Package: flowCore

Version: 1.14.1

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings flowCore_1.14.1.tar.gz

StartedAt: 2010-10-04 16:52:08 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 16:56:23 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 255.1 seconds

RetCode: 0

Status:  OK

CheckDir: flowCore.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/flowCore.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c biexponential.c -o biexponential.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c inPolygon.c -o inPolygon.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c inPolytope.c -o inPolytope.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c init.c -o init.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o flowCore.so biexponential.o inPolygon.o inPolytope.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.6-bioc/meat/flowCore.Rcheck/flowCore/libs/i386
*** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c biexponential.c -o biexponential.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c inPolygon.c -o inPolygon.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c inPolytope.c -o inPolytope.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c init.c -o init.o
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o flowCore.so biexponential.o inPolygon.o inPolytope.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.6-bioc/meat/flowCore.Rcheck/flowCore/libs/ppc
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c biexponential.c -o biexponential.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c inPolygon.c -o inPolygon.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c inPolytope.c -o inPolytope.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c init.c -o init.o
gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o flowCore.so biexponential.o inPolygon.o inPolytope.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.6-bioc/meat/flowCore.Rcheck/flowCore/libs/x86_64
** 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	0.228	0.024	0.265
Subset-methods	1.703	0.177	1.911
actionItem-class	0.003	0.000	0.003
arcsinhTransform	0.219	0.050	0.270
asinht-class	0.079	0.022	0.102
biexponentialTransform	13.097	3.259	16.611
boundaryFilter-class	0.307	0.032	0.340
characterOrTransformation-class	0.003	0.000	0.002
coerce	0.238	0.083	0.329
compensateActionItem-class	0.002	0.001	0.003
compensateView-class	0.002	0.000	0.002
compensatedParameter-class	0.451	0.161	0.617
compensation-class	1.046	0.326	1.474
curv1Filter-class	1.437	0.264	1.953
curv2Filter-class	5.950	0.708	7.333
dg1polynomial-class	0.076	0.018	0.094
each_col-methods	0.091	0.026	0.119
ellipsoidGate	0.197	0.053	0.261
exponential-class	0.074	0.019	0.098
expressionFilter-class	0.199	0.057	0.296
fcReference-class	0.003	0.001	0.003
filter-methods	2.226	0.111	2.445
filter-on-methods	0.389	0.048	0.438
filterList-class	0.027	0.001	0.028
filterResult-class	0.002	0.001	0.002
filterResultList-class	3.424	0.651	4.162
filterSet-class	0.137	0.001	0.148
filterSummary-class	0.973	0.160	1.194
filterSummaryList-class	2.861	0.462	3.354
flowFrame-class	6.828	0.730	7.688
flowSet-class	7.817	0.738	8.637
fsApply	0.448	0.154	0.610
gateActionItem-class	0.002	0.000	0.003
gateView-class	0.002	0.001	0.002
hyperlog-class	2.895	0.045	2.967
identifier-methods	0.061	0.018	0.078
inverseLogicleTransform	1.683	0.087	1.786
invsplitscale-class	0.076	0.019	0.097
keyword-methods	1.765	0.214	1.995
kmeansFilter	0.535	0.086	0.626
linearTransform	0.114	0.035	0.149
lnTransform	4.900	1.730	6.727
logTransform	0.209	0.075	0.286
logarithm-class	0.074	0.019	0.092
logicalFilterResult-class	0.002	0.000	0.002
logicleTransform	1.669	0.095	1.775
manyFilterResult-class	0.002	0.000	0.002
multipleFilterResult-class	0.002	0.000	0.002
norm2Filter-class	0.405	0.084	0.499
normalizeActionItem-class	0.002	0.000	0.003
normalizeView-class	0.002	0.000	0.002
parameters-methods	0.075	0.019	0.094
polygonGate	0.209	0.045	0.254
quadGate	0.633	0.101	0.741
quadratic-class	0.083	0.020	0.104
quadraticTransform	0.128	0.051	0.180
ratio-class	0.088	0.023	0.113
read.FCS	0.149	0.022	0.174
read.FCSheader	0.017	0.010	0.029
read.flowSet	0.352	0.119	0.481
rectangleGate	0.375	0.049	0.430
sampleFilter-class	0.167	0.043	0.234
scaleTransform	0.123	0.037	0.171
singleParameterTransform-class	0.003	0.000	0.003
sinht-class	0.082	0.018	0.100
split-methods	3.160	0.380	3.575
splitScaleTransform	5.256	1.764	7.150
splitscale-class	0.089	0.022	0.110
squareroot-class	0.179	0.053	0.231
subsettingActionItem-class	0.002	0.001	0.003
subsettingView-class	0.002	0.000	0.003
timeFilter-class	4.515	0.333	4.902
transform-class	0.005	0.001	0.006
transformActionItem-class	0.002	0.000	0.002
transformFilter-class	0.300	0.053	0.355
transformList-class	1.597	0.075	1.682
transformMap-class	0.001	0.000	0.001
transformView-class	0.002	0.000	0.003
truncateTransform	0.129	0.054	0.184
unitytransform-class	0.074	0.022	0.099
view-class	0.003	0.001	0.003
workFlow-class	0.002	0.000	0.003
write.FCS	0.133	0.042	0.182
write.flowSet	2.142	0.227	2.384