beadarray.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-2.12-bioc/meat/beadarray.buildbin-libdir/beadarray/libs/x64/beadarray.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.  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 installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [529s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
squeezedVarOutlierMethod 82.24   0.32   82.55
outlierplot              63.95   0.66   65.46
summarize                53.96   1.06   55.03
calculateOutlierStats    32.20   1.17   33.37
controlProbeDetection    23.56   0.34   23.90
poscontPlot              21.93   0.36   22.32
identifyControlBeads     21.94   0.30   22.23
insertSectionData        21.25   0.45   21.70
makeQCTable              18.99   0.59   19.57
showArrayMask            19.17   0.36   19.53
normaliseIllumina        17.85   0.22   18.08
quickSummary             14.65   0.21   14.86
calculateDetection       14.56   0.25   14.82
addFeatureData           13.51   0.22   14.03
imageplot                13.03   0.27   13.29
annotationInterface       8.88   0.36    9.24
combine                   8.03   0.57    8.59
boxplot                   7.22   0.59    7.83
plotMAXY                  5.49   0.13    5.61
plotBeadIntensities       5.32   0.28    5.60
illuminaOutlierMethod     4.85   0.23    5.08
** running examples for arch 'x64' ... [563s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
squeezedVarOutlierMethod 86.64   0.46   87.16
outlierplot              70.70   0.76   71.48
summarize                58.79   2.27   61.06
calculateOutlierStats    29.73   1.05   31.73
showArrayMask            22.10   0.88   22.98
controlProbeDetection    20.92   0.62   21.57
makeQCTable              20.64   0.69   21.33
poscontPlot              20.84   0.39   21.23
normaliseIllumina        19.97   0.60   20.61
insertSectionData        19.55   0.86   20.45
identifyControlBeads     19.48   0.34   19.84
calculateDetection       18.86   0.23   19.10
addFeatureData           18.33   0.24   18.57
quickSummary             15.55   0.67   16.70
annotationInterface      12.20   0.22   12.42
imageplot                 9.63   0.47   10.09
combine                   8.48   0.69    9.16
boxplot                   8.22   0.52    8.73
plotBeadIntensities       6.63   0.45    7.08
plotMAXY                  5.71   0.23    5.94
illuminaOutlierMethod     5.15   0.42    5.57
transformationFunctions   4.97   0.28    5.24
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/beadarray.Rcheck/00check.log'
for details.

beadarray.Rcheck/00install.out:


install for i386

* installing *source* package 'beadarray' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c BASH.c -o BASH.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c HULK.c -o HULK.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c determiningGridPositions.c -o determiningGridPositions.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c: In function 'findBeadStatus':
findAllOutliers.c:196:29: warning: 'ma' may be used uninitialized in this function [-Wuninitialized]
findAllOutliers.c:196:53: warning: 'm' may be used uninitialized in this function [-Wuninitialized]
findAllOutliers.c: In function 'findAllOutliers':
findAllOutliers.c:247:13: warning: 'status' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function 'illuminaBackground':
imageProcessing.c:88:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
imageProcessing.c: In function 'medianBackground':
imageProcessing.c:135:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
imageProcessing.c: In function 'illuminaSharpen':
imageProcessing.c:244:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
imageProcessing.c:251:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
gcc -m32 -shared -s -static-libgcc -o beadarray.dll tmp.def BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.12-bioc/meat/beadarray.buildbin-libdir/beadarray/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'beadarray' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c BASH.c -o BASH.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c HULK.c -o HULK.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c determiningGridPositions.c -o determiningGridPositions.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c: In function 'findBeadStatus':
findAllOutliers.c:196:29: warning: 'ma' may be used uninitialized in this function [-Wuninitialized]
findAllOutliers.c:196:53: warning: 'm' may be used uninitialized in this function [-Wuninitialized]
findAllOutliers.c: In function 'findAllOutliers':
findAllOutliers.c:247:13: warning: 'status' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function 'illuminaBackground':
imageProcessing.c:88:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
imageProcessing.c: In function 'medianBackground':
imageProcessing.c:135:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
imageProcessing.c: In function 'illuminaSharpen':
imageProcessing.c:244:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
imageProcessing.c:251:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
gcc -m64 -shared -s -static-libgcc -o beadarray.dll tmp.def BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.12-bioc/meat/beadarray.buildbin-libdir/beadarray/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'beadarray' as beadarray_2.10.0.zip
* DONE (beadarray)