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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: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings beadarray_2.8.1.tar.gz
StartedAt: 2013-03-24 23:31:14 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 23:40:04 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 530.3 seconds
RetCode: 0
Status:  OK 
CheckDir: beadarray.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/beadarray.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘2.8.1’
* 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  5.7Mb
  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 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
squeezedVarOutlierMethod 60.668  0.120  61.608
summarize                44.119  0.492  45.730
calculateOutlierStats    22.953  1.024  24.312
outlierplot              22.497  0.060  22.706
calculateDetection       16.937  0.048  17.240
controlProbeDetection    15.397  0.260  16.141
addFeatureData           14.245  0.208  14.750
normaliseIllumina        14.193  0.104  14.542
identifyControlBeads     13.661  0.140  13.902
makeQCTable              12.768  0.372  13.263
poscontPlot              12.681  0.204  13.617
insertSectionData        12.657  0.176  12.889
annotationInterface      10.932  0.836  12.288
quickSummary              8.772  0.148   8.940
showArrayMask             8.173  0.520   9.219
imageplot                 8.409  0.100   8.831
combine                   8.181  0.228   9.416
boxplot                   5.349  0.052   6.159
* 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
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/beadarray.Rcheck/00check.log’
for details.

beadarray.Rcheck/00install.out:

* installing *source* package ‘beadarray’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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-2.11-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-2.11-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-2.11-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: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 -std=gnu99 -I/home/biocbuild/bbs-2.11-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 [-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 -std=gnu99 -shared -L/usr/local/lib64 -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-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
BASH000
BASHCompact000
BASHDiffuse000
BASHExtended000
HULK000
addFeatureData14.245 0.20814.750
annotationInterface10.932 0.83612.288
backgroundCorrectSingleSection000
beadarrayUsersGuide0.0040.0040.019
boxplot5.3490.0526.159
calculateDetection16.937 0.04817.240
calculateOutlierStats22.953 1.02424.312
class-beadLevelData2.8280.0803.129
class-illuminaChannel0.0040.0000.004
combine8.1810.2289.416
controlProbeDetection15.397 0.26016.141
createTargetsFile000
expressionQCPipeline0.0560.0000.068
generateNeighbours000
getBeadData2.5480.0883.027
identifyControlBeads13.661 0.14013.902
illuminaOutlierMethod3.6880.1363.863
imageplot8.4090.1008.831
insertBeadData2.9160.1323.096
insertSectionData12.657 0.17612.889
makeControlProfile0.6720.0200.746
makeQCTable12.768 0.37213.263
medianNormalise2.5890.0122.651
metrics1.9600.0202.018
noOutlierMethod1.9720.0161.995
normaliseIllumina14.193 0.10414.542
numBeads2.6480.0162.675
outlierplot22.497 0.06022.706
plotBeadIntensities3.6970.0643.875
plotBeadLocations2.9920.1003.114
plotChipLayout000
plotMAXY3.0880.0563.211
poscontPlot12.681 0.20413.617
quickSummary8.7720.1488.940
readBeadSummaryData000
sectionNames2.6240.0242.789
showArrayMask8.1730.5209.219
squeezedVarOutlierMethod60.668 0.12061.608
summarize44.119 0.49245.730
transformationFunctions4.4000.0724.504
weightsOutlierMethod000