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Package 55/609HostnameOS / ArchBUILDCHECKBUILD BIN
beadarray 2.8.1
Mark Dunning
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/beadarray
Last Changed Rev: 70288 / Revision: 74773
Last Changed Date: 2012-10-08 13:39:30 -0700 (Mon, 08 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: beadarray
Version: 2.8.1
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch beadarray_2.8.1.tar.gz
StartedAt: 2013-03-24 22:39:07 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 22:49:45 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 637.9 seconds
RetCode: 0
Status:  OK 
CheckDir: beadarray.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/beadarray.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'beadarray/DESCRIPTION' ... OK
* this is package 'beadarray' version '2.8.1'
* 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 whether package 'beadarray' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    2.6Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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
* 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 ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
squeezedVarOutlierMethod 71.037  2.012  73.747
summarize                47.406  8.531  57.352
outlierplot              27.588  3.145  31.522
calculateOutlierStats    21.262  5.303  27.220
normaliseIllumina        14.577  3.449  18.866
calculateDetection       15.027  1.027  16.288
poscontPlot              13.886  2.146  16.848
makeQCTable              12.018  3.501  16.465
addFeatureData           14.200  0.889  20.386
controlProbeDetection    12.855  2.157  15.766
insertSectionData        11.629  3.367  15.825
showArrayMask            10.642  2.976  13.858
quickSummary             10.345  1.983  12.504
identifyControlBeads     11.095  0.903  12.497
combine                   8.918  2.576  12.173
annotationInterface      10.138  1.331  11.969
imageplot                 8.634  2.211  11.235
boxplot                   6.597  2.226  10.231
plotBeadIntensities       5.119  1.428   6.679
transformationFunctions   4.359  1.515   6.669
illuminaOutlierMethod     4.309  1.330   5.856
plotMAXY                  4.326  1.302   6.809
insertBeadData            3.778  1.206   5.267
plotBeadLocations         3.764  1.027   5.159
* 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 3 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/beadarray.Rcheck/00check.log'
for details.

beadarray.Rcheck/00install.out:

* installing *source* package 'beadarray' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c BASH.c -o BASH.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c HULK.c -o HULK.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c determiningGridPositions.c -o determiningGridPositions.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c: In function 'findBeadStatus':
findAllOutliers.c:155: warning: 'ma' may be used uninitialized in this function
findAllOutliers.c:155: warning: 'm' may be used uninitialized in this function
findAllOutliers.c: In function 'findAllOutliers':
findAllOutliers.c:226: warning: 'status' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function 'illuminaBackground':
imageProcessing.c:88: warning: ignoring #pragma omp parallel
imageProcessing.c: In function 'medianBackground':
imageProcessing.c:135: warning: ignoring #pragma omp parallel
imageProcessing.c: In function 'illuminaSharpen':
imageProcessing.c:244: warning: ignoring #pragma omp parallel
imageProcessing.c:251: warning: ignoring #pragma omp parallel
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/beadarray.Rcheck/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
   'ImageProcessing.rnw' 
   'beadarray.rnw' 
   'beadlevel.rnw' 
   'beadsummary.rnw' 
** testing if installed package can be loaded

* DONE (beadarray)

beadarray.Rcheck/beadarray-Ex.timings:

nameusersystemelapsed
BASH0.0000.0000.001
BASHCompact0.0000.0010.000
BASHDiffuse0.0000.0000.001
BASHExtended0.0000.0000.001
HULK0.0000.0010.001
addFeatureData14.200 0.88920.386
annotationInterface10.138 1.33111.969
backgroundCorrectSingleSection0.0000.0000.001
beadarrayUsersGuide0.0050.0040.010
boxplot 6.597 2.22610.231
calculateDetection15.027 1.02716.288
calculateOutlierStats21.262 5.30327.220
class-beadLevelData3.4490.8254.592
class-illuminaChannel0.0030.0000.003
combine 8.918 2.57612.173
controlProbeDetection12.855 2.15715.766
createTargetsFile000
expressionQCPipeline0.0520.0060.063
generateNeighbours000
getBeadData3.4530.6994.342
identifyControlBeads11.095 0.90312.497
illuminaOutlierMethod4.3091.3305.856
imageplot 8.634 2.21111.235
insertBeadData3.7781.2065.267
insertSectionData11.629 3.36715.825
makeControlProfile0.7960.0570.873
makeQCTable12.018 3.50116.465
medianNormalise2.7961.0524.162
metrics3.1620.4784.142
noOutlierMethod2.8770.3913.596
normaliseIllumina14.577 3.44918.866
numBeads4.0850.4194.850
outlierplot27.588 3.14531.522
plotBeadIntensities5.1191.4286.679
plotBeadLocations3.7641.0275.159
plotChipLayout0.0010.0010.000
plotMAXY4.3261.3026.809
poscontPlot13.886 2.14616.848
quickSummary10.345 1.98312.504
readBeadSummaryData0.0000.0010.000
sectionNames3.3630.4694.014
showArrayMask10.642 2.97613.858
squeezedVarOutlierMethod71.037 2.01273.747
summarize47.406 8.53157.352
transformationFunctions4.3591.5156.669
weightsOutlierMethod000