Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-22 11:36:36 -0400 (Wed, 22 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4665 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4400 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4427 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 147/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
beadarray 2.55.0 (landing page) Mark Dunning
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the beadarray package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: beadarray |
Version: 2.55.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:beadarray.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings beadarray_2.55.0.tar.gz |
StartedAt: 2024-05-20 22:27:00 -0400 (Mon, 20 May 2024) |
EndedAt: 2024-05-20 22:35:59 -0400 (Mon, 20 May 2024) |
EllapsedTime: 539.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: beadarray.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:beadarray.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings beadarray_2.55.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/beadarray.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'beadarray/DESCRIPTION' ... OK * this is package 'beadarray' version '2.55.0' * 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 whether package 'beadarray' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.2.0' * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 whether startup messages can be suppressed ... 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) createTargetsFile.Rd:49: Lost braces 49 | code{metricsflag}: This gives the key word that can be used to identify metrics files. | ^ 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/beadarray/libs/x64/beadarray.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed outlierplot 66.21 0.81 67.02 squeezedVarOutlierMethod 39.38 0.53 39.92 summarize 25.78 2.66 28.91 showArrayMask 22.10 0.88 22.97 limmaDE 17.09 0.54 17.64 calculateOutlierStats 14.68 1.36 16.05 normaliseIllumina 12.89 1.18 14.07 controlProbeDetection 12.20 0.64 12.84 identifyControlBeads 11.00 0.45 11.44 calculateDetection 9.90 1.20 11.11 insertSectionData 9.58 0.94 10.51 makeQCTable 8.86 1.02 9.86 poscontPlot 8.85 0.55 9.39 imageplot 7.28 0.69 7.96 quickSummary 7.04 0.59 7.66 addFeatureData 6.83 0.33 7.50 annotationInterface 6.75 0.38 7.84 maplots 5.00 0.89 5.90 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 6 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/beadarray.Rcheck/00check.log' for details.
beadarray.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL beadarray ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'beadarray' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BASH.c -o BASH.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c HULK.c -o HULK.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c determiningGridPositions.c -o determiningGridPositions.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c findAllOutliers.c -o findAllOutliers.o findAllOutliers.c: In function 'findBeadStatus': findAllOutliers.c:196:35: warning: 'm' may be used uninitialized [-Wmaybe-uninitialized] 196 | if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){ | ~~~^~~~~~~~~~~~ findAllOutliers.c:155:16: note: 'm' was declared here 155 | double m, ma; | ^ findAllOutliers.c:189:15: warning: 'ma' may be used uninitialized [-Wmaybe-uninitialized] 189 | if(ma==0) { | ^ findAllOutliers.c:155:19: note: 'ma' was declared here 155 | double m, ma; | ^~ findAllOutliers.c: In function 'findAllOutliers': findAllOutliers.c:246:20: warning: 'status' may be used uninitialized [-Wmaybe-uninitialized] 246 | free(status->validInds); | ~~~~~~^~~~~~~~~~~ findAllOutliers.c:226:27: note: 'status' was declared here 226 | beadStatusStruct *status; | ^~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 -s -static-libgcc -o beadarray.dll tmp.def BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-beadarray/00new/beadarray/libs/x64 ** 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 ** 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 | 0.00 | 0.01 | 0.01 | |
HULK | 0 | 0 | 0 | |
addFeatureData | 6.83 | 0.33 | 7.50 | |
annotationInterface | 6.75 | 0.38 | 7.84 | |
backgroundCorrectSingleSection | 0 | 0 | 0 | |
beadarrayUsersGuide | 0 | 0 | 0 | |
boxplot | 3.21 | 0.20 | 3.41 | |
calculateDetection | 9.90 | 1.20 | 11.11 | |
calculateOutlierStats | 14.68 | 1.36 | 16.05 | |
class-beadLevelData | 2.29 | 0.22 | 2.51 | |
class-illuminaChannel | 0 | 0 | 0 | |
combine | 3.47 | 0.42 | 3.89 | |
controlProbeDetection | 12.20 | 0.64 | 12.84 | |
createTargetsFile | 0 | 0 | 0 | |
expressionQCPipeline | 0.03 | 0.00 | 0.03 | |
generateNeighbours | 0 | 0 | 0 | |
getBeadData | 2.18 | 0.27 | 2.47 | |
identifyControlBeads | 11.00 | 0.45 | 11.44 | |
illuminaOutlierMethod | 3.08 | 0.44 | 3.52 | |
imageplot | 7.28 | 0.69 | 7.96 | |
insertBeadData | 2.87 | 0.45 | 3.33 | |
insertSectionData | 9.58 | 0.94 | 10.51 | |
limmaDE | 17.09 | 0.54 | 17.64 | |
makeControlProfile | 0.47 | 0.00 | 0.47 | |
makeQCTable | 8.86 | 1.02 | 9.86 | |
maplots | 5.00 | 0.89 | 5.90 | |
medianNormalise | 1.53 | 0.11 | 1.65 | |
metrics | 1.89 | 0.11 | 2.00 | |
noOutlierMethod | 1.85 | 0.12 | 1.96 | |
normaliseIllumina | 12.89 | 1.18 | 14.07 | |
numBeads | 1.89 | 0.14 | 2.03 | |
outlierplot | 66.21 | 0.81 | 67.02 | |
plotBeadIntensities | 2.48 | 0.39 | 2.87 | |
plotBeadLocations | 3.42 | 0.20 | 3.63 | |
plotChipLayout | 0 | 0 | 0 | |
plotMAXY | 0 | 0 | 0 | |
poscontPlot | 8.85 | 0.55 | 9.39 | |
quickSummary | 7.04 | 0.59 | 7.66 | |
readBeadSummaryData | 0.02 | 0.00 | 0.01 | |
sectionNames | 1.90 | 0.14 | 2.05 | |
showArrayMask | 22.10 | 0.88 | 22.97 | |
squeezedVarOutlierMethod | 39.38 | 0.53 | 39.92 | |
summarize | 25.78 | 2.66 | 28.91 | |
transformationFunctions | 3.84 | 0.51 | 4.51 | |
weightsOutlierMethod | 0 | 0 | 0 | |