Package: flowCore

Version: 1.19.2

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch flowCore_1.19.2.tar.gz

StartedAt: 2011-07-07 03:48:53 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 03:52:55 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 241.6 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/flowCore.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* 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 '1.19.2'
* 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 installed package size ... NOTE
  installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data      8.0Mb
    doc       1.2Mb
    extdata   1.1Mb
* 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 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
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c FastLogicle.cpp -o FastLogicle.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c Logicle.cpp -o Logicle.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -c biexponential.c -o biexponential.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -c inPolygon.c -o inPolygon.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -c inPolytope.c -o inPolytope.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -c init.c -o init.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-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˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-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 1.3-01)
** 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 1.3-01)

* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.34	0.01	0.36
Subset-methods	1.61	0.03	1.64
actionItem-class	0	0	0
arcsinhTransform	0.24	0.00	0.24
asinht-class	0.10	0.00	0.12
biexponentialTransform	10.96	0.38	11.38
boundaryFilter-class	0.23	0.00	0.23
characterOrTransformation-class	0	0	0
coerce	0.19	0.00	0.18
compensateActionItem-class	0	0	0
compensateView-class	0	0	0
compensatedParameter-class	0.42	0.09	0.51
compensation-class	0.85	0.03	0.88
curv1Filter-class	0.95	0.00	0.97
curv2Filter-class	3.95	0.03	4.08
dg1polynomial-class	0.1	0.0	0.1
each_col-methods	0.09	0.00	0.09
ellipsoidGate	0.17	0.00	0.17
exponential-class	0.1	0.0	0.1
expressionFilter-class	0.17	0.00	0.17
fcReference-class	0	0	0
filter-methods	1.44	0.00	1.44
filter-on-methods	0.27	0.00	0.27
filterList-class	0.01	0.00	0.01
filterResult-class	0	0	0
filterResultList-class	2.11	0.16	2.27
filterSet-class	0.08	0.00	0.08
filterSummary-class	0.56	0.00	0.58
filterSummaryList-class	1.61	0.08	1.68
flowFrame-class	4.85	0.14	6.64
flowSet-class	4.89	0.05	4.96
fsApply	0.43	0.03	0.59
gateActionItem-class	0	0	0
gateView-class	0	0	0
hyperlog-class	2.15	0.00	2.81
identifier-methods	0.09	0.00	0.09
inverseLogicleTransform	1.00	0.01	1.05
invsplitscale-class	0.15	0.00	0.14
keyword-methods	1.17	0.03	1.71
kmeansFilter	0.61	0.00	1.14
linearTransform	0.12	0.00	0.16
lnTransform	3.83	0.18	4.45
logTransform	0.25	0.00	0.25
logarithm-class	0.09	0.01	0.11
logicalFilterResult-class	0	0	0
logicleTransform	1.00	0.02	1.03
manyFilterResult-class	0	0	0
multipleFilterResult-class	0	0	0
norm2Filter-class	0.30	0.00	0.33
normalizeActionItem-class	0	0	0
normalizeView-class	0	0	0
parameters-methods	0.08	0.00	0.09
polygonGate	0.15	0.00	0.16
quadGate	0.41	0.00	0.41
quadratic-class	0.11	0.00	0.11
quadraticTransform	0.13	0.00	0.12
ratio-class	0.09	0.00	0.09
read.FCS	0.12	0.00	0.15
read.FCSheader	0.00	0.03	0.03
read.flowSet	0.30	0.03	0.32
rectangleGate	0.26	0.02	0.28
sampleFilter-class	0.14	0.00	0.14
scaleTransform	0.13	0.00	0.13
singleParameterTransform-class	0	0	0
sinht-class	0.11	0.00	0.14
split-methods	1.90	0.06	1.97
splitScaleTransform	3.63	0.08	3.70
splitscale-class	0.23	0.01	0.25
squareroot-class	0.10	0.00	0.09
subsettingActionItem-class	0	0	0
subsettingView-class	0	0	0
timeFilter-class	2.89	0.02	2.91
transform-class	0	0	0
transformActionItem-class	0	0	0
transformFilter-class	0.22	0.00	0.22
transformList-class	0.93	0.00	0.94
transformMap-class	0	0	0
transformView-class	0	0	0
truncateTransform	0.16	0.00	0.15
unitytransform-class	0.09	0.00	0.10
view-class	0	0	0
workFlow-class	0	0	0
write.FCS	0.08	0.00	0.07
write.flowSet	1.26	0.01	1.28