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Package 52/609HostnameOS / ArchBUILDCHECKBUILD BIN
BayesPeak 1.10.0
Jonathan Cairns
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/BayesPeak
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
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: BayesPeak
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BayesPeak_1.10.0.tar.gz
StartedAt: 2013-03-24 22:38:15 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 22:45:18 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 422.1 seconds
RetCode: 0
Status:  OK 
CheckDir: BayesPeak.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/BayesPeak.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 'BayesPeak/DESCRIPTION' ... OK
* this is package 'BayesPeak' version '1.10.0'
* 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 'BayesPeak' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   5.0Mb
* 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 ... 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 ... NOTE
S3 methods shown with full name in documentation object 'overfittingDiagnostics':
  'plot.overfitdiag' 'identify.overfitdiag'

S3 methods shown with full name in documentation object 'plot.PP':
  'plot.PP'

S3 methods shown with full name in documentation object 'plot.bed':
  'plot.bed'

S3 methods shown with full name in documentation object 'plot.job':
  'plot.job'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... NOTE
File '/Users/biocbuild/bbs-2.11-bioc/meat/BayesPeak.Rcheck/BayesPeak/libs/i386/BayesPeak.so':
  Found '___stdoutp', possibly from 'stdout' (C)
    Object: 'bayespeak.o'

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
bayespeak       157.890  0.722 172.588
summarise.peaks 156.131  0.616 158.498
plot.job         11.677  0.402  12.632
* 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 3 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/BayesPeak.Rcheck/00check.log'
for details.

BayesPeak.Rcheck/00install.out:

* installing *source* package 'BayesPeak' ...
** libs
*** arch - i386
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 bayespeak.c -o bayespeak.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 BayesPeak.so bayespeak.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/BayesPeak.Rcheck/BayesPeak/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'BayesPeak.Rnw' 
** testing if installed package can be loaded

* DONE (BayesPeak)

BayesPeak.Rcheck/BayesPeak-Ex.timings:

nameusersystemelapsed
bayespeak157.890 0.722172.588
overfitting0.1360.0150.155
plot.PP0.1280.0160.152
plot.bed1.0550.0941.163
plot.job11.677 0.40212.632
read.bed0.8520.0491.003
summarise.peaks156.131 0.616158.498