Package: flowCore

Version: 1.20.0

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch flowCore_1.20.0.tar.gz

StartedAt: 2012-01-09 03:02:56 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 03:05:46 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 170.5 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/flowCore.Rcheck'
* using R version 2.14.1 (2011-12-22)
* 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 '1.20.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'flowCore' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data      5.0Mb
    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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 compiled code ... 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
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c FastLogicle.cpp -o FastLogicle.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c Logicle.cpp -o Logicle.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c biexponential.c -o biexponential.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c inPolygon.c -o inPolygon.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c inPolytope.c -o inPolytope.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -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˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/flowCore.Rcheck/flowCore/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
Warning: replacing previous import '.__C__character' when loading 'methods'
Creating a new generic function for 'filter' in package 'flowCore'
** 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)
Warning message:
replacing previous import '.__C__character' when loading 'methods' 

* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.21	0.00	0.20
Subset-methods	1.03	0.03	1.07
actionItem-class	0	0	0
arcsinhTransform	0.17	0.01	0.18
asinht-class	0.05	0.00	0.05
biexponentialTransform	15.50	0.15	15.67
boundaryFilter-class	0.14	0.00	0.14
characterOrTransformation-class	0	0	0
coerce	0.21	0.01	0.22
compensateActionItem-class	0	0	0
compensateView-class	0	0	0
compensatedParameter-class	0.28	0.00	0.28
compensation-class	0.53	0.00	0.53
curv1Filter-class	0.44	0.02	0.45
curv2Filter-class	2.48	0.01	2.50
dg1polynomial-class	0.06	0.00	0.07
each_col-methods	0.06	0.00	0.06
ellipsoidGate	0.08	0.02	0.09
exponential-class	0.07	0.00	0.06
expressionFilter-class	0.10	0.00	0.11
fcReference-class	0	0	0
filter-methods	1.82	0.06	1.88
filter-on-methods	0.15	0.02	0.17
filterList-class	0.02	0.00	0.02
filterResult-class	0	0	0
filterResultList-class	2.61	0.09	2.71
filterSet-class	0.05	0.00	0.05
filterSummary-class	0.2	0.0	0.2
filterSummaryList-class	2.31	0.00	2.32
flowFrame-class	5.44	0.05	5.51
flowSet-class	4.27	0.01	4.30
fsApply	0.25	0.00	0.25
gateActionItem-class	0.02	0.00	0.01
gateView-class	0	0	0
hyperlog-class	1.60	0.02	1.66
identifier-methods	0.05	0.00	0.04
inverseLogicleTransform	1.63	0.06	1.69
invsplitscale-class	0.06	0.00	0.06
keyword-methods	1.80	0.02	1.82
kmeansFilter	0.23	0.00	0.23
linearTransform	0.06	0.00	0.06
lnTransform	4.17	0.09	4.28
logTransform	0.07	0.00	0.07
logarithm-class	0.15	0.01	0.17
logicalFilterResult-class	0	0	0
logicleTransform	1.72	0.03	1.75
manyFilterResult-class	0	0	0
multipleFilterResult-class	0	0	0
norm2Filter-class	0.21	0.00	0.25
normalizeActionItem-class	0	0	0
normalizeView-class	0	0	0
parameters-methods	0.04	0.00	0.05
polygonGate	0.1	0.0	0.1
quadGate	0.25	0.00	0.25
quadratic-class	0.06	0.00	0.06
quadraticTransform	0.06	0.00	0.06
ratio-class	0.05	0.00	0.05
read.FCS	0.04	0.03	0.08
read.FCSheader	0.02	0.00	0.01
read.flowSet	0.19	0.00	0.19
rectangleGate	0.14	0.00	0.14
sampleFilter-class	0.08	0.00	0.08
scaleTransform	0.06	0.00	0.06
singleParameterTransform-class	0	0	0
sinht-class	0.06	0.00	0.06
split-methods	2.35	0.07	2.41
splitScaleTransform	3.75	0.09	3.84
splitscale-class	0.15	0.02	0.17
squareroot-class	0.05	0.00	0.05
subsettingActionItem-class	0	0	0
subsettingView-class	0	0	0
timeFilter-class	2.95	0.02	2.97
transform-class	0	0	0
transformActionItem-class	0	0	0
transformFilter-class	0.17	0.00	0.17
transformList-class	1.68	0.01	1.68
transformMap-class	0	0	0
transformView-class	0	0	0
truncateTransform	0.06	0.00	0.07
unitytransform-class	0.04	0.00	0.04
view-class	0	0	0
workFlow-class	0	0	0
write.FCS	0.08	0.02	0.10
write.flowSet	1.94	0.01	1.95