BioC 2.11: CHECK report for beadarray on lamb1

* 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.

* 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)

name	user	system	elapsed
BASH	0	0	0
BASHCompact	0	0	0
BASHDiffuse	0	0	0
BASHExtended	0	0	0
HULK	0	0	0
addFeatureData	14.245	0.208	14.750
annotationInterface	10.932	0.836	12.288
backgroundCorrectSingleSection	0	0	0
beadarrayUsersGuide	0.004	0.004	0.019
boxplot	5.349	0.052	6.159
calculateDetection	16.937	0.048	17.240
calculateOutlierStats	22.953	1.024	24.312
class-beadLevelData	2.828	0.080	3.129
class-illuminaChannel	0.004	0.000	0.004
combine	8.181	0.228	9.416
controlProbeDetection	15.397	0.260	16.141
createTargetsFile	0	0	0
expressionQCPipeline	0.056	0.000	0.068
generateNeighbours	0	0	0
getBeadData	2.548	0.088	3.027
identifyControlBeads	13.661	0.140	13.902
illuminaOutlierMethod	3.688	0.136	3.863
imageplot	8.409	0.100	8.831
insertBeadData	2.916	0.132	3.096
insertSectionData	12.657	0.176	12.889
makeControlProfile	0.672	0.020	0.746
makeQCTable	12.768	0.372	13.263
medianNormalise	2.589	0.012	2.651
metrics	1.960	0.020	2.018
noOutlierMethod	1.972	0.016	1.995
normaliseIllumina	14.193	0.104	14.542
numBeads	2.648	0.016	2.675
outlierplot	22.497	0.060	22.706
plotBeadIntensities	3.697	0.064	3.875
plotBeadLocations	2.992	0.100	3.114
plotChipLayout	0	0	0
plotMAXY	3.088	0.056	3.211
poscontPlot	12.681	0.204	13.617
quickSummary	8.772	0.148	8.940
readBeadSummaryData	0	0	0
sectionNames	2.624	0.024	2.789
showArrayMask	8.173	0.520	9.219
squeezedVarOutlierMethod	60.668	0.120	61.608
summarize	44.119	0.492	45.730
transformationFunctions	4.400	0.072	4.504
weightsOutlierMethod	0	0	0

Summary

Command output