Back to the "Multiple platform build/check report" A [B] C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 49/467HostnameOS / ArchBUILDCHECKBUILD BIN
beadarray 2.2.0
Mark Dunning
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/beadarray
Last Changed Rev: 55866 / Revision: 59457
Last Changed Date: 2011-05-27 08:12:50 -0700 (Fri, 27 May 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: beadarray
Version: 2.2.0
Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch beadarray_2.2.0.tar.gz
StartedAt: 2011-10-20 14:08:29 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 14:12:09 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 219.4 seconds
RetCode: 0
Status:  OK  
CheckDir: beadarray.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/beadarray.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'beadarray/DESCRIPTION' ... OK
* this is package 'beadarray' version '2.2.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'beadarray' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 14.6Mb
  sub-directories of 1Mb or more:
    data      7.0Mb
    doc       3.3Mb
    extdata   4.0Mb
* checking package directory ... OK
* checking for portable file names ... 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
checkPlatform: no visible binding for global variable 'platformSigs'
makeControlProfile: no visible binding for global variable
  'ExpressionControlData'
poscontPlot: no visible binding for global variable
  'ExpressionControlData'
quickSummary: no visible binding for global variable
  'ExpressionControlData'
setAnnotation: no visible binding for global variable
  'ExpressionControlData'
showArrayMask: no visible binding for global variable 'SAM'
summarize: no visible binding for global variable
  'ExpressionControlData'
viewBeads: no visible global function definition for 'getArrayData'
* 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 examples ... OK
* 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

beadarray.Rcheck/00install.out:

* installing *source* package 'beadarray' ...
** libs
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c BASH.c -o BASH.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c HULK.c -o HULK.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c determiningGridPositions.c -o determiningGridPositions.o
determiningGridPositions.c: In function 'roundLocsFileValues':
determiningGridPositions.c:7:12: warning: unused variable 'vecLength'
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -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 -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function 'illuminaBackground':
imageProcessing.c:82:0: warning: ignoring #pragma omp parallel
imageProcessing.c: In function 'medianBackground':
imageProcessing.c:126:0: warning: ignoring #pragma omp parallel
imageProcessing.c: In function 'illuminaSharpen':
imageProcessing.c:224:0: warning: ignoring #pragma omp parallel
imageProcessing.c:231:0: warning: ignoring #pragma omp parallel
gcc -shared -s -static-libgcc -o beadarray.dll tmp.def BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -LE:/biocbld/BBS-2˜1.8-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.8-bioc/meat/beadarray.Rcheck/beadarray/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "boxplot" in "beadarray"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Welcome to beadarray version 2.2.0
There have been major changes to beadarray since Bioconductor 2.6 (April 2010). Please see package vignette for details

* DONE (beadarray)

beadarray.Rcheck/beadarray-Ex.timings:

nameusersystemelapsed
BASH000
BASHCompact4.510.068.15
BASHDiffuse6.130.056.35
BASHExtended 7.06 0.0211.07
ExpressionControlData0.030.000.07
HULK6.440.039.81
backgroundCorrectSingleSection2.920.084.50
beadStatusVector2.330.002.37
beadarrayUsersGuide0.010.000.02
calculateDetection0.140.000.14
calculateOutlierStats3.600.013.69
class-beadLevelData2.310.002.34
class-illuminaChannel5.340.025.61
combine2.910.042.95
controlProbeDetection2.660.042.71
controlProfile0.010.000.01
createTargetsFile000
expressionQCPipeline2.200.032.24
generateNeighbours2.520.012.53
getBeadData2.220.032.26
illuminaOutlierMethod2.280.042.38
imageplot6.340.016.39
insertSectionData2.880.062.94
makeQCTable2.920.073.01
medianNormalise0.080.000.08
normaliseIllumina4.340.144.53
numBeads3.440.043.48
outlierplot4.260.054.33
plotBeadIntensities2.770.062.82
plotBeadLocations2.400.002.41
plotChipLayout000
plotMAXY000
poscontPlot2.770.022.80
quickSummary2.410.012.42
readBeadSummaryData000
sectionNames2.310.042.36
showArrayMask8.620.068.75
summarize5.990.086.15
transformationFunctions2.360.042.41