Package: flowCore

Version: 1.17.2

Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings flowCore_1.17.2.tar.gz

StartedAt: 2011-02-24 17:53:57 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 17:57:15 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 197.9 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/flowCore.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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"E:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c FastLogicle.cpp -o FastLogicle.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c Logicle.cpp -o Logicle.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c biexponential.c -o biexponential.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c inPolygon.c -o inPolygon.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c inPolytope.c -o inPolytope.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c init.c -o init.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c logicleTransform.cpp -o logicleTransform.o
g++ -shared -s -static-libgcc -o flowCore.dll tmp.def FastLogicle.o Logicle.o biexponential.o inPolygon.o inPolytope.o init.o logicleTransform.o -LE:/biocbld/BBS-2˜1.8-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.8-bioc/meat/flowCore.Rcheck/flowCore/libs/i386
** 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	0.23	0.00	0.25
Subset-methods	1.20	0.03	1.27
actionItem-class	0	0	0
arcsinhTransform	0.16	0.00	0.17
asinht-class	0.05	0.02	0.06
biexponentialTransform	15.27	0.14	15.48
boundaryFilter-class	0.28	0.01	0.30
characterOrTransformation-class	0	0	0
coerce	0.09	0.03	0.12
compensateActionItem-class	0	0	0
compensateView-class	0	0	0
compensatedParameter-class	0.30	0.04	0.33
compensation-class	0.66	0.00	0.66
curv1Filter-class	0.97	0.00	0.97
curv2Filter-class	3.78	0.01	3.83
dg1polynomial-class	0.05	0.00	0.05
each_col-methods	0.08	0.00	0.08
ellipsoidGate	0.12	0.00	0.12
exponential-class	0.06	0.00	0.06
expressionFilter-class	0.15	0.00	0.14
fcReference-class	0	0	0
filter-methods	1.69	0.00	1.69
filter-on-methods	0.23	0.00	0.23
filterList-class	0.02	0.00	0.02
filterResult-class	0	0	0
filterResultList-class	2.70	0.00	2.71
filterSet-class	0.06	0.00	0.06
filterSummary-class	0.62	0.02	0.64
filterSummaryList-class	2.46	0.01	2.50
flowFrame-class	5.53	0.11	5.71
flowSet-class	5.03	0.02	5.04
fsApply	0.31	0.00	0.32
gateActionItem-class	0	0	0
gateView-class	0	0	0
hyperlog-class	1.84	0.00	1.85
identifier-methods	0.05	0.00	0.05
inverseLogicleTransform	1.30	0.03	1.33
invsplitscale-class	0.06	0.00	0.08
keyword-methods	1.53	0.05	1.92
kmeansFilter	0.3	0.0	0.3
linearTransform	0.08	0.00	0.07
lnTransform	3.53	0.03	3.58
logTransform	0.19	0.01	0.21
logarithm-class	0.04	0.00	0.04
logicalFilterResult-class	0.02	0.00	0.02
logicleTransform	1.39	0.00	1.40
manyFilterResult-class	0	0	0
multipleFilterResult-class	0	0	0
norm2Filter-class	0.23	0.02	0.29
normalizeActionItem-class	0	0	0
normalizeView-class	0	0	0
parameters-methods	0.07	0.00	0.06
polygonGate	0.12	0.00	0.12
quadGate	0.31	0.01	0.35
quadratic-class	0.07	0.00	0.06
quadraticTransform	0.07	0.00	0.08
ratio-class	0.05	0.02	0.06
read.FCS	0.09	0.00	0.09
read.FCSheader	0.04	0.00	0.04
read.flowSet	0.21	0.00	0.21
rectangleGate	0.24	0.00	0.24
sampleFilter-class	0.08	0.02	0.09
scaleTransform	0.09	0.00	0.10
singleParameterTransform-class	0	0	0
sinht-class	0.06	0.00	0.06
split-methods	2.16	0.04	2.20
splitScaleTransform	3.72	0.03	3.75
splitscale-class	0.06	0.00	0.06
squareroot-class	0.06	0.00	0.07
subsettingActionItem-class	0	0	0
subsettingView-class	0	0	0
timeFilter-class	3.42	0.00	3.44
transform-class	0	0	0
transformActionItem-class	0	0	0
transformFilter-class	0.2	0.0	0.2
transformList-class	1.27	0.02	1.28
transformMap-class	0.00	0.01	0.02
transformView-class	0	0	0
truncateTransform	0.09	0.00	0.09
unitytransform-class	0.05	0.02	0.07
view-class	0	0	0
workFlow-class	0	0	0
write.FCS	0.09	0.02	0.11
write.flowSet	1.64	0.03	1.67