Package: flowCore

Version: 1.19.1

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings flowCore_1.19.1.tar.gz

StartedAt: 2011-05-09 12:20:31 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 12:23:20 -0700 (Mon, 09 May 2011)

EllapsedTime: 169.8 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) (2011-04-18 r55504)
* 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 ‘1.19.1’
* 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 17.8Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    data      8.1Mb
    doc       7.2Mb
* 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 1.3-00)
** 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 1.3-00)

* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.252	0.008	0.262
Subset-methods	1.704	0.016	1.718
actionItem-class	0.004	0.000	0.001
arcsinhTransform	0.228	0.000	0.228
asinht-class	0.052	0.000	0.051
biexponentialTransform	11.737	0.256	12.005
boundaryFilter-class	0.344	0.012	0.356
characterOrTransformation-class	0.000	0.000	0.001
coerce	0.116	0.000	0.117
compensateActionItem-class	0.000	0.000	0.001
compensateView-class	0.000	0.000	0.001
compensatedParameter-class	0.296	0.004	0.302
compensation-class	0.716	0.012	0.734
curv1Filter-class	1.100	0.000	1.099
curv2Filter-class	3.880	0.000	3.879
dg1polynomial-class	0.048	0.004	0.051
each_col-methods	0.068	0.004	0.071
ellipsoidGate	0.128	0.004	0.129
exponential-class	0.044	0.000	0.050
expressionFilter-class	0.136	0.000	0.139
fcReference-class	0.000	0.000	0.002
filter-methods	1.116	0.016	1.130
filter-on-methods	0.24	0.00	0.24
filterList-class	0.016	0.000	0.017
filterResult-class	0.004	0.000	0.001
filterResultList-class	2.332	0.020	2.350
filterSet-class	0.088	0.000	0.087
filterSummary-class	0.608	0.000	0.607
filterSummaryList-class	1.880	0.000	1.879
flowFrame-class	4.353	0.028	4.384
flowSet-class	4.836	0.040	4.878
fsApply	0.304	0.004	0.310
gateActionItem-class	0.000	0.004	0.002
gateView-class	0.000	0.000	0.001
hyperlog-class	1.764	0.000	1.766
identifier-methods	0.040	0.004	0.044
inverseLogicleTransform	0.740	0.008	0.750
invsplitscale-class	0.052	0.000	0.051
keyword-methods	1.084	0.020	1.107
kmeansFilter	0.332	0.000	0.332
linearTransform	0.072	0.000	0.072
lnTransform	3.956	0.064	4.019
logTransform	0.076	0.004	0.078
logarithm-class	0.052	0.000	0.053
logicalFilterResult-class	0.000	0.000	0.001
logicleTransform	0.937	0.008	0.943
manyFilterResult-class	0.000	0.000	0.001
multipleFilterResult-class	0.000	0.000	0.001
norm2Filter-class	0.208	0.000	0.207
normalizeActionItem-class	0.000	0.000	0.001
normalizeView-class	0.000	0.000	0.001
parameters-methods	0.044	0.000	0.042
polygonGate	0.112	0.000	0.110
quadGate	0.32	0.00	0.32
quadratic-class	0.044	0.000	0.043
quadraticTransform	0.068	0.000	0.067
ratio-class	0.052	0.004	0.053
read.FCS	0.072	0.008	0.078
read.FCSheader	0.008	0.000	0.009
read.flowSet	0.188	0.004	0.192
rectangleGate	0.212	0.000	0.233
sampleFilter-class	0.100	0.004	0.102
scaleTransform	0.068	0.000	0.070
singleParameterTransform-class	0.000	0.000	0.002
sinht-class	0.048	0.000	0.047
split-methods	1.644	0.048	1.693
splitScaleTransform	3.58	0.06	3.64
splitscale-class	0.212	0.004	0.216
squareroot-class	0.048	0.000	0.045
subsettingActionItem-class	0.000	0.000	0.001
subsettingView-class	0.000	0.000	0.001
timeFilter-class	2.592	0.012	2.616
transform-class	0.004	0.000	0.003
transformActionItem-class	0.000	0.004	0.001
transformFilter-class	0.192	0.000	0.190
transformList-class	0.736	0.000	0.741
transformMap-class	0.000	0.000	0.001
transformView-class	0.000	0.004	0.001
truncateTransform	0.072	0.000	0.079
unitytransform-class	0.044	0.000	0.046
view-class	0.000	0.000	0.002
workFlow-class	0.004	0.000	0.001
write.FCS	0.092	0.000	0.090
write.flowSet	1.056	0.008	1.068