beadarray 2.14.1
Mark Dunning
| Snapshot Date: 2014-08-25 17:20:39 -0700 (Mon, 25 Aug 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/beadarray | | Last Changed Rev: 91415 / Revision: 93596 | | Last Changed Date: 2014-06-15 12:18:18 -0700 (Sun, 15 Jun 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK |
| morelia | Mac OS X Mavericks (10.9.2) / x86_64 | OK | OK | OK | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch beadarray_2.14.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/beadarray.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beadarray/DESCRIPTION’ ... OK
* this is package ‘beadarray’ version ‘2.14.1’
* 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 ... [30s/31s] 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
Packages in Depends field not imported from:
‘ggplot2’ ‘methods’
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.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘illuminaForeground_6x6’ ‘locsIndicesToGrid’ ‘obtainLocs’
‘simpleXMLparse’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 the chapter ‘System and foreign language interfaces’ of 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’
getPlatformSigs: no visible global function definition for
‘lumiHumanIDMapping_dbconn’
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 ‘value’
maplots: no visible binding for global variable ‘value.1’
maplots: no visible binding for global variable ‘value’
plotProbe: no visible binding for global variable ‘genesymbol’
plotProbe: no visible binding for global variable ‘PROBEQUALITY’
[,ExpressionSetIllumina-ANY: no visible global function definition for
‘assayDataEnvLock’
* 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13m/13m] OK
Examples with CPU or elapsed time > 5s
user system elapsed
squeezedVarOutlierMethod 127.307 1.601 132.785
summarize 84.574 6.228 92.590
limmaDE 61.433 0.903 63.974
calculateOutlierStats 39.110 3.291 43.602
calculateDetection 38.776 1.002 41.132
outlierplot 37.121 2.038 39.519
normaliseIllumina 34.517 1.628 37.014
maplots 27.073 5.021 32.451
addFeatureData 24.207 0.583 25.181
makeQCTable 21.257 2.644 24.144
controlProbeDetection 21.386 1.839 24.367
insertSectionData 20.014 2.436 22.699
poscontPlot 18.106 1.535 19.720
identifyControlBeads 17.996 0.817 18.978
annotationInterface 15.006 0.945 16.186
imageplot 14.474 1.437 16.107
quickSummary 14.084 1.607 15.821
showArrayMask 12.676 1.852 21.258
combine 9.838 1.251 11.523
boxplot 7.579 0.481 8.200
illuminaOutlierMethod 6.221 0.932 7.191
transformationFunctions 5.995 1.149 7.180
plotBeadIntensities 5.897 0.910 6.830
insertBeadData 5.231 0.760 6.022
plotBeadLocations 4.904 0.710 5.638
class-beadLevelData 4.408 0.706 5.319
* 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
NOTE: There were 3 notes.
See
‘/Users/biocbuild/bbs-2.14-bioc/meat/beadarray.Rcheck/00check.log’
for details.
* installing *source* package ‘beadarray’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c BASH.c -o BASH.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c HULK.c -o HULK.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c determiningGridPositions.c -o determiningGridPositions.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c findAllOutliers.c -o findAllOutliers.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function ‘illuminaBackground’:
imageProcessing.c:88: warning: ignoring #pragma omp parallel
imageProcessing.c: In function ‘medianBackground’:
imageProcessing.c:135: warning: ignoring #pragma omp parallel
imageProcessing.c: In function ‘illuminaSharpen’:
imageProcessing.c:244: warning: ignoring #pragma omp parallel
imageProcessing.c:251: warning: ignoring #pragma omp parallel
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/beadarray.Rcheck/beadarray/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (beadarray)