Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:14:51 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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To the developers/maintainers of the beadarray package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/beadarray.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 132/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
beadarray 2.49.0 (landing page) Mark Dunning
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: beadarray |
Version: 2.49.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:beadarray.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings beadarray_2.49.0.tar.gz |
StartedAt: 2023-02-06 18:24:15 -0000 (Mon, 06 Feb 2023) |
EndedAt: 2023-02-06 18:36:47 -0000 (Mon, 06 Feb 2023) |
EllapsedTime: 752.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: beadarray.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:beadarray.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings beadarray_2.49.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/beadarray.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘beadarray/DESCRIPTION’ ... OK * this is package ‘beadarray’ version ‘2.49.0’ * 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 * used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ * 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 ... NOTE checkRd: (-1) readBeadSummaryData.Rd:70: Escaped LaTeX specials: \_ checkRd: (-1) readBeadSummaryData.Rd:71: Escaped LaTeX specials: \_ \_ checkRd: (-1) readBeadSummaryData.Rd:76: Escaped LaTeX specials: \_ \_ checkRd: (-1) sampleSheet.Rd:26: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ * 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 LazyData ... 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 105.112 0.148 106.845 summarize 30.207 0.264 30.580 limmaDE 20.331 0.004 21.753 normaliseIllumina 15.897 0.124 16.077 calculateOutlierStats 15.332 0.432 15.857 calculateDetection 12.165 0.071 13.690 outlierplot 11.753 0.168 11.930 controlProbeDetection 10.935 0.052 11.117 insertSectionData 10.268 0.236 10.527 identifyControlBeads 9.650 0.016 9.710 makeQCTable 9.411 0.160 10.281 poscontPlot 8.065 0.052 8.151 imageplot 7.492 0.012 7.547 annotationInterface 6.829 0.368 7.258 quickSummary 6.999 0.056 7.060 addFeatureData 6.169 0.180 9.030 showArrayMask 5.973 0.060 6.038 maplots 5.788 0.147 6.438 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘ImageProcessing.rnw’... OK ‘beadarray.rnw’... OK ‘beadlevel.rnw’... OK ‘beadsummary.rnw’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/beadarray.Rcheck/00check.log’ for details.
beadarray.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL beadarray ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘beadarray’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c BASH.c -o BASH.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c HULK.c -o HULK.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c determiningGridPositions.c -o determiningGridPositions.o gcc -I"/home/biocbuild/bbs-3.17-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:196:43: 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:196:67: 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:246:20: warning: ‘status’ may be used uninitialized [-Wmaybe-uninitialized] 246 | free(status->validInds); | ~~~~~~^~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.17-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-3.17-bioc/R/lib -L/usr/local/lib -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-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)
beadarray.Rcheck/beadarray-Ex.timings
name | user | system | elapsed | |
BASH | 0 | 0 | 0 | |
BASHCompact | 0 | 0 | 0 | |
BASHDiffuse | 0 | 0 | 0 | |
BASHExtended | 0 | 0 | 0 | |
GEO | 0 | 0 | 0 | |
GEOtemplate | 0.003 | 0.000 | 0.002 | |
HULK | 0.000 | 0.000 | 0.001 | |
addFeatureData | 6.169 | 0.180 | 9.030 | |
annotationInterface | 6.829 | 0.368 | 7.258 | |
backgroundCorrectSingleSection | 0 | 0 | 0 | |
beadarrayUsersGuide | 0.002 | 0.000 | 0.002 | |
boxplot | 3.454 | 0.076 | 3.747 | |
calculateDetection | 12.165 | 0.071 | 13.690 | |
calculateOutlierStats | 15.332 | 0.432 | 15.857 | |
class-beadLevelData | 2.513 | 0.068 | 2.581 | |
class-illuminaChannel | 0.003 | 0.000 | 0.002 | |
combine | 4.142 | 0.044 | 4.248 | |
controlProbeDetection | 10.935 | 0.052 | 11.117 | |
createTargetsFile | 0.000 | 0.000 | 0.001 | |
expressionQCPipeline | 0.026 | 0.000 | 0.027 | |
generateNeighbours | 0 | 0 | 0 | |
getBeadData | 2.079 | 0.028 | 2.108 | |
identifyControlBeads | 9.650 | 0.016 | 9.710 | |
illuminaOutlierMethod | 3.139 | 0.032 | 3.250 | |
imageplot | 7.492 | 0.012 | 7.547 | |
insertBeadData | 2.828 | 0.124 | 2.955 | |
insertSectionData | 10.268 | 0.236 | 10.527 | |
limmaDE | 20.331 | 0.004 | 21.753 | |
makeControlProfile | 0.392 | 0.004 | 0.480 | |
makeQCTable | 9.411 | 0.160 | 10.281 | |
maplots | 5.788 | 0.147 | 6.438 | |
medianNormalise | 1.509 | 0.040 | 1.751 | |
metrics | 1.733 | 0.036 | 2.126 | |
noOutlierMethod | 1.728 | 0.032 | 1.919 | |
normaliseIllumina | 15.897 | 0.124 | 16.077 | |
numBeads | 1.760 | 0.104 | 1.866 | |
outlierplot | 11.753 | 0.168 | 11.930 | |
plotBeadIntensities | 3.583 | 0.072 | 3.659 | |
plotBeadLocations | 2.066 | 0.024 | 2.092 | |
plotChipLayout | 0 | 0 | 0 | |
plotMAXY | 0 | 0 | 0 | |
poscontPlot | 8.065 | 0.052 | 8.151 | |
quickSummary | 6.999 | 0.056 | 7.060 | |
readBeadSummaryData | 0 | 0 | 0 | |
sectionNames | 1.716 | 0.012 | 1.730 | |
showArrayMask | 5.973 | 0.060 | 6.038 | |
squeezedVarOutlierMethod | 105.112 | 0.148 | 106.845 | |
summarize | 30.207 | 0.264 | 30.580 | |
transformationFunctions | 3.756 | 0.104 | 3.866 | |
weightsOutlierMethod | 0 | 0 | 0 | |