beadarray 2.12.0
Mark Dunning
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/beadarray | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ OK ] | OK |
* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/beadarray.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘2.12.0’
* 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 ... [20s/21s] OK
* checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
data 2.5Mb
doc 2.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘BiocGenerics’
A package should be listed in only one of these fields.
* 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.
‘:::’ call which should be ‘::’: ‘BeadDataPackR:::extractLocsFile’
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ‘:::’ calls:
‘BeadDataPackR:::combineFiles’ ‘BeadDataPackR:::readHeader’
‘BeadDataPackR:::readLocsFile’
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
expressionQCPipeline: warning in ggsave(im, file = fname.im, width = 4,
height = 1): partial argument match of 'file' to 'filename'
makeControlProfile: warning in packageDescription(annoPkg, field =
"Version"): partial argument match of 'field' to 'fields'
plotMAXY: warning in close.screen(all = TRUE): partial argument match
of 'all' to 'all.screens'
summarize: warning in packageDescription(annoPkg, field = "Version"):
partial argument match of 'field' to 'fields'
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’
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘beadarray.rnw’, ‘beadlevel.rnw’, ‘beadsummary.rnw’,
‘ImageProcessing.rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [509s/518s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
squeezedVarOutlierMethod 77.752 1.952 79.867
summarize 60.031 7.027 67.121
normaliseIllumina 32.109 3.567 36.351
outlierplot 30.948 2.184 34.535
calculateOutlierStats 25.462 4.447 30.558
addFeatureData 21.924 0.852 24.613
calculateDetection 17.034 3.062 20.318
insertSectionData 13.475 2.815 16.638
poscontPlot 14.451 1.563 16.050
controlProbeDetection 12.979 2.342 15.510
makeQCTable 12.487 2.780 15.438
showArrayMask 11.997 1.892 13.971
boxplot 11.709 2.119 14.023
quickSummary 11.400 1.679 13.162
combine 10.745 2.255 13.197
annotationInterface 11.470 1.054 12.889
imageplot 10.064 1.777 12.340
identifyControlBeads 10.720 0.974 11.989
transformationFunctions 4.989 1.292 6.290
plotBeadIntensities 4.702 0.946 5.653
illuminaOutlierMethod 4.402 1.030 5.519
* 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 6 notes.
See
‘/Users/biocbuild/bbs-2.13-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-2.13-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)