Back to the "Multiple platform build/check report" A [B] C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 2.13: CHECK report for beadarray on zin1

This page was generated on 2014-04-05 09:47:18 -0700 (Sat, 05 Apr 2014).

Package 65/750HostnameOS / ArchBUILDCHECKBUILD BIN
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 

Summary

Package: beadarray
Version: 2.12.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings beadarray_2.12.0.tar.gz
StartedAt: 2014-04-04 23:43:40 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 23:51:10 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 449.7 seconds
RetCode: 0
Status:  OK 
CheckDir: beadarray.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/beadarray.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beadarray/DESCRIPTION’ ... OK
* this is package ‘beadarray’ version ‘2.12.0’
* 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 ... [12s/12s] OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘ImageProcessing.rnw’, ‘beadarray.rnw’, ‘beadlevel.rnw’,
  ‘beadsummary.rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [328s/330s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
squeezedVarOutlierMethod 55.211  0.040  55.432
summarize                38.111  0.548  38.850
calculateOutlierStats    19.705  0.820  20.570
outlierplot              19.465  0.320  19.854
normaliseIllumina        18.418  0.208  18.739
controlProbeDetection    14.013  0.100  14.175
makeQCTable              13.201  0.156  13.519
poscontPlot              12.668  0.204  12.934
calculateDetection       12.377  0.028  12.453
insertSectionData        12.261  0.124  12.608
identifyControlBeads     11.901  0.044  11.970
addFeatureData           10.312  0.116  10.471
quickSummary              9.557  0.120   9.750
showArrayMask             8.677  0.076   8.827
annotationInterface       7.941  0.260   8.284
imageplot                 7.480  0.020   7.525
combine                   6.077  0.272   6.374
* 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
  ‘/home/biocbuild/bbs-2.13-bioc/meat/beadarray.Rcheck/00check.log’
for details.

beadarray.Rcheck/00install.out:

* installing *source* package ‘beadarray’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c BASH.c -o BASH.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c HULK.c -o HULK.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c determiningGridPositions.c -o determiningGridPositions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-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 [-Wuninitialized]
findAllOutliers.c:196:53: warning: ‘m’ may be used uninitialized in this function [-Wuninitialized]
findAllOutliers.c: In function ‘findAllOutliers’:
findAllOutliers.c:247:13: warning: ‘status’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-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]
imageProcessing.c: In function ‘medianBackground’:
imageProcessing.c:135:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
imageProcessing.c: In function ‘illuminaSharpen’:
imageProcessing.c:244:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
imageProcessing.c:251:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
gcc -std=gnu99 -shared -L/usr/local/lib -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/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)

beadarray.Rcheck/beadarray-Ex.timings:

nameusersystemelapsed
BASH0.1200.0000.122
BASHCompact0.0000.0000.003
BASHDiffuse0.0040.0000.003
BASHExtended0.0040.0000.004
HULK0.0000.0040.004
addFeatureData10.312 0.11610.471
annotationInterface7.9410.2608.284
backgroundCorrectSingleSection0.0000.0000.002
beadarrayUsersGuide0.0080.0000.008
boxplot4.6080.0164.696
calculateDetection12.377 0.02812.453
calculateOutlierStats19.705 0.82020.570
class-beadLevelData2.4520.0922.547
class-illuminaChannel0.0040.0000.004
combine6.0770.2726.374
controlProbeDetection14.013 0.10014.175
createTargetsFile0.0040.0000.001
expressionQCPipeline0.0520.0000.050
generateNeighbours0.0040.0000.001
getBeadData2.4880.0522.542
identifyControlBeads11.901 0.04411.970
illuminaOutlierMethod3.5000.0363.559
imageplot7.4800.0207.525
insertBeadData2.7680.0482.888
insertSectionData12.261 0.12412.608
makeControlProfile0.5800.0040.584
makeQCTable13.201 0.15613.519
medianNormalise2.1080.0122.121
metrics2.0160.0402.059
noOutlierMethod2.1320.0282.166
normaliseIllumina18.418 0.20818.739
numBeads2.5280.0322.565
outlierplot19.465 0.32019.854
plotBeadIntensities3.9400.0884.068
plotBeadLocations2.8160.1642.982
plotChipLayout0.0000.0000.001
plotMAXY3.5090.0603.595
poscontPlot12.668 0.20412.934
quickSummary9.5570.1209.750
readBeadSummaryData0.0000.0000.002
sectionNames2.5480.0282.580
showArrayMask8.6770.0768.827
squeezedVarOutlierMethod55.211 0.04055.432
summarize38.111 0.54838.850
transformationFunctions3.2920.1243.421
weightsOutlierMethod0.0000.0000.001