Package: flowCore

Version: 1.18.0

Command: D:\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 14:12:02 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 14:14:47 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 164.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowCore.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/flowCore.Rcheck'
* using R version 2.13.2 (2011-09-30)
* 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 '1.18.0'
* 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 11.2Mb
  sub-directories of 1Mb or more:
    data      8.0Mb
    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' ... WARNING
Package vignette(s) without corresponding PDF:
   HowTo-flowCore.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-bioc/meat/flowCore.Rcheck/00check.log'
for details

* installing *source* package 'flowCore' ...
** libs
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c FastLogicle.cpp -o FastLogicle.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c Logicle.cpp -o Logicle.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -std=gnu99 -c biexponential.c -o biexponential.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -std=gnu99 -c inPolygon.c -o inPolygon.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -std=gnu99 -c inPolytope.c -o inPolytope.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -std=gnu99 -c init.c -o init.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-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˜1.8-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.8-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)
** 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	0.27	0.00	0.27
Subset-methods	1.66	0.05	1.70
actionItem-class	0	0	0
arcsinhTransform	0.25	0.02	0.27
asinht-class	0.09	0.00	0.09
biexponentialTransform	11.34	0.22	11.60
boundaryFilter-class	0.37	0.03	0.41
characterOrTransformation-class	0	0	0
coerce	0.19	0.00	0.19
compensateActionItem-class	0	0	0
compensateView-class	0	0	0
compensatedParameter-class	0.52	0.00	0.51
compensation-class	0.84	0.00	0.84
curv1Filter-class	0.56	0.01	0.58
curv2Filter-class	3.36	0.05	3.41
dg1polynomial-class	0.11	0.00	0.11
each_col-methods	0.11	0.00	0.11
ellipsoidGate	0.17	0.00	0.17
exponential-class	0.10	0.00	0.09
expressionFilter-class	0.17	0.00	0.18
fcReference-class	0	0	0
filter-methods	1.30	0.02	1.31
filter-on-methods	0.28	0.00	0.28
filterList-class	0.02	0.00	0.02
filterResult-class	0	0	0
filterResultList-class	1.58	0.09	1.67
filterSet-class	0.06	0.00	0.06
filterSummary-class	0.19	0.01	0.21
filterSummaryList-class	1.22	0.04	1.25
flowFrame-class	4.90	0.04	4.97
flowSet-class	4.89	0.00	4.89
fsApply	0.44	0.00	0.44
gateActionItem-class	0	0	0
gateView-class	0	0	0
hyperlog-class	2.13	0.00	2.12
identifier-methods	0.07	0.00	0.08
inverseLogicleTransform	0.89	0.00	0.90
invsplitscale-class	0.11	0.00	0.10
keyword-methods	1.06	0.02	1.08
kmeansFilter	0.49	0.00	0.49
linearTransform	0.11	0.00	0.11
lnTransform	3.73	0.03	3.76
logTransform	0.27	0.00	0.27
logarithm-class	0.09	0.00	0.09
logicalFilterResult-class	0	0	0
logicleTransform	1.08	0.00	1.08
manyFilterResult-class	0	0	0
multipleFilterResult-class	0.01	0.00	0.01
norm2Filter-class	0.27	0.00	0.42
normalizeActionItem-class	0	0	0
normalizeView-class	0	0	0
parameters-methods	0.11	0.00	0.11
polygonGate	0.16	0.00	0.16
quadGate	0.39	0.00	0.39
quadratic-class	0.09	0.00	0.09
quadraticTransform	0.11	0.00	0.11
ratio-class	0.11	0.00	0.11
read.FCS	0.12	0.00	0.13
read.FCSheader	0	0	0
read.flowSet	0.34	0.00	0.35
rectangleGate	0.25	0.03	0.28
sampleFilter-class	0.14	0.00	0.14
scaleTransform	0.13	0.00	0.12
singleParameterTransform-class	0.00	0.01	0.02
sinht-class	0.09	0.00	0.09
split-methods	1.94	0.02	1.96
splitScaleTransform	3.48	0.06	3.54
splitscale-class	0.1	0.0	0.1
squareroot-class	0.09	0.00	0.09
subsettingActionItem-class	0	0	0
subsettingView-class	0	0	0
timeFilter-class	2.85	0.00	2.86
transform-class	0.01	0.00	0.01
transformActionItem-class	0	0	0
transformFilter-class	0.20	0.00	0.21
transformList-class	0.88	0.00	0.89
transformMap-class	0	0	0
transformView-class	0	0	0
truncateTransform	0.12	0.00	0.12
unitytransform-class	0.08	0.00	0.08
view-class	0	0	0
workFlow-class	0	0	0
write.FCS	0.08	0.00	0.08
write.flowSet	1.22	0.03	1.27