Package: flowCore

Version: 1.16.0

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings flowCore_1.16.0.tar.gz

StartedAt: 2011-03-31 05:43:00 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 05:45:36 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 156.9 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/flowCore.Rcheck’
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowCore/DESCRIPTION’ ... OK
* this is package ‘flowCore’ version ‘1.16.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘flowCore’ can be installed ... OK
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 data for non-ASCII characters ... 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 examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘flowCore’ ...
** libs
g++ -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c FastLogicle.cpp -o FastLogicle.o
g++ -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Logicle.cpp -o Logicle.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c biexponential.c -o biexponential.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c inPolygon.c -o inPolygon.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c inPolytope.c -o inPolytope.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c init.c -o init.o
g++ -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c logicleTransform.cpp -o logicleTransform.o
g++ -shared -L/usr/local/lib64 -o flowCore.so FastLogicle.o Logicle.o biexponential.o inPolygon.o inPolytope.o init.o logicleTransform.o -L/home/biocbuild/bbs-2.7-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.7-bioc/meat/flowCore.Rcheck/flowCore/libs
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: robustbase
Loading required package: pcaPP
Loading required package: mvtnorm
Scalable Robust Estimators with High Breakdown Point (version 1.1-00)
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.192	0.008	0.202
Subset-methods	1.532	0.032	1.563
actionItem-class	0.000	0.000	0.002
arcsinhTransform	0.184	0.000	0.186
asinht-class	0.044	0.004	0.047
biexponentialTransform	10.476	0.196	10.670
boundaryFilter-class	0.184	0.000	0.185
characterOrTransformation-class	0.000	0.000	0.001
coerce	0.220	0.000	0.218
compensateActionItem-class	0.000	0.000	0.001
compensateView-class	0.000	0.000	0.001
compensatedParameter-class	0.272	0.004	0.277
compensation-class	0.641	0.000	0.640
curv1Filter-class	0.888	0.000	0.890
curv2Filter-class	3.764	0.000	3.766
dg1polynomial-class	0.044	0.000	0.045
each_col-methods	0.060	0.000	0.061
ellipsoidGate	0.112	0.000	0.110
exponential-class	0.044	0.000	0.044
expressionFilter-class	0.116	0.000	0.115
fcReference-class	0.004	0.000	0.002
filter-methods	1.052	0.008	1.059
filter-on-methods	0.228	0.000	0.228
filterList-class	0.012	0.000	0.012
filterResult-class	0.000	0.000	0.001
filterResultList-class	1.872	0.008	1.878
filterSet-class	0.072	0.000	0.072
filterSummary-class	0.592	0.000	0.589
filterSummaryList-class	1.656	0.012	1.669
flowFrame-class	3.808	0.052	3.859
flowSet-class	4.229	0.012	4.238
fsApply	0.300	0.000	0.299
gateActionItem-class	0.004	0.000	0.002
gateView-class	0.000	0.000	0.001
hyperlog-class	1.884	0.008	1.889
identifier-methods	0.036	0.000	0.037
inverseLogicleTransform	0.708	0.004	0.712
invsplitscale-class	0.044	0.000	0.045
keyword-methods	0.812	0.004	0.815
kmeansFilter	0.276	0.004	0.281
linearTransform	0.064	0.000	0.065
lnTransform	3.824	0.008	3.831
logTransform	0.204	0.004	0.208
logarithm-class	0.044	0.000	0.044
logicalFilterResult-class	0.000	0.000	0.001
logicleTransform	0.760	0.004	0.766
manyFilterResult-class	0.000	0.000	0.001
multipleFilterResult-class	0.000	0.000	0.001
norm2Filter-class	0.224	0.000	0.222
normalizeActionItem-class	0.000	0.000	0.001
normalizeView-class	0.004	0.000	0.001
parameters-methods	0.040	0.004	0.046
polygonGate	0.108	0.000	0.109
quadGate	0.324	0.004	0.328
quadratic-class	0.040	0.000	0.044
quadraticTransform	0.068	0.000	0.070
ratio-class	0.044	0.000	0.045
read.FCS	0.08	0.00	0.08
read.FCSheader	0.000	0.008	0.009
read.flowSet	0.184	0.000	0.185
rectangleGate	0.212	0.000	0.210
sampleFilter-class	0.088	0.000	0.088
scaleTransform	0.068	0.000	0.067
singleParameterTransform-class	0.000	0.000	0.001
sinht-class	0.044	0.000	0.045
split-methods	1.500	0.000	1.502
splitScaleTransform	3.093	0.004	3.096
splitscale-class	0.196	0.004	0.202
squareroot-class	0.044	0.000	0.044
subsettingActionItem-class	0.000	0.000	0.001
subsettingView-class	0.004	0.000	0.001
timeFilter-class	2.360	0.008	2.370
transform-class	0.004	0.000	0.002
transformActionItem-class	0.000	0.000	0.001
transformFilter-class	0.168	0.004	0.171
transformList-class	0.696	0.000	0.696
transformMap-class	0.000	0.000	0.001
transformView-class	0.000	0.000	0.001
truncateTransform	0.072	0.000	0.074
unitytransform-class	0.040	0.000	0.039
view-class	0.004	0.000	0.001
workFlow-class	0.000	0.000	0.001
write.FCS	0.064	0.004	0.067
write.flowSet	1.016	0.004	1.020