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Package 52/553HostnameOS / ArchBUILDCHECKBUILD BIN
beadarray 2.6.0
Mark Dunning
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/beadarray
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: beadarray
Version: 2.6.0
Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings beadarray_2.6.0.tar.gz
StartedAt: 2012-09-23 23:30:32 -0700 (Sun, 23 Sep 2012)
EndedAt: 2012-09-23 23:39:42 -0700 (Sun, 23 Sep 2012)
EllapsedTime: 549.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: beadarray.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/beadarray.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beadarray/DESCRIPTION’ ... OK
* this is package ‘beadarray’ version ‘2.6.0’
* 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 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 for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... OK
* checking R code for possible problems ... NOTE
.onAttach: warning in packageDescription("beadarray", field =
  "Version"): partial argument match of 'field' to 'fields'
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'
processSwathData: warning in assignToImage(t1, an, inputDir = inputDir,
  twocolour = twoColour, locs = locslist, GrnTiffSuffix1 =
  GrnTiffSuffix1, GrnTiffSuffix2 = GrnTiffSuffix2, verbose = verbose):
  partial argument match of 'locs' to 'locslist'
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 installed files from ‘inst/doc’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: ‘opts’ is deprecated.
  Warning: ‘theme_blank’ is deprecated.
  Warning: ‘theme_blank’ is deprecated.
  Warning: ‘theme_blank’ is deprecated.
  Warning: ‘theme_blank’ is deprecated.
  Warning: ‘theme_blank’ is deprecated.
  Warning: ‘theme_blank’ is deprecated.
  Warning: ‘theme_blank’ is deprecated.
  Warning: ‘theme_blank’ is deprecated.
  Warning: ‘theme_blank’ is deprecated.
  Warning: ‘theme_blank’ is deprecated.
  Warning: ‘theme_blank’ is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ call not declared from: ‘gridExtra’
* 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

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/beadarray.Rcheck/00check.log’
for details.

beadarray.Rcheck/00install.out:

* installing *source* package ‘beadarray’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c BASH.c -o BASH.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c HULK.c -o HULK.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c determiningGridPositions.c -o determiningGridPositions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c: In function ‘findBeadStatus’:
findAllOutliers.c:155:9: warning: ‘m’ may be used uninitialized in this function
findAllOutliers.c:155:12: warning: ‘ma’ may be used uninitialized in this function
findAllOutliers.c: In function ‘findAllOutliers’:
findAllOutliers.c:226:20: warning: ‘status’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function ‘illuminaBackground’:
imageProcessing.c:88:0: warning: ignoring #pragma omp parallel
imageProcessing.c: In function ‘medianBackground’:
imageProcessing.c:135:0: warning: ignoring #pragma omp parallel
imageProcessing.c: In function ‘illuminaSharpen’:
imageProcessing.c:244:0: warning: ignoring #pragma omp parallel
imageProcessing.c:251:0: warning: ignoring #pragma omp parallel
gcc -std=gnu99 -shared -L/usr/local/lib64 -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/beadarray.Rcheck/beadarray/libs
** 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
BASHCompact000
BASHDiffuse000
BASHExtended0.0000.0040.000
HULK000
addFeatureData15.545 0.23216.038
annotationInterface11.081 0.46011.572
backgroundCorrectSingleSection000
beadarrayUsersGuide0.0040.0040.006
boxplot5.6080.0605.676
calculateDetection17.661 0.07217.807
calculateOutlierStats23.269 1.42024.864
class-beadLevelData2.6930.1922.917
class-illuminaChannel0.0040.0000.003
combine9.0400.7329.857
controlProbeDetection15.073 0.13615.218
createTargetsFile000
expressionQCPipeline0.0640.0000.063
generateNeighbours000
getBeadData2.8720.0642.936
identifyControlBeads11.893 0.15612.134
illuminaOutlierMethod3.9120.1324.048
imageplot8.5450.1568.793
insertBeadData3.2160.2843.537
insertSectionData13.517 0.40814.003
makeControlProfile0.7720.0040.778
makeQCTable13.325 0.38013.883
medianNormalise2.7720.0322.807
metrics2.0840.0162.101
noOutlierMethod2.1160.0122.128
normaliseIllumina22.478 0.11223.362
numBeads4.4760.0204.495
outlierplot25.605 0.23625.945
plotBeadIntensities4.1690.3244.528
plotBeadLocations2.9960.1163.116
plotChipLayout000
plotMAXY3.1040.0563.182
poscontPlot11.485 0.22411.731
quickSummary11.457 0.30011.760
readBeadSummaryData0.0000.0000.001
sectionNames2.5920.0682.694
showArrayMask9.0600.5769.833
squeezedVarOutlierMethod62.500 0.15663.076
summarize46.863 0.73648.339
transformationFunctions3.9880.2444.261
weightsOutlierMethod000