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Package 153/479HostnameOS / ArchBUILDCHECKBUILD BIN
flowCore 1.19.2
F. Hahne
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowCore
Last Changed Rev: 56203 / Revision: 56603
Last Changed Date: 2011-06-15 07:43:08 -0700 (Wed, 15 Jun 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: flowCore
Version: 1.19.2
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowCore_1.19.2.tar.gz
StartedAt: 2011-07-07 02:51:24 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 02:57:06 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 342.3 seconds
RetCode: 0
Status:  OK 
CheckDir: flowCore.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/flowCore.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 11.6Mb
  sub-directories of 1Mb or more:
    data      8.1Mb
    doc       1.2Mb
    extdata   1.1Mb
* 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 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 sizes of PDF files under 'inst/doc' ... 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

flowCore.Rcheck/00install.out:

* installing *source* package 'flowCore' ...
** libs
*** arch - i386
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c FastLogicle.cpp -o FastLogicle.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c Logicle.cpp -o Logicle.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c biexponential.c -o biexponential.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c inPolygon.c -o inPolygon.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c inPolytope.c -o inPolytope.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c init.c -o init.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c logicleTransform.cpp -o logicleTransform.o
g++-4.2 -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o flowCore.so FastLogicle.o Logicle.o biexponential.o inPolygon.o inPolytope.o init.o logicleTransform.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/flowCore.Rcheck/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)

* DONE (flowCore)

flowCore.Rcheck/flowCore-Ex.timings:

nameusersystemelapsed
EHtrans-class0.2310.0250.277
Subset-methods1.6760.1621.919
actionItem-class0.0020.0000.003
arcsinhTransform0.2190.0510.332
asinht-class0.0760.0240.119
biexponentialTransform12.268 3.14916.314
boundaryFilter-class0.3660.0670.442
characterOrTransformation-class0.0020.0010.002
coerce0.1420.0410.190
compensateActionItem-class0.0050.0080.013
compensateView-class0.0020.0000.002
compensatedParameter-class0.3960.1410.562
compensation-class0.8950.3061.243
curv1Filter-class1.2930.2711.584
curv2Filter-class5.5830.7156.465
dg1polynomial-class0.0710.0180.094
each_col-methods0.0860.0240.112
ellipsoidGate0.1710.0480.236
exponential-class0.0670.0170.085
expressionFilter-class0.1780.0560.237
fcReference-class0.0020.0010.002
filter-methods2.2560.1122.393
filter-on-methods0.3680.0500.430
filterList-class0.0190.0010.021
filterResult-class0.0010.0000.001
filterResultList-class3.4860.7734.324
filterSet-class0.1090.0060.115
filterSummary-class0.7900.1050.907
filterSummaryList-class2.8710.4793.393
flowFrame-class6.7910.7317.911
flowSet-class6.9740.6677.781
fsApply0.4050.1350.551
gateActionItem-class0.0010.0010.002
gateView-class0.0010.0000.002
hyperlog-class2.8660.0452.936
identifier-methods0.0560.0160.072
inverseLogicleTransform1.7010.0901.824
invsplitscale-class0.0750.0320.108
keyword-methods1.8820.2572.206
kmeansFilter0.5600.1050.697
linearTransform0.1050.0350.144
lnTransform5.0501.5886.922
logTransform0.2020.0690.303
logarithm-class0.0690.0190.111
logicalFilterResult-class0.0010.0000.001
logicleTransform1.7910.1062.118
manyFilterResult-class0.0010.0010.002
multipleFilterResult-class0.0010.0000.002
norm2Filter-class0.3850.0640.459
normalizeActionItem-class0.0020.0000.031
normalizeView-class0.0010.0010.002
parameters-methods0.0650.0170.093
polygonGate0.1770.0470.227
quadGate0.6180.0960.730
quadratic-class0.0680.0170.087
quadraticTransform0.1100.0400.152
ratio-class0.0720.0320.107
read.FCS0.1240.0210.146
read.FCSheader0.0100.0040.015
read.flowSet0.2730.0980.374
rectangleGate0.3210.0460.370
sampleFilter-class0.1410.0400.189
scaleTransform0.1010.0340.138
singleParameterTransform-class0.0020.0010.002
sinht-class0.0680.0180.086
split-methods2.9700.3843.493
splitScaleTransform5.0671.6657.175
splitscale-class0.0690.0190.093
squareroot-class0.0730.0210.107
subsettingActionItem-class0.0010.0000.003
subsettingView-class0.0010.0010.002
timeFilter-class4.3880.3434.886
transform-class0.0040.0000.004
transformActionItem-class0.0010.0010.001
transformFilter-class0.2740.0440.328
transformList-class1.6740.0871.815
transformMap-class0.0010.0000.002
transformView-class0.0020.0010.002
truncateTransform0.1300.0610.204
unitytransform-class0.0600.0160.076
view-class0.0010.0000.001
workFlow-class0.0010.0010.002
write.FCS0.1060.0350.163
write.flowSet2.1340.2222.421