Package: flowCore

Version: 1.18.0

Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch flowCore_1.18.0.tar.gz

StartedAt: 2011-10-20 14:59:23 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 15:02:24 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 181.5 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/flowCore.Rcheck'
* using R version 2.13.2 (2011-09-30)
* 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 '1.18.0'
* checking package namespace 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 18.1Mb
  sub-directories of 1Mb or more:
    data      8.0Mb
    doc       7.2Mb
    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 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˜1.8-B/R/include"          -O2 -Wall  -c FastLogicle.cpp -o FastLogicle.o
g++ -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c Logicle.cpp -o Logicle.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c biexponential.c -o biexponential.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c inPolygon.c -o inPolygon.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c inPolytope.c -o inPolytope.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c init.c -o init.o
g++ -I"E:/biocbld/BBS-2˜1.8-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˜1.8-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.8-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)
** help
*** installing help indices
** building package indices ...
** 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	0.18	0.00	0.17
Subset-methods	1.37	0.01	1.39
actionItem-class	0	0	0
arcsinhTransform	0.17	0.00	0.17
asinht-class	0.07	0.00	0.06
biexponentialTransform	14.85	0.27	15.19
boundaryFilter-class	0.29	0.00	0.28
characterOrTransformation-class	0	0	0
coerce	0.12	0.00	0.13
compensateActionItem-class	0	0	0
compensateView-class	0	0	0
compensatedParameter-class	0.31	0.01	0.32
compensation-class	0.64	0.00	0.64
curv1Filter-class	0.57	0.02	0.58
curv2Filter-class	3.09	0.01	3.14
dg1polynomial-class	0.05	0.02	0.07
each_col-methods	0.08	0.00	0.07
ellipsoidGate	0.09	0.02	0.11
exponential-class	0.06	0.00	0.07
expressionFilter-class	0.10	0.01	0.15
fcReference-class	0	0	0
filter-methods	1.68	0.02	1.72
filter-on-methods	0.25	0.00	0.25
filterList-class	0	0	0
filterResult-class	0.02	0.00	0.02
filterResultList-class	2.30	0.06	2.37
filterSet-class	0.06	0.00	0.06
filterSummary-class	0.25	0.00	0.25
filterSummaryList-class	2.01	0.03	2.05
flowFrame-class	5.66	0.05	5.77
flowSet-class	5.03	0.01	5.06
fsApply	0.3	0.0	0.3
gateActionItem-class	0.01	0.00	0.01
gateView-class	0	0	0
hyperlog-class	1.8	0.0	1.8
identifier-methods	0.05	0.02	0.06
inverseLogicleTransform	1.33	0.00	1.34
invsplitscale-class	0.07	0.00	0.11
keyword-methods	1.52	0.03	1.57
kmeansFilter	0.33	0.00	0.32
linearTransform	0.08	0.00	0.08
lnTransform	4.06	0.02	4.16
logTransform	0.19	0.00	0.19
logarithm-class	0.04	0.00	0.04
logicalFilterResult-class	0.02	0.00	0.02
logicleTransform	1.40	0.00	1.41
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	0.05	0.00	0.04
polygonGate	0.12	0.00	0.15
quadGate	0.36	0.00	0.35
quadratic-class	0.06	0.00	0.07
quadraticTransform	0.08	0.00	0.08
ratio-class	0.06	0.00	0.06
read.FCS	0.10	0.00	0.09
read.FCSheader	0.00	0.01	0.02
read.flowSet	0.20	0.00	0.22
rectangleGate	0.22	0.00	0.21
sampleFilter-class	0.11	0.00	0.11
scaleTransform	0.08	0.00	0.08
singleParameterTransform-class	0	0	0
sinht-class	0.06	0.00	0.06
split-methods	2.16	0.00	2.20
splitScaleTransform	3.75	0.03	3.82
splitscale-class	0.17	0.00	0.17
squareroot-class	0.06	0.00	0.06
subsettingActionItem-class	0	0	0
subsettingView-class	0	0	0
timeFilter-class	3.45	0.03	3.52
transform-class	0	0	0
transformActionItem-class	0	0	0
transformFilter-class	0.21	0.00	0.20
transformList-class	1.29	0.02	1.33
transformMap-class	0	0	0
transformView-class	0	0	0
truncateTransform	0.08	0.00	0.08
unitytransform-class	0.04	0.00	0.06
view-class	0	0	0
workFlow-class	0	0	0
write.FCS	0.1	0.0	0.1
write.flowSet	1.69	0.00	1.72