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CHECK report for beadarray on nebbiolo1

This page was generated on 2020-12-01 11:55:50 -0500 (Tue, 01 Dec 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE beadarray PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 134/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
beadarray 2.40.0
Mark Dunning
Snapshot Date: 2020-11-30 14:42:56 -0500 (Mon, 30 Nov 2020)
URL: https://git.bioconductor.org/packages/beadarray
Branch: RELEASE_3_12
Last Commit: 785579b
Last Changed Date: 2020-10-27 10:28:02 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: beadarray
Version: 2.40.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:beadarray.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings beadarray_2.40.0.tar.gz
StartedAt: 2020-11-30 20:02:23 -0500 (Mon, 30 Nov 2020)
EndedAt: 2020-11-30 20:11:29 -0500 (Mon, 30 Nov 2020)
EllapsedTime: 546.0 seconds
RetCode: 0
Status:  OK 
CheckDir: beadarray.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:beadarray.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings beadarray_2.40.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/beadarray.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘2.40.0’
* 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 ... 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 ‘Negative’
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:
  IMAGE.TYPE.RASTER 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 (user + system) or elapsed time > 5s
                           user system elapsed
squeezedVarOutlierMethod 49.894  0.150  50.046
calculateOutlierStats    17.706  0.491  18.284
summarize                17.649  0.370  18.146
limmaDE                  16.628  0.056  17.025
controlProbeDetection    15.917  0.183  16.266
identifyControlBeads     14.110  0.111  15.804
calculateDetection       13.391  0.128  13.540
normaliseIllumina        12.816  0.204  14.674
makeQCTable              11.816  0.482  12.831
insertSectionData        10.965  0.319  11.292
outlierplot              10.149  0.599  10.749
annotationInterface       8.151  0.916   9.097
poscontPlot               8.314  0.072   8.386
imageplot                 7.185  0.160   7.461
addFeatureData            5.766  0.203   5.980
maplots                   5.029  0.204   5.465
quickSummary              4.982  0.096   5.078
* 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-3.12-bioc/meat/beadarray.Rcheck/00check.log’
for details.



Installation output

beadarray.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL beadarray
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘beadarray’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c BASH.c -o BASH.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c HULK.c -o HULK.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c determiningGridPositions.c -o determiningGridPositions.o
gcc -I"/home/biocbuild/bbs-3.12-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]
  196 |   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]
  196 |   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]
  226 |  beadStatusStruct *status;
      |                    ^~~~~~
gcc -I"/home/biocbuild/bbs-3.12-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: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
   88 |     #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
      | 
imageProcessing.c: In function ‘medianBackground’:
imageProcessing.c:135: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  135 |     #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
      | 
imageProcessing.c: In function ‘illuminaSharpen’:
imageProcessing.c:244: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  244 |     #pragma omp parallel for private(i, j) shared(sharpened) num_threads(2)
      | 
imageProcessing.c:251: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  251 |     #pragma omp parallel for private(i, j, sum) shared(sharpened) num_threads(2)
      | 
gcc -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-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
BASH0.0010.0010.001
BASHCompact0.0000.0000.001
BASHDiffuse0.0010.0000.000
BASHExtended0.0010.0000.000
GEO000
GEOtemplate0.0000.0030.003
HULK0.0000.0000.001
addFeatureData5.7660.2035.980
annotationInterface8.1510.9169.097
backgroundCorrectSingleSection0.0010.0000.001
beadarrayUsersGuide0.0020.0000.002
boxplot3.3660.0923.465
calculateDetection13.391 0.12813.540
calculateOutlierStats17.706 0.49118.284
class-beadLevelData2.9860.0843.098
class-illuminaChannel0.0050.0000.004
combine4.2210.1394.455
controlProbeDetection15.917 0.18316.266
createTargetsFile000
expressionQCPipeline0.0250.0020.027
generateNeighbours0.0000.0000.001
getBeadData2.7050.0562.768
identifyControlBeads14.110 0.11115.804
illuminaOutlierMethod3.4250.0443.589
imageplot7.1850.1607.461
insertBeadData2.3480.1202.469
insertSectionData10.965 0.31911.292
limmaDE16.628 0.05617.025
makeControlProfile0.5510.0000.552
makeQCTable11.816 0.48212.831
maplots5.0290.2045.465
medianNormalise1.7640.0152.028
metrics2.1960.0162.263
noOutlierMethod2.2400.0242.767
normaliseIllumina12.816 0.20414.674
numBeads1.8690.1041.973
outlierplot10.149 0.59910.749
plotBeadIntensities3.1710.1763.346
plotBeadLocations1.8400.1281.968
plotChipLayout000
plotMAXY0.0010.0000.000
poscontPlot8.3140.0728.386
quickSummary4.9820.0965.078
readBeadSummaryData000
sectionNames1.7640.0281.792
showArrayMask3.6930.1683.862
squeezedVarOutlierMethod49.894 0.15050.046
summarize17.649 0.37018.146
transformationFunctions2.6080.1042.713
weightsOutlierMethod000