Package: flowCore

Version: 1.16.0

Command: E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings flowCore_1.16.0.tar.gz

StartedAt: 2011-04-07 06:53:32 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 06:57:10 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 217.7 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.7-bioc/meat/flowCore.Rcheck'
* using R version 2.12.2 (2011-02-25)
* 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 '1.16.0'
* 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) and $(LAPACK_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˜1.7-B/R/include"         -O2 -Wall  -c FastLogicle.cpp -o FastLogicle.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c Logicle.cpp -o Logicle.o
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O3 -Wall  -std=gnu99 -c biexponential.c -o biexponential.o
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O3 -Wall  -std=gnu99 -c inPolygon.c -o inPolygon.o
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O3 -Wall  -std=gnu99 -c inPolytope.c -o inPolytope.o
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O3 -Wall  -std=gnu99 -c init.c -o init.o
g++ -I"E:/biocbld/BBS-2˜1.7-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˜1.7-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.7-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
  'openVignette()'. 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 1.2-01)
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.21	0.00	0.22
Subset-methods	1.60	0.02	1.61
actionItem-class	0	0	0
arcsinhTransform	0.17	0.00	0.17
asinht-class	0.06	0.01	0.08
biexponentialTransform	15.53	0.24	15.79
boundaryFilter-class	0.38	0.03	0.41
characterOrTransformation-class	0	0	0
coerce	0.14	0.00	0.14
compensateActionItem-class	0	0	0
compensateView-class	0	0	0
compensatedParameter-class	0.34	0.00	0.34
compensation-class	0.78	0.00	0.78
curv1Filter-class	1.19	0.00	1.20
curv2Filter-class	5.14	0.02	5.18
dg1polynomial-class	0.06	0.00	0.06
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	0.14	0.00	0.14
fcReference-class	0	0	0
filter-methods	1.77	0.03	1.81
filter-on-methods	0.29	0.00	0.31
filterList-class	0.02	0.00	0.02
filterResult-class	0	0	0
filterResultList-class	2.89	0.01	2.92
filterSet-class	0.08	0.00	0.08
filterSummary-class	0.94	0.00	0.94
filterSummaryList-class	2.62	0.00	2.64
flowFrame-class	10.80	0.16	11.39
flowSet-class	6.80	0.00	7.45
fsApply	0.31	0.01	0.33
gateActionItem-class	0	0	0
gateView-class	0	0	0
hyperlog-class	1.93	0.00	1.92
identifier-methods	0.04	0.00	0.04
inverseLogicleTransform	1.28	0.00	1.29
invsplitscale-class	0.07	0.00	0.06
keyword-methods	1.49	0.02	1.52
kmeansFilter	0.34	0.00	0.34
linearTransform	0.09	0.00	0.10
lnTransform	3.88	0.02	3.93
logTransform	0.08	0.01	0.10
logarithm-class	0.06	0.00	0.07
logicalFilterResult-class	0	0	0
logicleTransform	1.36	0.00	1.36
manyFilterResult-class	0	0	0
multipleFilterResult-class	0	0	0
norm2Filter-class	0.27	0.00	0.31
normalizeActionItem-class	0	0	0
normalizeView-class	0	0	0
parameters-methods	0.06	0.00	0.06
polygonGate	0.13	0.00	0.13
quadGate	0.37	0.00	0.37
quadratic-class	0.05	0.00	0.08
quadraticTransform	0.09	0.00	0.09
ratio-class	0.07	0.00	0.07
read.FCS	0.1	0.0	0.1
read.FCSheader	0	0	0
read.flowSet	0.22	0.00	0.21
rectangleGate	0.29	0.00	0.28
sampleFilter-class	0.11	0.00	0.13
scaleTransform	0.09	0.00	0.09
singleParameterTransform-class	0	0	0
sinht-class	0.06	0.00	0.06
split-methods	2.16	0.00	2.19
splitScaleTransform	3.76	0.05	3.81
splitscale-class	0.07	0.00	0.07
squareroot-class	0.14	0.03	0.17
subsettingActionItem-class	0	0	0
subsettingView-class	0	0	0
timeFilter-class	4.86	0.00	4.86
transform-class	0	0	0
transformActionItem-class	0	0	0
transformFilter-class	0.20	0.00	0.21
transformList-class	1.24	0.03	1.27
transformMap-class	0	0	0
transformView-class	0	0	0
truncateTransform	0.08	0.00	0.08
unitytransform-class	0.07	0.00	0.06
view-class	0	0	0
workFlow-class	0	0	0
write.FCS	0.07	0.01	0.10
write.flowSet	1.63	0.00	1.67