Package: flowCore

Version: 1.16.0

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

StartedAt: 2011-03-31 07:37:31 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 07:41:34 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 243.0 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.7-bioc/meat/flowCore.Rcheck'
* using R version 2.12.2 (2011-02-25)
* 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 '1.16.0'
* 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
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c FastLogicle.cpp -o FastLogicle.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c Logicle.cpp -o Logicle.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -std=gnu99 -c biexponential.c -o biexponential.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -std=gnu99 -c inPolygon.c -o inPolygon.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -std=gnu99 -c inPolytope.c -o inPolytope.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -std=gnu99 -c init.c -o init.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.7-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˜1.7-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.7-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
  '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 1.1-00)
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.25	0.00	0.25
Subset-methods	1.57	0.05	1.60
actionItem-class	0	0	0
arcsinhTransform	0.23	0.00	0.24
asinht-class	0.09	0.00	0.09
biexponentialTransform	11.44	0.28	11.72
boundaryFilter-class	0.24	0.02	0.25
characterOrTransformation-class	0	0	0
coerce	0.31	0.01	0.33
compensateActionItem-class	0	0	0
compensateView-class	0	0	0
compensatedParameter-class	0.5	0.0	0.5
compensation-class	0.86	0.00	0.86
curv1Filter-class	0.94	0.02	0.95
curv2Filter-class	4.04	0.03	4.08
dg1polynomial-class	0.10	0.00	0.09
each_col-methods	0.11	0.00	0.11
ellipsoidGate	0.15	0.00	0.16
exponential-class	0.10	0.00	0.09
expressionFilter-class	0.16	0.00	0.16
fcReference-class	0	0	0
filter-methods	1.28	0.03	1.31
filter-on-methods	0.28	0.00	0.28
filterList-class	0.02	0.00	0.01
filterResult-class	0	0	0
filterResultList-class	1.98	0.08	2.07
filterSet-class	0.08	0.00	0.08
filterSummary-class	0.64	0.01	0.65
filterSummaryList-class	1.80	0.02	1.83
flowFrame-class	4.64	0.08	4.72
flowSet-class	4.79	0.04	4.84
fsApply	0.43	0.02	0.44
gateActionItem-class	0	0	0
gateView-class	0.01	0.00	0.02
hyperlog-class	2.14	0.00	2.14
identifier-methods	0.10	0.00	0.09
inverseLogicleTransform	0.89	0.00	0.89
invsplitscale-class	0.09	0.00	0.09
keyword-methods	1.05	0.00	1.05
kmeansFilter	0.34	0.00	0.34
linearTransform	0.13	0.00	0.13
lnTransform	3.64	0.11	3.75
logTransform	0.21	0.03	0.25
logarithm-class	0.10	0.00	0.09
logicalFilterResult-class	0.01	0.00	0.02
logicleTransform	0.94	0.02	0.95
manyFilterResult-class	0	0	0
multipleFilterResult-class	0	0	0
norm2Filter-class	0.28	0.00	0.28
normalizeActionItem-class	0	0	0
normalizeView-class	0	0	0
parameters-methods	0.08	0.01	0.10
polygonGate	0.16	0.02	0.17
quadGate	0.39	0.00	0.39
quadratic-class	0.09	0.00	0.09
quadraticTransform	0.11	0.01	0.13
ratio-class	0.09	0.00	0.09
read.FCS	0.15	0.00	0.14
read.FCSheader	0.01	0.00	0.02
read.flowSet	0.34	0.00	0.34
rectangleGate	0.27	0.00	0.27
sampleFilter-class	0.14	0.00	0.14
scaleTransform	0.11	0.00	0.11
singleParameterTransform-class	0.02	0.00	0.01
sinht-class	0.09	0.00	0.10
split-methods	1.69	0.05	1.75
splitScaleTransform	3.14	0.16	3.29
splitscale-class	0.08	0.01	0.10
squareroot-class	0.11	0.00	0.11
subsettingActionItem-class	0	0	0
subsettingView-class	0	0	0
timeFilter-class	2.76	0.05	2.81
transform-class	0.02	0.00	0.02
transformActionItem-class	0	0	0
transformFilter-class	0.22	0.00	0.21
transformList-class	0.89	0.00	0.91
transformMap-class	0	0	0
transformView-class	0	0	0
truncateTransform	0.11	0.00	0.11
unitytransform-class	0.13	0.00	0.12
view-class	0	0	0
workFlow-class	0	0	0
write.FCS	0.07	0.00	0.08
write.flowSet	1.19	0.00	1.24