Package: flowCore

Version: 1.19.2

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings flowCore_1.19.2.tar.gz

StartedAt: 2011-07-07 00:24:29 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 00:27:16 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 167.3 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/flowCore.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* 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 ‘1.19.2’
* 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 installed package size ... NOTE
  installed size is 11.8Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    data      8.1Mb
    doc       1.2Mb
* 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 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 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

* installing *source* package ‘flowCore’ ...
** libs
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c FastLogicle.cpp -o FastLogicle.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c Logicle.cpp -o Logicle.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c biexponential.c -o biexponential.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c inPolygon.c -o inPolygon.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c inPolytope.c -o inPolytope.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c init.c -o init.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-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 1.3-01)
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘HowTo-flowCore.Rnw’ 
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)

* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.220	0.012	0.230
Subset-methods	1.760	0.020	1.786
actionItem-class	0.000	0.000	0.002
arcsinhTransform	0.212	0.000	0.216
asinht-class	0.048	0.000	0.050
biexponentialTransform	11.553	0.232	11.809
boundaryFilter-class	0.200	0.004	0.204
characterOrTransformation-class	0.000	0.000	0.001
coerce	0.244	0.024	0.266
compensateActionItem-class	0.000	0.000	0.001
compensateView-class	0.000	0.000	0.001
compensatedParameter-class	0.288	0.004	0.293
compensation-class	0.708	0.004	0.714
curv1Filter-class	0.948	0.000	0.948
curv2Filter-class	3.764	0.040	3.819
dg1polynomial-class	0.048	0.000	0.049
each_col-methods	0.064	0.004	0.067
ellipsoidGate	0.124	0.000	0.121
exponential-class	0.052	0.000	0.052
expressionFilter-class	0.128	0.004	0.131
fcReference-class	0.004	0.000	0.001
filter-methods	1.144	0.004	1.152
filter-on-methods	0.244	0.008	0.252
filterList-class	0.012	0.000	0.012
filterResult-class	0.000	0.000	0.001
filterResultList-class	2.184	0.004	2.196
filterSet-class	0.076	0.000	0.076
filterSummary-class	0.560	0.000	0.574
filterSummaryList-class	1.940	0.004	1.945
flowFrame-class	4.265	0.048	4.323
flowSet-class	4.700	0.012	4.722
fsApply	0.372	0.000	0.371
gateActionItem-class	0.000	0.000	0.001
gateView-class	0.000	0.000	0.001
hyperlog-class	1.976	0.004	1.980
identifier-methods	0.044	0.000	0.045
inverseLogicleTransform	0.768	0.008	0.776
invsplitscale-class	0.056	0.000	0.057
keyword-methods	1.092	0.004	1.093
kmeansFilter	0.316	0.000	0.314
linearTransform	0.084	0.000	0.085
lnTransform	4.392	0.024	4.415
logTransform	0.248	0.008	0.261
logarithm-class	0.044	0.000	0.047
logicalFilterResult-class	0.000	0.000	0.001
logicleTransform	0.821	0.008	0.827
manyFilterResult-class	0.000	0.000	0.001
multipleFilterResult-class	0.000	0.000	0.001
norm2Filter-class	0.216	0.000	0.218
normalizeActionItem-class	0.000	0.000	0.002
normalizeView-class	0.000	0.000	0.001
parameters-methods	0.048	0.000	0.048
polygonGate	0.120	0.004	0.126
quadGate	0.364	0.004	0.369
quadratic-class	0.052	0.000	0.051
quadraticTransform	0.080	0.000	0.081
ratio-class	0.056	0.000	0.055
read.FCS	0.080	0.004	0.085
read.FCSheader	0.008	0.000	0.010
read.flowSet	0.220	0.008	0.228
rectangleGate	0.236	0.004	0.244
sampleFilter-class	0.100	0.004	0.103
scaleTransform	0.072	0.000	0.074
singleParameterTransform-class	0.004	0.000	0.002
sinht-class	0.052	0.000	0.055
split-methods	1.716	0.012	1.733
splitScaleTransform	3.592	0.040	3.635
splitscale-class	0.196	0.008	0.204
squareroot-class	0.052	0.000	0.050
subsettingActionItem-class	0.000	0.000	0.001
subsettingView-class	0.000	0.000	0.001
timeFilter-class	2.620	0.004	2.711
transform-class	0.000	0.000	0.003
transformActionItem-class	0.000	0.000	0.001
transformFilter-class	0.168	0.004	0.170
transformList-class	0.744	0.004	0.754
transformMap-class	0.000	0.000	0.001
transformView-class	0.004	0.000	0.001
truncateTransform	0.244	0.000	0.243
unitytransform-class	0.044	0.000	0.046
view-class	0.000	0.000	0.001
workFlow-class	0.004	0.000	0.002
write.FCS	0.068	0.004	0.071
write.flowSet	1.020	0.004	1.024