Back to Multiple platform build/check report for BioC 3.10
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for beadarray on malbec1

This page was generated on 2020-04-15 12:04:37 -0400 (Wed, 15 Apr 2020).

Package 127/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
beadarray 2.36.1
Mark Dunning
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/beadarray
Branch: RELEASE_3_10
Last Commit: 1939559
Last Changed Date: 2020-04-13 17:37:12 -0400 (Mon, 13 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]YES, new version is higher than in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK YES, new version is higher than in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK YES, new version is higher than in internal repository

Summary

Package: beadarray
Version: 2.36.1
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:beadarray.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings beadarray_2.36.1.tar.gz
StartedAt: 2020-04-15 00:17:55 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:25:46 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 471.5 seconds
RetCode: 0
Status:  OK 
CheckDir: beadarray.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:beadarray.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings beadarray_2.36.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/beadarray.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.36.1’
* 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 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 55.680  0.080  55.871
summarize                28.696  0.104  28.870
limmaDE                  23.728  0.044  23.823
identifyControlBeads     17.460  0.048  17.551
calculateOutlierStats    16.192  0.396  16.635
outlierplot              16.108  0.212  16.383
controlProbeDetection    15.236  0.024  15.276
normaliseIllumina        13.828  0.460  14.346
insertSectionData        13.688  0.204  13.935
poscontPlot              12.484  0.188  12.710
calculateDetection       12.444  0.068  12.532
makeQCTable              11.440  0.116  11.580
imageplot                 9.180  0.036   9.245
quickSummary              9.124  0.076   9.221
annotationInterface       7.064  0.344   7.627
addFeatureData            6.732  0.124   7.004
showArrayMask             5.860  0.028   5.904
* 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-3.10-bioc/meat/beadarray.Rcheck/00check.log’
for details.



Installation output

beadarray.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL beadarray
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘beadarray’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c BASH.c -o BASH.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c HULK.c -o HULK.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c determiningGridPositions.c -o determiningGridPositions.o
gcc -I"/home/biocbuild/bbs-3.10-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-3.10-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-3.10-bioc/R/lib -L/usr/local/lib -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-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)

Tests output


Example timings

beadarray.Rcheck/beadarray-Ex.timings

nameusersystemelapsed
BASH0.0000.0000.001
BASHCompact000
BASHDiffuse000
BASHExtended000
GEO000
GEOtemplate0.0040.0000.003
HULK000
addFeatureData6.7320.1247.004
annotationInterface7.0640.3447.627
backgroundCorrectSingleSection000
beadarrayUsersGuide0.0000.0000.003
boxplot4.5720.0564.640
calculateDetection12.444 0.06812.532
calculateOutlierStats16.192 0.39616.635
class-beadLevelData3.0480.0763.128
class-illuminaChannel0.0000.0000.002
combine3.0320.0603.096
controlProbeDetection15.236 0.02415.276
createTargetsFile000
expressionQCPipeline0.0160.0000.019
generateNeighbours000
getBeadData2.9360.0162.979
identifyControlBeads17.460 0.04817.551
illuminaOutlierMethod4.0240.0964.125
imageplot9.1800.0369.245
insertBeadData4.1000.1364.243
insertSectionData13.688 0.20413.935
limmaDE23.728 0.04423.823
makeControlProfile0.5040.0040.513
makeQCTable11.440 0.11611.580
maplots4.0200.0444.071
medianNormalise1.6480.0121.663
metrics2.2120.0202.240
noOutlierMethod2.7680.0202.797
normaliseIllumina13.828 0.46014.346
numBeads2.3640.0402.409
outlierplot16.108 0.21216.383
plotBeadIntensities3.5360.0523.595
plotBeadLocations3.2800.0803.373
plotChipLayout000
plotMAXY000
poscontPlot12.484 0.18812.710
quickSummary9.1240.0769.221
readBeadSummaryData000
sectionNames2.3440.0442.390
showArrayMask5.8600.0285.904
squeezedVarOutlierMethod55.680 0.08055.871
summarize28.696 0.10428.870
transformationFunctions4.0400.1004.158
weightsOutlierMethod000