BioC 2.9: CHECK report for flowCore on moscato1

Package: flowCore

Version: 1.19.2

Command: mkdir flowCore.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowCore.buildbin-libdir flowCore_1.19.2.tar.gz >flowCore-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=flowCore.buildbin-libdir --install="check:flowCore-install.out" --force-multiarch --no-vignettes --timings flowCore_1.19.2.tar.gz && mv flowCore.buildbin-libdir/* flowCore.Rcheck/ && rmdir flowCore.buildbin-libdir

StartedAt: 2011-07-07 04:53:32 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 04:59:06 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 333.6 seconds

RetCode: 0

Status: OK

CheckDir: flowCore.Rcheck

Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/flowCore.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* 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 '1.19.2'
* 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 installed package size ... NOTE
  installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data      8.0Mb
    doc       1.2Mb
    extdata   1.1Mb
    libs      1.2Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or R CMD build --resave-data
           old_size new_size compress
  GvHD.rda    8.0Mb    5.0Mb       xz
* 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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


install for i386

* installing *source* package 'flowCore' ...
** libs
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c FastLogicle.cpp -o FastLogicle.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c Logicle.cpp -o Logicle.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c biexponential.c -o biexponential.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c inPolygon.c -o inPolygon.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c inPolytope.c -o inPolytope.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
g++  -I"D:/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 -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/flowCore.buildbin-libdir/flowCore/libs/i386
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. 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 1.3-01)
** 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)

add DLL for x64

* 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.buildbin-libdir/flowCore/libs/x64
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
* MD5 sums
packaged installation of 'flowCore' as flowCore_1.19.2.zip

* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.19	0.00	0.19
Subset-methods	1.17	0.02	1.19
actionItem-class	0.01	0.00	0.01
arcsinhTransform	0.16	0.00	0.16
asinht-class	0.06	0.00	0.06
biexponentialTransform	8.57	0.15	8.74
boundaryFilter-class	0.28	0.00	0.28
characterOrTransformation-class	0	0	0
coerce	0.12	0.00	0.12
compensateActionItem-class	0	0	0
compensateView-class	0	0	0
compensatedParameter-class	0.33	0.00	0.33
compensation-class	0.64	0.02	0.65
curv1Filter-class	0.79	0.02	0.87
curv2Filter-class	3.78	0.01	3.80
dg1polynomial-class	0.07	0.00	0.07
each_col-methods	0.08	0.00	0.08
ellipsoidGate	0.13	0.00	0.13
exponential-class	0.06	0.00	0.06
expressionFilter-class	0.12	0.00	0.12
fcReference-class	0	0	0
filter-methods	1.28	0.02	1.31
filter-on-methods	0.22	0.00	0.22
filterList-class	0.02	0.00	0.02
filterResult-class	0	0	0
filterResultList-class	1.85	0.01	1.87
filterSet-class	0.07	0.00	0.06
filterSummary-class	0.5	0.0	0.5
filterSummaryList-class	1.57	0.02	1.59
flowFrame-class	4.79	0.06	4.85
flowSet-class	4.32	0.00	4.33
fsApply	0.31	0.00	0.31
gateActionItem-class	0	0	0
gateView-class	0	0	0
hyperlog-class	1.81	0.00	1.81
identifier-methods	0.05	0.00	0.05
inverseLogicleTransform	0.85	0.00	0.86
invsplitscale-class	0.07	0.00	0.06
keyword-methods	1.06	0.00	1.06
kmeansFilter	0.28	0.00	0.28
linearTransform	0.08	0.00	0.08
lnTransform	2.62	0.05	2.67
logTransform	0.09	0.00	0.09
logarithm-class	0.16	0.00	0.16
logicalFilterResult-class	0	0	0
logicleTransform	1.37	0.00	1.45
manyFilterResult-class	0	0	0
multipleFilterResult-class	0	0	0
norm2Filter-class	0.35	0.00	0.38
normalizeActionItem-class	0	0	0
normalizeView-class	0	0	0
parameters-methods	0.08	0.00	0.08
polygonGate	0.12	0.00	0.12
quadGate	0.34	0.00	0.34
quadratic-class	0.07	0.00	0.07
quadraticTransform	0.09	0.00	0.09
ratio-class	0.05	0.01	0.06
read.FCS	0.09	0.02	0.11
read.FCSheader	0.00	0.01	0.02
read.flowSet	0.23	0.00	0.23
rectangleGate	0.22	0.02	0.30
sampleFilter-class	0.11	0.00	0.11
scaleTransform	0.10	0.00	0.09
singleParameterTransform-class	0	0	0
sinht-class	0.06	0.00	0.06
split-methods	1.65	0.00	1.66
splitScaleTransform	3.11	0.02	3.12
splitscale-class	0.2	0.0	0.2
squareroot-class	0.09	0.00	0.09
subsettingActionItem-class	0	0	0
subsettingView-class	0	0	0
timeFilter-class	3.51	0.02	3.52
transform-class	0.00	0.00	0.02
transformActionItem-class	0	0	0
transformFilter-class	0.17	0.00	0.17
transformList-class	0.89	0.00	0.89
transformMap-class	0	0	0
transformView-class	0	0	0
truncateTransform	0.09	0.00	0.09
unitytransform-class	0.06	0.00	0.07
view-class	0	0	0
workFlow-class	0	0	0
write.FCS	0.07	0.00	0.06
write.flowSet	1.14	0.00	1.17

Summary

Command output