Package: flowCore

Version: 1.23.1

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowCore_1.23.1.tar.gz

StartedAt: 2012-06-20 23:41:21 -0700 (Wed, 20 Jun 2012)

EndedAt: 2012-06-20 23:45:21 -0700 (Wed, 20 Jun 2012)

EllapsedTime: 240.0 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/flowCore.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'flowCore/DESCRIPTION' ... OK
* this is package 'flowCore' version '1.23.1'
* 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 whether package 'flowCore' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data      5.0Mb
    doc       1.2Mb
    extdata   1.1Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 examples ... OK
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/flowCore.Rcheck/00check.log'
for details.

* installing *source* package 'flowCore' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c FastLogicle.cpp -o FastLogicle.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c Logicle.cpp -o Logicle.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c biexponential.c -o biexponential.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c inPolygon.c -o inPolygon.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c inPolytope.c -o inPolytope.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c init.c -o init.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c logicleTransform.cpp -o logicleTransform.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o flowCore.so FastLogicle.o Logicle.o biexponential.o inPolygon.o inPolytope.o init.o logicleTransform.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/flowCore.Rcheck/flowCore/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'filter' in package 'flowCore'
** help
*** installing help indices
** building package indices
** installing vignettes
   'HowTo-flowCore.Rnw' 
** testing if installed package can be loaded

* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.255	0.024	0.279
Subset-methods	1.634	0.165	1.804
actionItem-class	0.002	0.000	0.002
arcsinhTransform	0.226	0.046	0.272
asinht-class	0.070	0.021	0.091
biexponentialTransform	12.413	3.313	15.906
boundaryFilter-class	0.322	0.073	0.398
characterOrTransformation-class	0.002	0.000	0.001
coerce	0.135	0.042	0.178
compensateActionItem-class	0.000	0.000	0.002
compensateView-class	0.001	0.001	0.002
compensatedParameter-class	0.374	0.149	0.527
compensation-class	0.810	0.328	1.144
curv1Filter-class	0.665	0.262	0.961
curv2Filter-class	3.882	0.721	4.653
dg1polynomial-class	0.063	0.019	0.081
each_col-methods	0.082	0.037	0.122
ellipsoidGate	0.143	0.037	0.182
exponential-class	0.063	0.018	0.084
expressionFilter-class	0.166	0.061	0.239
fcReference-class	0.002	0.000	0.002
filter-methods	1.527	0.170	1.729
filter-on-methods	0.265	0.050	0.316
filterList-class	0.014	0.000	0.014
filterResult-class	0.001	0.000	0.001
filterResultList-class	2.286	0.896	3.214
filterSet-class	0.208	0.023	0.232
filterSummary-class	0.235	0.103	0.341
filterSummaryList-class	1.762	0.564	2.385
flowFrame-class	5.784	0.798	6.662
flowSet-class	5.294	0.763	6.142
fsApply	0.376	0.151	0.536
gateActionItem-class	0.001	0.000	0.002
gateView-class	0.001	0.000	0.001
hyperlog-class	2.675	0.057	2.816
identifier-methods	0.054	0.017	0.072
inverseLogicleTransform	1.190	0.162	1.399
invsplitscale-class	0.064	0.018	0.082
keyword-methods	1.344	0.336	1.710
kmeansFilter	0.376	0.077	0.467
linearTransform	0.096	0.042	0.151
lnTransform	4.649	1.791	7.375
logTransform	0.091	0.034	0.126
logarithm-class	0.064	0.019	0.083
logicalFilterResult-class	0.001	0.000	0.001
logicleTransform	1.260	0.168	1.563
manyFilterResult-class	0.001	0.000	0.001
multipleFilterResult-class	0.002	0.001	0.002
norm2Filter-class	0.332	0.060	0.490
normalizeActionItem-class	0.001	0.000	0.001
normalizeView-class	0.001	0.000	0.001
parameters-methods	0.060	0.019	0.090
polygonGate	0.154	0.050	0.215
quadGate	0.452	0.093	0.650
quadratic-class	0.062	0.017	0.081
quadraticTransform	0.100	0.044	0.146
ratio-class	0.073	0.039	0.114
read.FCS	0.115	0.021	0.137
read.FCSheader	0.009	0.004	0.014
read.flowSet	0.256	0.105	0.365
rectangleGate	0.231	0.046	0.277
sampleFilter-class	0.129	0.044	0.172
scaleTransform	0.093	0.036	0.130
singleParameterTransform-class	0.002	0.000	0.001
sinht-class	0.068	0.021	0.111
split-methods	2.461	0.492	2.987
splitScaleTransform	3.710	1.922	5.730
splitscale-class	0.066	0.022	0.090
squareroot-class	0.068	0.022	0.091
subsettingActionItem-class	0.002	0.000	0.001
subsettingView-class	0.001	0.000	0.001
timeFilter-class	3.169	0.410	3.609
transform-class	0.003	0.001	0.003
transformActionItem-class	0.000	0.000	0.001
transformFilter-class	0.294	0.076	0.373
transformList-class	1.163	0.147	1.331
transformMap-class	0.001	0.000	0.001
transformView-class	0.001	0.000	0.001
truncateTransform	0.101	0.059	0.166
unitytransform-class	0.057	0.019	0.076
view-class	0.001	0.001	0.002
workFlow-class	0.001	0.001	0.002
write.FCS	0.220	0.039	0.268
write.flowSet	2.235	0.299	2.570