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Package 54/467HostnameOS / ArchBUILDCHECKBUILD BIN
BGmix 1.12.0
Alex Lewin
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/BGmix
Last Changed Rev: 54800 / Revision: 59457
Last Changed Date: 2011-04-13 15:27:35 -0700 (Wed, 13 Apr 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 N O T   S U P P O R T E D
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: BGmix
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BGmix_1.12.0.tar.gz
StartedAt: 2011-10-20 13:40:53 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 13:42:47 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 113.3 seconds
RetCode: 0
Status:  OK 
CheckDir: BGmix.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/BGmix.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'BGmix/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BGmix' version '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'BGmix' can be installed ... OK
* checking installed package size ... 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 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 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking sizes of PDF files under inst/doc ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'BGmix.pdf' from 696Kb to 245Kb
  consider running tools::compactPDF() on these files
* 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

BGmix.Rcheck/00install.out:

* installing *source* package 'BGmix' ...
checking for gcc... gcc-4.2 -arch i386 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc-4.2 -arch i386 -std=gnu99 accepts -g... yes
checking for gcc-4.2 -arch i386 -std=gnu99 option to accept ISO C89... none needed
checking for gcc-4.2 -arch i386 -std=gnu99 option to accept ISO C99... none needed
checking for cos in -lm... yes
Untarring Boost header files...
checking for an ANSI C-conforming const... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I ../boostIncl -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -DUSING_R -c BGmix_main.cpp -o BGmix_main.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I ../boostIncl -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -DUSING_R -c rundir.cpp -o rundir.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I ../boostIncl -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -DUSING_R -c updates_BGmix.cpp -o updates_BGmix.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 BGmix.so BGmix_main.o rundir.o updates_BGmix.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
rm -r ../boostIncl 
installing to /Users/biocbuild/bbs-2.8-bioc/meat/BGmix.Rcheck/BGmix/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (BGmix)

BGmix.Rcheck/BGmix-Ex.timings:

nameusersystemelapsed
BGmix-package3.6620.3174.901
BGmix 9.562 0.38310.611
EstimatePi05.2820.7177.496
FDRforTailPP12.411 1.90814.872
FDRplotTailPP4.9930.7666.204
TailPP5.0020.7436.154
calcFDR1.0070.0601.115
ccParams1.0020.0571.476
ccPred1.0050.0551.353
ccSummary0.9850.0571.340
ccTrace1.3260.0891.816
histTailPP4.9960.7366.472
plotBasic1.0160.0761.160
plotCompare0.0020.0000.002
plotFDR1.0260.0661.476
plotMixDensity3.3290.3034.554
plotPredChecks1.0330.0651.644
plotTrace1.3940.1202.226