Package: flowCore

Version: 1.20.0

Command: D:\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 02:42:27 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 02:45:25 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 178.7 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 2.14.1 (2011-12-22)
* 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 '1.20.0'
* 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  9.3Mb
  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
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c FastLogicle.cpp -o FastLogicle.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -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 -mtune=core2 -c init.c -o init.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -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
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	0.3	0.0	0.3
Subset-methods	1.27	0.05	1.32
actionItem-class	0	0	0
arcsinhTransform	0.12	0.00	0.12
asinht-class	0.21	0.00	0.21
biexponentialTransform	12.73	0.34	13.07
boundaryFilter-class	0.33	0.02	0.35
characterOrTransformation-class	0	0	0
coerce	0.2	0.0	0.2
compensateActionItem-class	0	0	0
compensateView-class	0	0	0
compensatedParameter-class	0.5	0.0	0.5
compensation-class	0.83	0.02	0.84
curv1Filter-class	0.45	0.04	0.50
curv2Filter-class	2.92	0.02	2.94
dg1polynomial-class	0.1	0.0	0.1
each_col-methods	0.12	0.00	0.12
ellipsoidGate	0.14	0.00	0.14
exponential-class	0.09	0.00	0.09
expressionFilter-class	0.19	0.00	0.19
fcReference-class	0	0	0
filter-methods	1.83	0.04	1.87
filter-on-methods	0.23	0.00	0.24
filterList-class	0	0	0
filterResult-class	0	0	0
filterResultList-class	2.38	0.13	2.50
filterSet-class	0.05	0.00	0.05
filterSummary-class	0.2	0.0	0.2
filterSummaryList-class	1.94	0.14	2.08
flowFrame-class	4.95	0.11	5.06
flowSet-class	4.68	0.05	4.72
fsApply	0.40	0.00	0.41
gateActionItem-class	0	0	0
gateView-class	0	0	0
hyperlog-class	1.92	0.00	1.92
identifier-methods	0.10	0.00	0.09
inverseLogicleTransform	1.47	0.06	1.54
invsplitscale-class	0.08	0.01	0.09
keyword-methods	1.70	0.07	1.76
kmeansFilter	0.33	0.01	0.35
linearTransform	0.12	0.00	0.12
lnTransform	3.49	0.11	3.60
logTransform	0.11	0.00	0.11
logarithm-class	0.09	0.00	0.09
logicalFilterResult-class	0	0	0
logicleTransform	1.73	0.02	1.75
manyFilterResult-class	0	0	0
multipleFilterResult-class	0	0	0
norm2Filter-class	0.25	0.00	0.33
normalizeActionItem-class	0	0	0
normalizeView-class	0	0	0
parameters-methods	0.08	0.00	0.08
polygonGate	0.15	0.00	0.16
quadGate	0.35	0.00	0.34
quadratic-class	0.09	0.00	0.10
quadraticTransform	0.11	0.00	0.11
ratio-class	0.09	0.00	0.09
read.FCS	0.13	0.00	0.12
read.FCSheader	0.01	0.00	0.02
read.flowSet	0.32	0.00	0.31
rectangleGate	0.20	0.00	0.22
sampleFilter-class	0.13	0.00	0.13
scaleTransform	0.10	0.00	0.11
singleParameterTransform-class	0	0	0
sinht-class	0.10	0.00	0.09
split-methods	2.25	0.01	2.26
splitScaleTransform	3.58	0.14	3.72
splitscale-class	0.22	0.02	0.24
squareroot-class	0.07	0.00	0.08
subsettingActionItem-class	0	0	0
subsettingView-class	0	0	0
timeFilter-class	2.73	0.03	2.77
transform-class	0.02	0.00	0.01
transformActionItem-class	0	0	0
transformFilter-class	0.20	0.00	0.21
transformList-class	1.5	0.0	1.5
transformMap-class	0	0	0
transformView-class	0	0	0
truncateTransform	0.11	0.00	0.11
unitytransform-class	0.08	0.00	0.07
view-class	0	0	0
workFlow-class	0	0	0
write.FCS	0.06	0.00	0.06
write.flowSet	1.77	0.02	1.78