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Package 216/658HostnameOS / ArchBUILDCHECKBUILD BIN
flagme 1.15.1
Mark Robinson
Snapshot Date: 2013-03-23 17:02:20 -0700 (Sat, 23 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flagme
Last Changed Rev: 73893 / Revision: 74756
Last Changed Date: 2013-03-04 09:49:21 -0800 (Mon, 04 Mar 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: flagme
Version: 1.15.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flagme_1.15.1.tar.gz
StartedAt: 2013-03-24 04:57:41 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 05:00:22 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 160.3 seconds
RetCode: 0
Status:  OK 
CheckDir: flagme.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/flagme.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'flagme/DESCRIPTION' ... OK
* this is package 'flagme' version '1.15.1'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'flagme' can be installed ... [11s/12s] OK
* checking installed package size ... OK
* checking package directory ... 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 ... 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 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 installed files from 'inst/doc' ... OK
* checking examples ... [49s/52s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
parseChromaTOF 7.880  0.057   8.442
parseELU       5.978  0.113   6.971
* 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

flagme.Rcheck/00install.out:

* installing *source* package 'flagme' ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c dp.c -o dp.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c init.c -o init.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o flagme.so dp.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/flagme.Rcheck/flagme/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'flagme'
** help
*** installing help indices
** building package indices
** installing vignettes
   'flagme.Rnw' using 'UTF-8' 
** testing if installed package can be loaded
* DONE (flagme)

flagme.Rcheck/flagme-Ex.timings:

nameusersystemelapsed
addAMDISPeaks1.5540.1111.773
addChromaTOFPeaks0.6610.0640.736
betweenAlignment0.0060.0130.020
calcTimeDiffs2.0010.2012.290
clusterAlignment2.1590.1662.367
compress2.2350.1652.443
dp2.3170.1672.531
gatherInfo2.3660.1702.593
imputePeaks3.2760.2373.723
multipleAlignment2.2300.1652.434
normDotProduct2.0980.1582.272
parseChromaTOF7.8800.0578.442
parseELU5.9780.1136.971
peaksAlignment0.0070.0070.015
peaksDataset0.7520.1321.085
plot1.4930.1981.837
plotImage0.4730.0950.602
progressiveAlignment2.3890.1742.626
rmaFitUnit2.2970.1812.503