Multiple platform build/check report for BioC 3.6 - CHECK report for beadarray on malbec1

Package: beadarray

Version: 2.28.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings beadarray_2.28.0.tar.gz

StartedAt: 2018-04-11 21:42:17 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 21:48:50 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 393.0 seconds

RetCode: 0

Status: OK

CheckDir: beadarray.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings beadarray_2.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/beadarray.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘2.28.0’
* 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 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
'library' or 'require' calls in package code:
  ‘Nozzle.R1’ ‘affy’ ‘ggbio’ ‘hwriter’ ‘lumi’ ‘vsn’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘ggplot2’ ‘methods’
  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.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘illuminaForeground_6x6’ ‘locsIndicesToGrid’ ‘obtainLocs’
  ‘simpleXMLparse’
* 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
.mergePhenodata: no visible global function definition for ‘new’
.onAttach: no visible global function definition for
  ‘packageDescription’
addFeatureData: no visible global function definition for ‘is’
addFeatureData: no visible global function definition for ‘new’
analyseDirectory: no visible global function definition for
  ‘read.table’
calculateDetection: no visible global function definition for
  ‘txtProgressBar’
calculateDetection: no visible global function definition for
  ‘setTxtProgressBar’
checkRegistration: no visible global function definition for ‘new’
combinedControlPlot: no visible binding for global variable ‘Control’
combinedControlPlot: no visible binding for global variable ‘Negative’
combinedControlPlot: no visible global function definition for
  ‘density’
combinedControlPlot: no visible global function definition for ‘ggplot’
combinedControlPlot: no visible global function definition for ‘aes’
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 global function definition for
  ‘geom_boxplot’
combinedControlPlot: no visible global function definition for
  ‘geom_hline’
combinedControlPlot: no visible global function definition for
  ‘facet_wrap’
combinedControlPlot: no visible global function definition for
  ‘geom_point’
combinedControlPlot: no visible binding for global variable ‘Masked’
convertBeadLevelList: no visible global function definition for ‘new’
createGEOMatrix: no visible global function definition for
  ‘write.table’
createGEOMeta: no visible global function definition for ‘data’
createGEOMeta: no visible binding for global variable ‘metaTemplate’
createTargetsFile: no visible global function definition for
  ‘read.table’
expressionQCPipeline: no visible global function definition for
  ‘ggsave’
expressionQCPipeline: no visible global function definition for ‘jpeg’
expressionQCPipeline: no visible global function definition for ‘pdf’
expressionQCPipeline: no visible global function definition for ‘png’
expressionQCPipeline: no visible global function definition for
  ‘dev.off’
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’
expressionQCPipeline: no visible global function definition for
  ‘write.csv’
generateE: no visible global function definition for ‘aggregate’
genericBeadIntensityPlot: no visible global function definition for
  ‘runif’
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 global function definition for ‘ggplot’
imageplot: no visible global function definition for ‘aes’
imageplot: no visible binding for global variable ‘Var1’
imageplot: no visible binding for global variable ‘Var2’
imageplot: no visible binding for global variable ‘value’
imageplot: no visible global function definition for ‘geom_tile’
imageplot: no visible global function definition for
  ‘scale_fill_gradient’
imageplot: no visible global function definition for ‘theme’
imageplot: no visible global function definition for ‘element_blank’
limmaDE: no visible global function definition for ‘model.matrix’
limmaDE: no visible global function definition for ‘new’
makeControlProfile: no visible global function definition for
  ‘packageDescription’
makeReport: no visible global function definition for ‘as’
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 ‘ggsave’
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 global function definition for ‘ggplot’
makeReport: no visible global function definition for ‘aes’
makeReport: no visible binding for global variable ‘value’
makeReport: no visible global function definition for ‘geom_boxplot’
makeReport: no visible global function definition for ‘facet_wrap’
makeReport: no visible global function definition for ‘writeReport’
maplots: no visible global function definition for ‘ggplot’
maplots: no visible global function definition for ‘aes’
maplots: no visible binding for global variable ‘value.1’
maplots: no visible binding for global variable ‘value’
maplots: no visible global function definition for ‘stat_binhex’
maplots: no visible global function definition for ‘theme_bw’
maplots: no visible global function definition for ‘xlab’
maplots: no visible global function definition for ‘ylab’
maplots: no visible global function definition for ‘facet_wrap’
maplots: no visible global function definition for ‘theme’
maplots: no visible global function definition for ‘ggtitle’
normaliseIllumina: no visible global function definition for ‘new’
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’
normaliseIllumina: no visible global function definition for ‘rsn’
numberOfChannels: no visible global function definition for
  ‘read.table’
numberOfColumns: no visible global function definition for ‘read.table’
outlierplot2: no visible global function definition for ‘geom_vline’
outlierplot2: no visible global function definition for ‘geom_hline’
plot.smooth.line: no visible global function definition for ‘approx’
plot.smooth.line: no visible global function definition for ‘lowess’
plotBeadIntensities: no visible global function definition for
  ‘rainbow’
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’
plotChipLayout: no visible global function definition for ‘rgb’
plotProbe: no visible global function definition for ‘data’
plotProbe: no visible binding for global variable ‘genesymbol’
plotProbe: no visible global function definition for ‘autoplot’
plotProbe: no visible global function definition for ‘tracks’
plotProbe: no visible global function definition for ‘aes’
plotProbe: no visible binding for global variable ‘PROBEQUALITY’
plotTIFF: no visible global function definition for ‘col2rgb’
plotTIFF: no visible global function definition for ‘rgb’
poscontPlot: no visible global function definition for ‘rainbow’
rankInvariantNormalise: no visible global function definition for
  ‘normalize.invariantset’
rankInvariantNormalise: no visible global function definition for
  ‘predict’
readBeadSummaryData: no visible global function definition for
  ‘read.table’
readBeadSummaryData: no visible global function definition for ‘new’
readIdatFiles: no visible global function definition for ‘new’
readIllumina: no visible global function definition for ‘new’
readQC: no visible global function definition for ‘read.table’
readQC: no visible global function definition for ‘new’
readSampleSheet: no visible global function definition for ‘read.csv’
setFeatureData: no visible global function definition for
  ‘packageDescription’
setFeatureData: no visible global function definition for ‘new’
squeezedVarOutlierMethod: no visible global function definition for
  ‘loess’
squeezedVarOutlierMethod: no visible global function definition for
  ‘predict’
suggestAnnotation: no visible binding for global variable
  ‘platformSigs’
suggestAnnotation_Vector: no visible global function definition for
  ‘data’
suggestAnnotation_Vector: no visible binding for global variable
  ‘platformSigs’
summarize: no visible global function definition for ‘new’
summarize: no visible global function definition for
  ‘packageDescription’
viewBeads: no visible global function definition for ‘col2rgb’
viewBeads: no visible global function definition for ‘menu’
viewBeads: no visible global function definition for ‘rgb’
writeOutFiles: no visible global function definition for ‘write.table’
[,ExpressionSetIllumina-ANY: no visible global function definition for
  ‘assayDataEnvLock’
boxplot,ExpressionSetIllumina: no visible global function definition
  for ‘ggplot’
boxplot,ExpressionSetIllumina: no visible global function definition
  for ‘aes’
boxplot,ExpressionSetIllumina: no visible binding for global variable
  ‘Var2’
boxplot,ExpressionSetIllumina: no visible binding for global variable
  ‘value’
boxplot,ExpressionSetIllumina: no visible global function definition
  for ‘geom_boxplot’
boxplot,ExpressionSetIllumina: no visible global function definition
  for ‘scale_fill_discrete’
boxplot,ExpressionSetIllumina: no visible global function definition
  for ‘facet_wrap’
boxplot,ExpressionSetIllumina: no visible global function definition
  for ‘theme’
boxplot,ExpressionSetIllumina: no visible global function definition
  for ‘element_blank’
boxplot,ExpressionSetIllumina: no visible global function definition
  for ‘element_text’
boxplot,ExpressionSetIllumina: no visible global function definition
  for ‘ylab’
channel,ExpressionSetIllumina-ANY: no visible global function
  definition for ‘new’
coerce,ExpressionSet-ExpressionSetIllumina: no visible global function
  definition for ‘new’
coerce,limmaResults-GRanges: no visible global function definition for
  ‘new’
combine,beadLevelData-beadLevelData: no visible global function
  definition for ‘new’
initialize,ExpressionSetIllumina: no visible global function definition
  for ‘new’
initialize,ExpressionSetIllumina: no visible global function definition
  for ‘callNextMethod’
initialize,limmaResults: no visible global function definition for
  ‘new’
initialize,limmaResults: no visible global function definition for
  ‘callNextMethod’
plot,limmaResults-ANY: no visible global function definition for
  ‘ggplot’
plot,limmaResults-ANY: no visible global function definition for ‘aes’
plot,limmaResults-ANY: no visible global function definition for
  ‘geom_point’
plot,limmaResults-ANY: no visible global function definition for
  ‘facet_wrap’
plotMA,ExpressionSetIllumina: no visible global function definition for
  ‘ggplot’
plotMA,ExpressionSetIllumina: no visible global function definition for
  ‘aes’
plotMA,ExpressionSetIllumina: no visible binding for global variable
  ‘value.1’
plotMA,ExpressionSetIllumina: no visible binding for global variable
  ‘value’
plotMA,ExpressionSetIllumina: no visible global function definition for
  ‘stat_binhex’
plotMA,ExpressionSetIllumina: no visible global function definition for
  ‘theme_bw’
plotMA,ExpressionSetIllumina: no visible global function definition for
  ‘xlab’
plotMA,ExpressionSetIllumina: no visible global function definition for
  ‘ylab’
plotMA,ExpressionSetIllumina: no visible global function definition for
  ‘facet_wrap’
plotMA,ExpressionSetIllumina: no visible global function definition for
  ‘theme’
plotMA,ExpressionSetIllumina: no visible global function definition for
  ‘ggtitle’
show,ExpressionSetIllumina: no visible global function definition for
  ‘callNextMethod’
show,limmaResults: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  Control ControlType ID IMAGE.TYPE.RASTER Log2Intensity Masked
  Negative PROBEQUALITY PROTECTION.PUBLIC Var1 Var2 addTo aes aggregate
  approx as assayDataEnvLock autoplot callNextMethod closePage col2rgb
  data dbGetQuery dbListFields dbListTables density dev.off
  element_blank element_text facet_wrap genesymbol geom_boxplot
  geom_hline geom_point geom_tile geom_vline ggplot ggsave ggtitle
  hwrite hwriteImage is jpeg loess lowess lumiHumanIDMapping_dbconn
  lumiMouseIDMapping_dbconn lumiRatIDMapping_dbconn lumiT menu
  metaTemplate model.matrix new newCustomReport newFigure newParagraph
  newSection newTable normalize.invariantset normalize.qspline openPage
  opts p.adjust packageDescription pdf platformSigs plotIdeogram png
  predict qplot rainbow read.csv read.table rgb rsn runif
  scale_fill_discrete scale_fill_gradient setTxtProgressBar stat_binhex
  theme theme_blank theme_bw tracks txtProgressBar value value.1 vsn2
  write.csv write.table writeReport xlab ylab
Consider adding
  importFrom("grDevices", "col2rgb", "dev.off", "jpeg", "pdf", "png",
             "rainbow", "rgb")
  importFrom("methods", "as", "callNextMethod", "is", "new")
  importFrom("stats", "aggregate", "approx", "density", "loess",
             "lowess", "model.matrix", "p.adjust", "predict", "runif")
  importFrom("utils", "data", "menu", "packageDescription", "read.csv",
             "read.table", "setTxtProgressBar", "txtProgressBar",
             "write.csv", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
squeezedVarOutlierMethod 48.928  0.152  49.110
summarize                27.708  0.604  28.337
limmaDE                  19.668  0.008  19.691
calculateOutlierStats    15.008  0.620  15.662
controlProbeDetection    12.764  0.076  12.853
outlierplot              11.300  0.420  11.729
normaliseIllumina        11.376  0.076  11.916
calculateDetection       11.084  0.040  11.135
identifyControlBeads     10.752  0.012  10.768
maplots                  10.596  0.084  10.702
makeQCTable              10.064  0.156  10.240
insertSectionData         9.592  0.292   9.895
poscontPlot               8.940  0.160   9.106
annotationInterface       7.600  0.200   7.809
addFeatureData            7.416  0.160   7.722
quickSummary              6.412  0.180   6.596
imageplot                 5.988  0.032   6.023
showArrayMask             4.996  0.472   5.470
boxplot                   5.296  0.032   5.337
* 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-3.6-bioc/meat/beadarray.Rcheck/00check.log’
for details.

* installing *source* package ‘beadarray’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c BASH.c -o BASH.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c HULK.c -o HULK.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c determiningGridPositions.c -o determiningGridPositions.o
gcc -I/home/biocbuild/bbs-3.6-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-3.6-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)
 ^
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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
** testing if installed package can be loaded
* DONE (beadarray)

name	user	system	elapsed
BASH	0.000	0.000	0.001
BASHCompact	0.004	0.000	0.001
BASHDiffuse	0.004	0.000	0.001
BASHExtended	0	0	0
GEO	0.000	0.000	0.001
GEOtemplate	0.000	0.000	0.003
HULK	0.000	0.000	0.001
addFeatureData	7.416	0.160	7.722
annotationInterface	7.600	0.200	7.809
backgroundCorrectSingleSection	0.000	0.000	0.001
beadarrayUsersGuide	0.004	0.000	0.003
boxplot	5.296	0.032	5.337
calculateDetection	11.084	0.040	11.135
calculateOutlierStats	15.008	0.620	15.662
class-beadLevelData	2.312	0.056	2.372
class-illuminaChannel	0.004	0.000	0.003
combine	3.244	0.164	3.419
controlProbeDetection	12.764	0.076	12.853
createTargetsFile	0	0	0
expressionQCPipeline	0.036	0.000	0.037
generateNeighbours	0.000	0.000	0.001
getBeadData	2.260	0.020	2.282
identifyControlBeads	10.752	0.012	10.768
illuminaOutlierMethod	2.688	0.004	2.693
imageplot	5.988	0.032	6.023
insertBeadData	2.700	0.076	2.777
insertSectionData	9.592	0.292	9.895
limmaDE	19.668	0.008	19.691
makeControlProfile	0.512	0.000	0.511
makeQCTable	10.064	0.156	10.240
maplots	10.596	0.084	10.702
medianNormalise	1.572	0.020	1.590
metrics	2.096	0.040	2.136
noOutlierMethod	2.036	0.028	2.067
normaliseIllumina	11.376	0.076	11.916
numBeads	1.940	0.036	1.975
outlierplot	11.300	0.420	11.729
plotBeadIntensities	3.528	0.128	3.656
plotBeadLocations	2.656	0.088	2.743
plotChipLayout	0.004	0.000	0.000
plotMAXY	0.000	0.000	0.001
poscontPlot	8.940	0.160	9.106
quickSummary	6.412	0.180	6.596
readBeadSummaryData	0.000	0.000	0.001
sectionNames	1.876	0.048	1.926
showArrayMask	4.996	0.472	5.470
squeezedVarOutlierMethod	48.928	0.152	49.110
summarize	27.708	0.604	28.337
transformationFunctions	3.048	0.168	3.219
weightsOutlierMethod	0.000	0.000	0.001

CHECK report for beadarray on malbec1

Summary

Command output

Installation output

Tests output

Example timings