Package: flowCore

Version: 1.17.2

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

StartedAt: 2011-02-24 19:34:33 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 19:37:41 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 188.2 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/flowCore.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-pc-mingw32 (64-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
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c FastLogicle.cpp -o FastLogicle.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c Logicle.cpp -o Logicle.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -std=gnu99 -c biexponential.c -o biexponential.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -std=gnu99 -c inPolygon.c -o inPolygon.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -std=gnu99 -c inPolytope.c -o inPolytope.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -std=gnu99 -c init.c -o init.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c logicleTransform.cpp -o logicleTransform.o
x86_64-w64-mingw32-g++ -shared -s -static-libgcc -o flowCore.dll tmp.def FastLogicle.o Logicle.o biexponential.o inPolygon.o inPolytope.o init.o logicleTransform.o -LD:/biocbld/BBS-2˜1.8-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.8-bioc/meat/flowCore.Rcheck/flowCore/libs/x64
** 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	0.26	0.00	0.27
Subset-methods	1.64	0.04	1.67
actionItem-class	0	0	0
arcsinhTransform	0.24	0.01	0.25
asinht-class	0.11	0.00	0.11
biexponentialTransform	11.69	0.25	11.96
boundaryFilter-class	0.34	0.02	0.43
characterOrTransformation-class	0	0	0
coerce	0.22	0.00	0.22
compensateActionItem-class	0	0	0
compensateView-class	0	0	0
compensatedParameter-class	0.57	0.00	0.57
compensation-class	0.85	0.00	0.85
curv1Filter-class	1.05	0.00	1.05
curv2Filter-class	4.22	0.01	4.24
dg1polynomial-class	0.08	0.02	0.09
each_col-methods	0.09	0.00	0.09
ellipsoidGate	0.17	0.00	0.17
exponential-class	0.10	0.00	0.09
expressionFilter-class	0.17	0.00	0.18
fcReference-class	0.02	0.00	0.01
filter-methods	1.32	0.00	1.35
filter-on-methods	0.32	0.00	0.31
filterList-class	0.01	0.00	0.01
filterResult-class	0	0	0
filterResultList-class	2.17	0.00	2.18
filterSet-class	0.08	0.00	0.07
filterSummary-class	0.67	0.02	0.69
filterSummaryList-class	1.75	0.03	1.81
flowFrame-class	5.05	0.08	5.24
flowSet-class	4.84	0.03	4.89
fsApply	0.46	0.00	0.45
gateActionItem-class	0	0	0
gateView-class	0	0	0
hyperlog-class	2.07	0.00	2.06
identifier-methods	0.09	0.00	0.09
inverseLogicleTransform	0.96	0.00	0.97
invsplitscale-class	0.09	0.02	0.11
keyword-methods	1.24	0.01	1.25
kmeansFilter	0.34	0.00	0.34
linearTransform	0.11	0.02	0.13
lnTransform	3.48	0.11	3.59
logTransform	0.24	0.01	0.25
logarithm-class	0.11	0.00	0.11
logicalFilterResult-class	0	0	0
logicleTransform	0.99	0.02	1.00
manyFilterResult-class	0	0	0
multipleFilterResult-class	0	0	0
norm2Filter-class	0.26	0.01	0.42
normalizeActionItem-class	0	0	0
normalizeView-class	0	0	0
parameters-methods	0.09	0.00	0.10
polygonGate	0.17	0.00	0.17
quadGate	0.39	0.00	0.39
quadratic-class	0.11	0.00	0.11
quadraticTransform	0.11	0.00	0.11
ratio-class	0.10	0.02	0.11
read.FCS	0.12	0.01	0.14
read.FCSheader	0.02	0.00	0.01
read.flowSet	0.36	0.00	0.36
rectangleGate	0.26	0.00	0.27
sampleFilter-class	0.14	0.02	0.15
scaleTransform	0.14	0.00	0.14
singleParameterTransform-class	0	0	0
sinht-class	0.1	0.0	0.1
split-methods	1.81	0.05	1.86
splitScaleTransform	3.58	0.09	3.67
splitscale-class	0.22	0.02	0.23
squareroot-class	0.09	0.00	0.10
subsettingActionItem-class	0	0	0
subsettingView-class	0	0	0
timeFilter-class	2.81	0.00	2.81
transform-class	0.01	0.00	0.02
transformActionItem-class	0	0	0
transformFilter-class	0.22	0.01	0.23
transformList-class	0.88	0.02	0.90
transformMap-class	0	0	0
transformView-class	0	0	0
truncateTransform	0.26	0.03	0.29
unitytransform-class	0.1	0.0	0.1
view-class	0	0	0
workFlow-class	0	0	0
write.FCS	0.08	0.00	0.08
write.flowSet	1.20	0.03	1.27