Package: flowCore

Version: 1.17.2

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings flowCore_1.17.2.tar.gz

StartedAt: 2011-02-24 19:23:35 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 19:26:16 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 160.1 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/flowCore.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘1.17.2’
* 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 ... 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-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c FastLogicle.cpp -o FastLogicle.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Logicle.cpp -o Logicle.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c biexponential.c -o biexponential.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c inPolygon.c -o inPolygon.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c inPolytope.c -o inPolytope.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c init.c -o init.o
g++ -I/home/biocbuild/bbs-2.8-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-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/flowCore.Rcheck/flowCore/libs
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. 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	0.216	0.000	0.214
Subset-methods	1.516	0.032	1.563
actionItem-class	0.004	0.000	0.002
arcsinhTransform	0.200	0.004	0.203
asinht-class	0.048	0.000	0.047
biexponentialTransform	10.468	0.244	10.755
boundaryFilter-class	0.308	0.004	0.312
characterOrTransformation-class	0.004	0.000	0.001
coerce	0.1	0.0	0.1
compensateActionItem-class	0.000	0.000	0.001
compensateView-class	0.000	0.000	0.001
compensatedParameter-class	0.272	0.000	0.271
compensation-class	0.665	0.004	0.667
curv1Filter-class	0.940	0.004	0.946
curv2Filter-class	3.948	0.000	3.954
dg1polynomial-class	0.044	0.000	0.045
each_col-methods	0.06	0.00	0.06
ellipsoidGate	0.112	0.008	0.117
exponential-class	0.044	0.000	0.044
expressionFilter-class	0.120	0.000	0.121
fcReference-class	0.000	0.000	0.002
filter-methods	1.060	0.012	1.070
filter-on-methods	0.232	0.004	0.235
filterList-class	0.012	0.000	0.011
filterResult-class	0.004	0.000	0.001
filterResultList-class	2.064	0.004	2.072
filterSet-class	0.072	0.000	0.073
filterSummary-class	0.588	0.000	0.591
filterSummaryList-class	1.688	0.004	1.697
flowFrame-class	3.928	0.040	3.975
flowSet-class	4.237	0.020	4.529
fsApply	0.288	0.004	0.293
gateActionItem-class	0.000	0.004	0.001
gateView-class	0.000	0.000	0.001
hyperlog-class	1.804	0.004	1.805
identifier-methods	0.040	0.000	0.039
inverseLogicleTransform	0.724	0.008	0.732
invsplitscale-class	0.044	0.004	0.047
keyword-methods	1.012	0.020	1.033
kmeansFilter	0.292	0.004	0.295
linearTransform	0.068	0.000	0.069
lnTransform	3.564	0.048	3.610
logTransform	0.220	0.012	0.231
logarithm-class	0.044	0.000	0.045
logicalFilterResult-class	0.000	0.000	0.001
logicleTransform	0.768	0.008	0.776
manyFilterResult-class	0.000	0.000	0.001
multipleFilterResult-class	0.000	0.000	0.001
norm2Filter-class	0.228	0.004	0.231
normalizeActionItem-class	0.000	0.004	0.001
normalizeView-class	0.000	0.000	0.001
parameters-methods	0.044	0.004	0.046
polygonGate	0.108	0.008	0.113
quadGate	0.344	0.004	0.346
quadratic-class	0.044	0.000	0.045
quadraticTransform	0.076	0.000	0.076
ratio-class	0.044	0.000	0.045
read.FCS	0.080	0.004	0.084
read.FCSheader	0.008	0.000	0.010
read.flowSet	0.188	0.004	0.189
rectangleGate	0.212	0.000	0.214
sampleFilter-class	0.092	0.000	0.094
scaleTransform	0.064	0.004	0.069
singleParameterTransform-class	0.000	0.000	0.001
sinht-class	0.048	0.000	0.047
split-methods	1.580	0.036	1.616
splitScaleTransform	3.325	0.028	3.354
splitscale-class	0.196	0.008	0.202
squareroot-class	0.044	0.000	0.043
subsettingActionItem-class	0.000	0.000	0.001
subsettingView-class	0.000	0.000	0.001
timeFilter-class	2.416	0.004	2.429
transform-class	0.000	0.000	0.003
transformActionItem-class	0.000	0.000	0.001
transformFilter-class	0.176	0.008	0.191
transformList-class	0.696	0.008	0.718
transformMap-class	0.000	0.000	0.001
transformView-class	0.000	0.004	0.001
truncateTransform	0.240	0.000	0.241
unitytransform-class	0.040	0.000	0.039
view-class	0.000	0.004	0.001
workFlow-class	0.000	0.000	0.001
write.FCS	0.068	0.004	0.070
write.flowSet	1.016	0.004	1.023