Mark Dunning
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/beadarray |
| git_branch: master |
| git_last_commit: 3ac2907 |
| git_last_commit_date: 2021-10-26 11:49:14 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:00 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 130/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| beadarray 2.45.0 (landing page) Mark Dunning
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: beadarray |
| Version: 2.45.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:beadarray.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings beadarray_2.45.0.tar.gz |
| StartedAt: 2022-03-17 18:30:27 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:36:23 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 356.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: beadarray.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:beadarray.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings beadarray_2.45.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/beadarray.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'beadarray/DESCRIPTION' ... OK
* this is package 'beadarray' version '2.45.0'
* 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
* 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 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 'D:/biocbuild/bbs-3.15-bioc/R/library/beadarray/libs/x64/beadarray.dll':
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. 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
squeezedVarOutlierMethod 36.48 0.55 37.03
outlierplot 20.92 1.33 22.25
summarize 16.44 3.67 20.11
calculateOutlierStats 10.27 2.21 12.48
limmaDE 9.20 0.25 9.45
showArrayMask 7.91 1.01 8.93
calculateDetection 7.55 1.29 8.83
normaliseIllumina 7.60 1.13 8.72
controlProbeDetection 7.97 0.73 8.71
identifyControlBeads 8.22 0.33 8.55
insertSectionData 6.74 1.16 7.89
makeQCTable 6.12 1.03 7.16
poscontPlot 5.69 0.63 6.31
quickSummary 4.44 0.82 5.27
annotationInterface 4.52 0.72 5.24
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/beadarray.Rcheck/00check.log'
for details.
beadarray.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL beadarray
###
##############################################################################
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'beadarray' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c BASH.c -o BASH.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c HULK.c -o HULK.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c determiningGridPositions.c -o determiningGridPositions.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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;
^~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function 'illuminaBackground':
imageProcessing.c:88: 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: 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: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(i, j) shared(sharpened) num_threads(2)
imageProcessing.c:251: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(i, j, sum) shared(sharpened) num_threads(2)
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o beadarray.dll tmp.def BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-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
converting help for package 'beadarray'
finding HTML links ... done
BASH html
BASHCompact html
BASHDiffuse html
BASHExtended html
GEO html
GEOtemplate html
HULK html
addFeatureData html
annotationInterface html
backgroundCorrectSingleSection html
beadarray-package html
beadarrayUsersGuide html
boxplot html
calculateDetection html
calculateOutlierStats html
checkRegistration html
class-BeadLevelList html
class-ExpressionSetIllumina html
class-beadLevelData html
class-beadRegistrationData html
class-illuminaChannel html
class-limmaResults html
combine html
controlProbeDetection html
convertBeadLevelList html
createTargetsFile html
deprecatedFunctions html
dim html
expressionQCPipeline html
generateNeighbours html
getBeadData html
identifyControlBeads html
illuminaOutlierMethod html
imageProcessing html
imageplot html
insertBeadData html
insertSectionData html
limmaDE html
makeControlProfile html
makeQCTable html
maplots html
medianNormalise html
metrics html
noOutlierMethod html
normaliseIllumina html
numBeads html
outlierplot html
platformSigs html
plotBeadIntensities html
plotBeadLocations html
plotChipLayout html
plotMAXY html
plotTIFF html
poscontPlot html
processSwathData html
quickSummary html
readBeadSummaryData html
readIdatFiles html
readIllumina html
readLocsFile html
readTIFF html
sampleSheet html
sectionNames html
setWeights html
show html
showArrayMask html
squeezedVarOutlierMethod html
summarize html
transformationFunctions html
weightsOutlierMethod html
** 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)
Making 'packages.html' ... done
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 | 0.02 | |
| HULK | 0 | 0 | 0 | |
| addFeatureData | 4.26 | 0.19 | 4.45 | |
| annotationInterface | 4.52 | 0.72 | 5.24 | |
| backgroundCorrectSingleSection | 0.00 | 0.02 | 0.01 | |
| beadarrayUsersGuide | 0 | 0 | 0 | |
| boxplot | 2.14 | 0.21 | 2.36 | |
| calculateDetection | 7.55 | 1.29 | 8.83 | |
| calculateOutlierStats | 10.27 | 2.21 | 12.48 | |
| class-beadLevelData | 1.98 | 0.24 | 2.22 | |
| class-illuminaChannel | 0 | 0 | 0 | |
| combine | 2.84 | 0.61 | 3.45 | |
| controlProbeDetection | 7.97 | 0.73 | 8.71 | |
| createTargetsFile | 0 | 0 | 0 | |
| expressionQCPipeline | 0.01 | 0.00 | 0.02 | |
| generateNeighbours | 0 | 0 | 0 | |
| getBeadData | 1.72 | 0.22 | 1.93 | |
| identifyControlBeads | 8.22 | 0.33 | 8.55 | |
| illuminaOutlierMethod | 2.30 | 0.37 | 2.67 | |
| imageplot | 4.30 | 0.63 | 4.93 | |
| insertBeadData | 2.57 | 0.45 | 3.03 | |
| insertSectionData | 6.74 | 1.16 | 7.89 | |
| limmaDE | 9.20 | 0.25 | 9.45 | |
| makeControlProfile | 0.24 | 0.00 | 0.23 | |
| makeQCTable | 6.12 | 1.03 | 7.16 | |
| maplots | 2.63 | 1.38 | 4.00 | |
| medianNormalise | 1.11 | 0.10 | 1.22 | |
| metrics | 1.26 | 0.25 | 1.52 | |
| noOutlierMethod | 1.26 | 0.16 | 1.42 | |
| normaliseIllumina | 7.60 | 1.13 | 8.72 | |
| numBeads | 1.25 | 0.28 | 1.53 | |
| outlierplot | 20.92 | 1.33 | 22.25 | |
| plotBeadIntensities | 2.33 | 0.56 | 2.89 | |
| plotBeadLocations | 1.32 | 0.44 | 1.77 | |
| plotChipLayout | 0 | 0 | 0 | |
| plotMAXY | 0 | 0 | 0 | |
| poscontPlot | 5.69 | 0.63 | 6.31 | |
| quickSummary | 4.44 | 0.82 | 5.27 | |
| readBeadSummaryData | 0 | 0 | 0 | |
| sectionNames | 1.23 | 0.18 | 1.40 | |
| showArrayMask | 7.91 | 1.01 | 8.93 | |
| squeezedVarOutlierMethod | 36.48 | 0.55 | 37.03 | |
| summarize | 16.44 | 3.67 | 20.11 | |
| transformationFunctions | 2.50 | 0.64 | 3.14 | |
| weightsOutlierMethod | 0 | 0 | 0 | |