Package: beadarray

Version: 2.33.2

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:beadarray.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings beadarray_2.33.2.tar.gz

StartedAt: 2019-04-08 22:56:41 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:04:29 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 468.3 seconds

RetCode: 0

Status:  OK

CheckDir: beadarray.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:beadarray.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings beadarray_2.33.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/beadarray.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beadarray/DESCRIPTION’ ... OK
* this is package ‘beadarray’ version ‘2.33.2’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘beadarray’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘hexbin’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘BeadDataPackR:::combineFiles’ ‘BeadDataPackR:::readHeader’
  ‘Biobase:::assayDataStorageMode’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("roundLocsFileValues", ..., PACKAGE = "BeadDataPackR")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
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’
createGEOMeta: no visible binding for global variable ‘metaTemplate’
expressionQCPipeline: no visible global function definition for
  ‘openPage’
expressionQCPipeline: no visible global function definition for
  ‘hwrite’
expressionQCPipeline: no visible global function definition for
  ‘hwriteImage’
expressionQCPipeline: no visible global function definition for
  ‘closePage’
getPlatformSigs: no visible global function definition for
  ‘lumiHumanIDMapping_dbconn’
getPlatformSigs: no visible global function definition for
  ‘dbListTables’
getPlatformSigs: no visible global function definition for
  ‘dbListFields’
getPlatformSigs: no visible global function definition for ‘dbGetQuery’
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’
makeReport: no visible binding for global variable ‘Nozzle.R1’
makeReport: no visible binding for global variable ‘ggbio’
makeReport: no visible global function definition for ‘newCustomReport’
makeReport: no visible global function definition for ‘newSection’
makeReport: no visible global function definition for ‘newTable’
makeReport: no visible global function definition for ‘newParagraph’
makeReport: no visible global function definition for ‘addTo’
makeReport: no visible global function definition for ‘autoplot’
makeReport: no visible global function definition for ‘plotIdeogram’
makeReport: no visible global function definition for ‘tracks’
makeReport: no visible global function definition for ‘newFigure’
makeReport: no visible binding for global variable ‘IMAGE.TYPE.RASTER’
makeReport: no visible binding for global variable ‘PROTECTION.PUBLIC’
makeReport: no visible binding for global variable ‘value’
makeReport: no visible global function definition for ‘writeReport’
maplots: no visible binding for global variable ‘value.1’
maplots: no visible binding for global variable ‘value’
normaliseIllumina: no visible global function definition for ‘lumiT’
normaliseIllumina: no visible global function definition for
  ‘normalize.qspline’
normaliseIllumina: no visible global function definition for ‘vsn2’
plotBeadLocations2: no visible global function definition for ‘qplot’
plotBeadLocations2: no visible global function definition for ‘opts’
plotBeadLocations2: no visible global function definition for
  ‘theme_blank’
plotProbe: no visible global function definition for ‘autoplot’
plotProbe: no visible binding for global variable ‘genesymbol’
plotProbe: no visible global function definition for ‘tracks’
plotProbe: no visible binding for global variable ‘PROBEQUALITY’
rankInvariantNormalise: no visible global function definition for
  ‘normalize.invariantset’
suggestAnnotation: no visible binding for global variable
  ‘platformSigs’
suggestAnnotation_Vector: no visible binding for global variable
  ‘platformSigs’
[,ExpressionSetIllumina-ANY: no visible global function definition for
  ‘assayDataEnvLock’
boxplot,ExpressionSetIllumina: no visible binding for global variable
  ‘Var2’
boxplot,ExpressionSetIllumina: no visible binding for global variable
  ‘value’
plotMA,ExpressionSetIllumina: no visible binding for global variable
  ‘value.1’
plotMA,ExpressionSetIllumina: no visible binding for global variable
  ‘value’
Undefined global functions or variables:
  Control ControlType ID IMAGE.TYPE.RASTER Log2Intensity Masked
  Negative Nozzle.R1 PROBEQUALITY PROTECTION.PUBLIC Var1 Var2 addTo
  assayDataEnvLock autoplot closePage dbGetQuery dbListFields
  dbListTables genesymbol ggbio hwrite hwriteImage
  lumiHumanIDMapping_dbconn lumiMouseIDMapping_dbconn
  lumiRatIDMapping_dbconn lumiT metaTemplate newCustomReport newFigure
  newParagraph newSection newTable normalize.invariantset
  normalize.qspline openPage opts platformSigs plotIdeogram qplot
  theme_blank tracks value value.1 vsn2 writeReport
* 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
squeezedVarOutlierMethod 53.109  0.108  53.389
summarize                28.436  0.324  28.828
limmaDE                  24.692  0.031  24.899
calculateOutlierStats    16.336  0.456  16.792
controlProbeDetection    16.534  0.120  16.666
normaliseIllumina        14.315  0.567  15.068
outlierplot              14.576  0.076  14.685
identifyControlBeads     13.742  0.036  13.782
insertSectionData        13.296  0.292  13.638
makeQCTable              12.949  0.175  13.265
calculateDetection       12.055  0.023  12.083
poscontPlot              11.827  0.016  11.950
quickSummary              9.153  0.052   9.253
imageplot                 8.578  0.028   8.642
annotationInterface       7.118  0.289   7.575
addFeatureData            7.082  0.156   7.847
showArrayMask             6.800  0.140   6.964
maplots                   5.069  0.000   5.097
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/beadarray.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL beadarray
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘beadarray’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c BASH.c -o BASH.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c HULK.c -o HULK.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c determiningGridPositions.c -o determiningGridPositions.o
gcc -I"/home/biocbuild/bbs-3.9-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 [-Wmaybe-uninitialized]
   if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){
                       ˜˜˜˜˜˜^˜˜
findAllOutliers.c:196:53: warning: ‘m’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){
                                                  ˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
findAllOutliers.c: In function ‘findAllOutliers’:
findAllOutliers.c:226:20: warning: ‘status’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  beadStatusStruct *status;
                    ^˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-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]
     #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
 
imageProcessing.c: In function ‘medianBackground’:
imageProcessing.c:135:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
 
imageProcessing.c: In function ‘illuminaSharpen’:
imageProcessing.c:244:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel for private(i, j) shared(sharpened) num_threads(2)
 
imageProcessing.c:251:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel for private(i, j, sum) shared(sharpened) num_threads(2)
 
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-beadarray/00new/beadarray/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (beadarray)

name	user	system	elapsed
BASH	0	0	0
BASHCompact	0.001	0.001	0.000
BASHDiffuse	0.001	0.000	0.000
BASHExtended	0	0	0
GEO	0	0	0
GEOtemplate	0.000	0.002	0.003
HULK	0.000	0.001	0.001
addFeatureData	7.082	0.156	7.847
annotationInterface	7.118	0.289	7.575
backgroundCorrectSingleSection	0.000	0.000	0.001
beadarrayUsersGuide	0.002	0.000	0.003
boxplot	4.542	0.064	4.606
calculateDetection	12.055	0.023	12.083
calculateOutlierStats	16.336	0.456	16.792
class-beadLevelData	2.435	0.088	2.523
class-illuminaChannel	0.000	0.002	0.003
combine	3.447	0.116	3.563
controlProbeDetection	16.534	0.120	16.666
createTargetsFile	0.001	0.000	0.000
expressionQCPipeline	0.030	0.000	0.029
generateNeighbours	0.001	0.000	0.000
getBeadData	3.265	0.036	3.302
identifyControlBeads	13.742	0.036	13.782
illuminaOutlierMethod	3.542	0.104	3.646
imageplot	8.578	0.028	8.642
insertBeadData	4.231	0.148	4.432
insertSectionData	13.296	0.292	13.638
limmaDE	24.692	0.031	24.899
makeControlProfile	0.395	0.004	0.408
makeQCTable	12.949	0.175	13.265
maplots	5.069	0.000	5.097
medianNormalise	2.160	0.012	2.175
metrics	2.642	0.067	2.733
noOutlierMethod	2.638	0.024	2.694
normaliseIllumina	14.315	0.567	15.068
numBeads	2.676	0.068	2.757
outlierplot	14.576	0.076	14.685
plotBeadIntensities	2.792	0.088	2.880
plotBeadLocations	3.641	0.072	3.728
plotChipLayout	0	0	0
plotMAXY	0	0	0
poscontPlot	11.827	0.016	11.950
quickSummary	9.153	0.052	9.253
readBeadSummaryData	0	0	0
sectionNames	2.544	0.027	2.614
showArrayMask	6.800	0.140	6.964
squeezedVarOutlierMethod	53.109	0.108	53.389
summarize	28.436	0.324	28.828
transformationFunctions	3.616	0.132	3.749
weightsOutlierMethod	0	0	0