Package: flowCore

Version: 1.14.1

Command: E:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings flowCore_1.14.1.tar.gz

StartedAt: 2010-10-04 18:00:09 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 18:03:29 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 200.1 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.6-bioc/meat/flowCore.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowCore/DESCRIPTION' ... OK
* this is package 'flowCore' version '1.14.1'
* 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 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 ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* installing *source* package 'flowCore' ...
** libs
  making DLL ...
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"         -O3 -Wall  -std=gnu99 -c biexponential.c -o biexponential.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"         -O3 -Wall  -std=gnu99 -c inPolygon.c -o inPolygon.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"         -O3 -Wall  -std=gnu99 -c inPolytope.c -o inPolytope.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"         -O3 -Wall  -std=gnu99 -c init.c -o init.o
gcc -shared -s -static-libgcc -o flowCore.dll tmp.def biexponential.o inPolygon.o inPolytope.o init.o -LE:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to E:/biocbld/bbs-2.6-bioc/meat/flowCore.Rcheck/flowCore/libs
  ... done
** 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	0.2	0.0	0.2
Subset-methods	1.33	0.03	1.36
actionItem-class	0	0	0
arcsinhTransform	0.17	0.00	0.18
asinht-class	0.06	0.00	0.06
biexponentialTransform	15.00	0.25	15.27
boundaryFilter-class	0.30	0.01	0.31
characterOrTransformation-class	0	0	0
coerce	0.11	0.02	0.12
compensateActionItem-class	0	0	0
compensateView-class	0	0	0
compensatedParameter-class	0.33	0.03	0.36
compensation-class	0.76	0.00	0.76
curv1Filter-class	1.03	0.01	1.05
curv2Filter-class	3.91	0.02	3.92
dg1polynomial-class	0.06	0.00	0.06
each_col-methods	0.08	0.00	0.08
ellipsoidGate	0.13	0.02	0.14
exponential-class	0.06	0.00	0.06
expressionFilter-class	0.14	0.00	0.14
fcReference-class	0	0	0
filter-methods	1.33	0.01	1.34
filter-on-methods	0.26	0.00	0.27
filterList-class	0.02	0.00	0.02
filterResult-class	0	0	0
filterResultList-class	2.25	0.04	2.29
filterSet-class	0.09	0.00	0.10
filterSummary-class	0.64	0.00	0.64
filterSummaryList-class	2.04	0.00	2.04
flowFrame-class	5.40	0.07	5.46
flowSet-class	5.25	0.00	5.27
fsApply	0.35	0.00	0.34
gateActionItem-class	0	0	0
gateView-class	0	0	0
hyperlog-class	1.85	0.00	1.86
identifier-methods	0.07	0.00	0.07
inverseLogicleTransform	0.90	0.01	0.92
invsplitscale-class	0.07	0.00	0.06
keyword-methods	0.98	0.03	1.02
kmeansFilter	0.36	0.00	0.36
linearTransform	0.08	0.02	0.09
lnTransform	3.29	0.12	3.42
logTransform	0.21	0.00	0.20
logarithm-class	0.08	0.00	0.08
logicalFilterResult-class	0	0	0
logicleTransform	0.90	0.03	0.94
manyFilterResult-class	0	0	0
multipleFilterResult-class	0	0	0
norm2Filter-class	0.28	0.00	0.33
normalizeActionItem-class	0	0	0
normalizeView-class	0	0	0
parameters-methods	0.07	0.00	0.06
polygonGate	0.14	0.00	0.14
quadGate	0.4	0.0	0.4
quadratic-class	0.07	0.00	0.07
quadraticTransform	0.07	0.02	0.09
ratio-class	0.05	0.02	0.06
read.FCS	0.11	0.00	0.11
read.FCSheader	0.02	0.00	0.01
read.flowSet	0.23	0.01	0.25
rectangleGate	0.25	0.00	0.25
sampleFilter-class	0.12	0.00	0.13
scaleTransform	0.10	0.00	0.09
singleParameterTransform-class	0	0	0
sinht-class	0.06	0.00	0.06
split-methods	1.94	0.02	1.95
splitScaleTransform	3.40	0.08	3.49
splitscale-class	0.07	0.00	0.06
squareroot-class	0.08	0.00	0.08
subsettingActionItem-class	0	0	0
subsettingView-class	0	0	0
timeFilter-class	2.98	0.06	3.04
transform-class	0	0	0
transformActionItem-class	0	0	0
transformFilter-class	0.19	0.02	0.22
transformList-class	0.9	0.0	0.9
transformMap-class	0	0	0
transformView-class	0.02	0.00	0.02
truncateTransform	0.09	0.00	0.09
unitytransform-class	0.07	0.00	0.07
view-class	0	0	0
workFlow-class	0	0	0
write.FCS	0.12	0.00	0.12
write.flowSet	1.27	0.08	1.38