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Package 200/609HostnameOS / ArchBUILDCHECKBUILD BIN
flowCore 1.24.2
M.Jiang
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/flowCore
Last Changed Rev: 73047 / Revision: 74773
Last Changed Date: 2013-01-31 10:28:45 -0800 (Thu, 31 Jan 2013)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: flowCore
Version: 1.24.2
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowCore_1.24.2.tar.gz
StartedAt: 2013-03-24 23:27:43 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 23:31:05 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 201.3 seconds
RetCode: 0
Status:  OK 
CheckDir: flowCore.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/flowCore.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.24.2'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'flowCore' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data      5.0Mb
    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 for left-over 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 ... NOTE
[[<-,filterSet-character-ANY-formula : harvest: warning in exists(f,
  env = x@env): partial argument match of 'env' to 'envir'
coerce,environment-flowSet: warning in ls(env = from): partial argument
  match of 'env' to 'envir'
coerce,environment-flowSet : <anonymous>: warning in get(f, env =
  from): partial argument match of 'env' to 'envir'
coerce,filterSet-list: warning in ls(env = from@env): partial argument
  match of 'env' to 'envir'
identifier,filterReference: warning in exists(object@name, env =
  object@env): partial argument match of 'env' to 'envir'
names,filterSet: warning in ls(env = x@env): partial argument match of
  'env' to 'envir'
plot,workFlow-missing : <anonymous>: warning in edgeData(..., at =
  "actionItem"): partial argument match of 'at' to 'attr'
show,filterReference: warning in exists(object@name, env = object@env):
  partial argument match of 'env' to 'envir'
summary,transform: warning in ls(env = e): partial argument match of
  'env' to 'envir'
* 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 compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
biexponentialTransform 9.963  2.818  13.972
flowFrame-class        4.397  0.856   5.552
lnTransform            3.536  1.526   5.438
splitScaleTransform    3.365  1.584   5.114
* 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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/flowCore.Rcheck/00check.log'
for details.

flowCore.Rcheck/00install.out:

* installing *source* package 'flowCore' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c FastLogicle.cpp -o FastLogicle.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c Logicle.cpp -o Logicle.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c init.c -o init.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c logicleTransform.cpp -o logicleTransform.o
g++ -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-2.11-bioc/meat/flowCore.Rcheck/flowCore/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'filter' in package 'flowCore'
** help
*** installing help indices
** building package indices
** installing vignettes
   'HowTo-flowCore.Rnw' 
** testing if installed package can be loaded

* DONE (flowCore)

flowCore.Rcheck/flowCore-Ex.timings:

nameusersystemelapsed
EHtrans-class0.3270.0260.363
Subset-methods1.2050.1511.473
actionItem-class0.0020.0000.002
arcsinhTransform0.1870.0410.270
asinht-class0.0470.0180.089
biexponentialTransform 9.963 2.81813.972
boundaryFilter-class0.2690.0900.412
characterOrTransformation-class0.0010.0010.002
coerce0.1000.0440.153
compensateActionItem-class0.0010.0000.004
compensateView-class0.0010.0000.002
compensatedParameter-class0.2740.1450.457
compensation-class0.6030.2970.909
curv1Filter-class0.4790.2810.819
curv2Filter-class2.7800.7133.585
dg1polynomial-class0.0480.0180.069
each_col-methods0.0610.0320.105
ellipsoidGate0.1130.0530.169
exponential-class0.0450.0170.067
expressionFilter-class0.1260.0550.190
fcReference-class0.0010.0000.002
filter-methods1.1070.1971.364
filter-on-methods0.2060.0580.303
filterList-class0.0100.0000.011
filterResult-class0.0000.0000.001
filterResultList-class1.7490.9042.832
filterSet-class0.0650.0010.066
filterSummary-class0.1430.0990.253
filterSummaryList-class1.2130.5372.055
flowFrame-class4.3970.8565.552
flowSet-class4.0090.8044.916
fsApply0.2640.1430.432
gateActionItem-class0.0010.0000.001
gateView-class0.0010.0000.001
hyperlog-class1.8430.0411.904
identifier-methods0.0400.0200.076
inverseLogicleTransform0.8460.1481.015
invsplitscale-class0.0480.0300.079
keyword-methods1.1380.3421.567
kmeansFilter0.2820.0760.361
linearTransform0.0680.0330.108
lnTransform3.5361.5265.438
logTransform0.0760.0410.122
logarithm-class0.0490.0230.075
logicalFilterResult-class0.0010.0000.001
logicleTransform1.0450.2001.335
manyFilterResult-class0.0000.0000.001
multipleFilterResult-class0.0010.0000.001
norm2Filter-class0.2570.0610.324
normalizeActionItem-class0.0010.0000.001
normalizeView-class0.0010.0000.001
parameters-methods0.0470.0240.078
polygonGate0.1140.0510.172
quadGate0.3300.0950.455
quadratic-class0.0450.0160.063
quadraticTransform0.0690.0340.113
ratio-class0.0450.0160.065
read.FCS0.0920.0420.151
read.FCSheader0.0070.0050.012
read.flowSet0.1910.0910.323
rectangleGate0.1710.0590.254
sampleFilter-class0.0960.0340.136
scaleTransform0.0700.0310.107
singleParameterTransform-class0.0010.0000.002
sinht-class0.0540.0440.102
split-methods1.7260.4262.391
splitScaleTransform3.3651.5845.114
splitscale-class0.2080.0670.298
squareroot-class0.0460.0160.067
subsettingActionItem-class0.0010.0000.001
subsettingView-class0.0010.0010.000
timeFilter-class2.2800.4152.892
transform-class0.0030.0000.002
transformActionItem-class0.0010.0000.001
transformFilter-class0.1850.0370.223
transformList-class0.8470.1621.045
transformMap-class0.0010.0000.001
transformView-class0.0000.0000.001
truncateTransform0.0800.0380.119
unitytransform-class0.0490.0320.082
view-class0.0000.0010.001
workFlow-class0.0010.0000.002
write.FCS0.1490.0310.185
write.flowSet1.5960.2951.943