| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:30 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 | ||||
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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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 143/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| beadarray 2.51.0 (landing page) Mark Dunning
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: beadarray |
| Version: 2.51.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:beadarray.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings beadarray_2.51.0.tar.gz |
| StartedAt: 2023-05-30 01:17:16 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 01:29:22 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 726.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: beadarray.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:beadarray.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings beadarray_2.51.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/beadarray.Rcheck’
* using R version 4.3.0 (2023-04-21)
* 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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘beadarray/DESCRIPTION’ ... OK
* this is package ‘beadarray’ version ‘2.51.0’
* 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 11.3.0-1ubuntu1~22.04.1) 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 loading without being on the library search path ... OK
* checking 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) 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 78.000 0.408 78.411
summarize 29.901 0.846 30.748
limmaDE 20.480 0.104 20.584
normaliseIllumina 16.981 0.308 17.294
calculateOutlierStats 14.056 0.616 14.673
outlierplot 13.368 0.416 13.784
calculateDetection 12.610 0.160 12.771
controlProbeDetection 10.876 0.180 11.056
insertSectionData 10.140 0.256 10.396
identifyControlBeads 9.680 0.048 9.729
makeQCTable 9.496 0.156 9.654
poscontPlot 9.367 0.115 9.482
imageplot 7.667 0.080 7.748
annotationInterface 6.767 0.504 7.273
quickSummary 7.162 0.089 7.252
maplots 6.276 0.124 6.401
showArrayMask 6.124 0.148 6.272
addFeatureData 6.018 0.179 6.210
* 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-3.18-bioc/meat/beadarray.Rcheck/00check.log’
for details.
beadarray.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL beadarray ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘beadarray’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’ gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c BASH.c -o BASH.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c HULK.c -o HULK.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c determiningGridPositions.c -o determiningGridPositions.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c findAllOutliers.c -o findAllOutliers.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c imageProcessing.c -o imageProcessing.o gcc -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/site-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 | 0.000 | 0.000 | 0.001 | |
| BASHCompact | 0 | 0 | 0 | |
| BASHDiffuse | 0 | 0 | 0 | |
| BASHExtended | 0.001 | 0.000 | 0.000 | |
| GEO | 0 | 0 | 0 | |
| GEOtemplate | 0.002 | 0.000 | 0.003 | |
| HULK | 0 | 0 | 0 | |
| addFeatureData | 6.018 | 0.179 | 6.210 | |
| annotationInterface | 6.767 | 0.504 | 7.273 | |
| backgroundCorrectSingleSection | 0.000 | 0.000 | 0.001 | |
| beadarrayUsersGuide | 0.002 | 0.000 | 0.003 | |
| boxplot | 3.667 | 0.132 | 3.799 | |
| calculateDetection | 12.610 | 0.160 | 12.771 | |
| calculateOutlierStats | 14.056 | 0.616 | 14.673 | |
| class-beadLevelData | 2.550 | 0.148 | 2.698 | |
| class-illuminaChannel | 0.003 | 0.000 | 0.003 | |
| combine | 3.724 | 0.152 | 3.876 | |
| controlProbeDetection | 10.876 | 0.180 | 11.056 | |
| createTargetsFile | 0 | 0 | 0 | |
| expressionQCPipeline | 0.024 | 0.000 | 0.025 | |
| generateNeighbours | 0 | 0 | 0 | |
| getBeadData | 2.097 | 0.036 | 2.133 | |
| identifyControlBeads | 9.680 | 0.048 | 9.729 | |
| illuminaOutlierMethod | 3.113 | 0.128 | 3.242 | |
| imageplot | 7.667 | 0.080 | 7.748 | |
| insertBeadData | 2.764 | 0.104 | 2.868 | |
| insertSectionData | 10.140 | 0.256 | 10.396 | |
| limmaDE | 20.480 | 0.104 | 20.584 | |
| makeControlProfile | 0.387 | 0.004 | 0.390 | |
| makeQCTable | 9.496 | 0.156 | 9.654 | |
| maplots | 6.276 | 0.124 | 6.401 | |
| medianNormalise | 1.443 | 0.032 | 1.475 | |
| metrics | 1.695 | 0.012 | 1.707 | |
| noOutlierMethod | 1.758 | 0.024 | 1.781 | |
| normaliseIllumina | 16.981 | 0.308 | 17.294 | |
| numBeads | 1.678 | 0.060 | 1.738 | |
| outlierplot | 13.368 | 0.416 | 13.784 | |
| plotBeadIntensities | 3.697 | 0.184 | 3.881 | |
| plotBeadLocations | 3.369 | 0.112 | 3.480 | |
| plotChipLayout | 0 | 0 | 0 | |
| plotMAXY | 0.000 | 0.000 | 0.001 | |
| poscontPlot | 9.367 | 0.115 | 9.482 | |
| quickSummary | 7.162 | 0.089 | 7.252 | |
| readBeadSummaryData | 0 | 0 | 0 | |
| sectionNames | 1.781 | 0.044 | 1.826 | |
| showArrayMask | 6.124 | 0.148 | 6.272 | |
| squeezedVarOutlierMethod | 78.000 | 0.408 | 78.411 | |
| summarize | 29.901 | 0.846 | 30.748 | |
| transformationFunctions | 3.830 | 0.208 | 4.038 | |
| weightsOutlierMethod | 0.001 | 0.000 | 0.000 | |