Mark Dunning
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/beadarray |
| Branch: RELEASE_3_9 |
| Last Commit: 0502079 |
| Last Changed Date: 2019-05-02 11:53:05 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 11:55:58 -0400 (Wed, 16 Oct 2019).
| Package 121/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| beadarray 2.34.0 Mark Dunning
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: beadarray |
| Version: 2.34.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:beadarray.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings beadarray_2.34.0.tar.gz |
| StartedAt: 2019-10-16 00:00:22 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 00:07:54 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 451.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: beadarray.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:beadarray.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings beadarray_2.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/beadarray.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.34.0’
* 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 ‘Control’
combinedControlPlot: no visible binding for global variable ‘Negative’
combinedControlPlot: no visible binding for global variable ‘ID’
combinedControlPlot: no visible binding for global variable
‘Log2Intensity’
combinedControlPlot: no visible binding for global variable
‘ControlType’
combinedControlPlot: no visible binding for global variable ‘Masked’
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:
Control ControlType ID IMAGE.TYPE.RASTER Log2Intensity Masked
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 or elapsed time > 5s
user system elapsed
squeezedVarOutlierMethod 52.704 0.036 53.017
limmaDE 24.031 0.032 24.256
summarize 23.955 0.076 24.104
controlProbeDetection 16.660 0.160 16.833
identifyControlBeads 15.463 0.008 15.536
calculateOutlierStats 14.480 0.348 14.828
poscontPlot 14.133 0.180 14.374
normaliseIllumina 13.852 0.448 14.523
outlierplot 13.364 0.248 13.624
makeQCTable 13.234 0.147 13.483
insertSectionData 12.991 0.227 13.295
calculateDetection 11.278 0.040 11.325
imageplot 8.876 0.048 8.950
quickSummary 8.127 0.116 8.245
annotationInterface 7.525 0.368 8.421
addFeatureData 6.792 0.131 7.516
showArrayMask 6.127 0.164 6.319
maplots 5.080 0.028 5.140
* 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-3.9-bioc/meat/beadarray.Rcheck/00check.log’
for details.
beadarray.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL beadarray
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘beadarray’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c BASH.c -o BASH.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c HULK.c -o HULK.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c determiningGridPositions.c -o determiningGridPositions.o
gcc -I"/home/biocbuild/bbs-3.9-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]
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;
^~~~~~
gcc -I"/home/biocbuild/bbs-3.9-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:88:0: 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:135:0: 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:244:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(i, j) shared(sharpened) num_threads(2)
imageProcessing.c:251:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(i, j, sum) shared(sharpened) num_threads(2)
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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 | 0.000 | 0.001 | 0.000 | |
| BASHCompact | 0 | 0 | 0 | |
| BASHDiffuse | 0 | 0 | 0 | |
| BASHExtended | 0.001 | 0.000 | 0.001 | |
| GEO | 0 | 0 | 0 | |
| GEOtemplate | 0.003 | 0.000 | 0.003 | |
| HULK | 0.000 | 0.001 | 0.001 | |
| addFeatureData | 6.792 | 0.131 | 7.516 | |
| annotationInterface | 7.525 | 0.368 | 8.421 | |
| backgroundCorrectSingleSection | 0.001 | 0.000 | 0.001 | |
| beadarrayUsersGuide | 0.002 | 0.000 | 0.002 | |
| boxplot | 3.562 | 0.032 | 3.602 | |
| calculateDetection | 11.278 | 0.040 | 11.325 | |
| calculateOutlierStats | 14.480 | 0.348 | 14.828 | |
| class-beadLevelData | 2.299 | 0.056 | 2.355 | |
| class-illuminaChannel | 0.002 | 0.000 | 0.002 | |
| combine | 3.880 | 0.056 | 3.940 | |
| controlProbeDetection | 16.660 | 0.160 | 16.833 | |
| createTargetsFile | 0 | 0 | 0 | |
| expressionQCPipeline | 0.017 | 0.000 | 0.017 | |
| generateNeighbours | 0 | 0 | 0 | |
| getBeadData | 2.064 | 0.012 | 2.075 | |
| identifyControlBeads | 15.463 | 0.008 | 15.536 | |
| illuminaOutlierMethod | 3.357 | 0.056 | 3.491 | |
| imageplot | 8.876 | 0.048 | 8.950 | |
| insertBeadData | 3.614 | 0.076 | 3.701 | |
| insertSectionData | 12.991 | 0.227 | 13.295 | |
| limmaDE | 24.031 | 0.032 | 24.256 | |
| makeControlProfile | 0.441 | 0.004 | 0.446 | |
| makeQCTable | 13.234 | 0.147 | 13.483 | |
| maplots | 5.080 | 0.028 | 5.140 | |
| medianNormalise | 2.132 | 0.032 | 2.174 | |
| metrics | 2.559 | 0.108 | 2.696 | |
| noOutlierMethod | 2.610 | 0.120 | 2.771 | |
| normaliseIllumina | 13.852 | 0.448 | 14.523 | |
| numBeads | 2.674 | 0.128 | 2.802 | |
| outlierplot | 13.364 | 0.248 | 13.624 | |
| plotBeadIntensities | 4.020 | 0.135 | 4.167 | |
| plotBeadLocations | 2.542 | 0.072 | 2.616 | |
| plotChipLayout | 0 | 0 | 0 | |
| plotMAXY | 0 | 0 | 0 | |
| poscontPlot | 14.133 | 0.180 | 14.374 | |
| quickSummary | 8.127 | 0.116 | 8.245 | |
| readBeadSummaryData | 0 | 0 | 0 | |
| sectionNames | 2.408 | 0.031 | 2.530 | |
| showArrayMask | 6.127 | 0.164 | 6.319 | |
| squeezedVarOutlierMethod | 52.704 | 0.036 | 53.017 | |
| summarize | 23.955 | 0.076 | 24.104 | |
| transformationFunctions | 4.078 | 0.020 | 4.131 | |
| weightsOutlierMethod | 0.001 | 0.000 | 0.000 | |