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BioC 2.12: CHECK report for EBcoexpress on petty

This page was generated on 2013-10-09 09:40:10 -0700 (Wed, 09 Oct 2013).

Package 198/671HostnameOS / ArchBUILDCHECKBUILD BIN
EBcoexpress 1.4.0
John A. Dawson
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/EBcoexpress
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: EBcoexpress
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch EBcoexpress_1.4.0.tar.gz
StartedAt: 2013-10-08 22:14:47 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 22:16:23 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 96.7 seconds
RetCode: 0
Status:  OK 
CheckDir: EBcoexpress.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/EBcoexpress.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'EBcoexpress/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EBcoexpress' version '1.4.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'EBcoexpress' can be installed ... [7s/7s] 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 ... NOTE
rankMyGenes: warning in sort(table(allNames), decr = TRUE): partial
  argument match of 'decr' to 'decreasing'
showPair : getUsed: warning in mad(aX, const = 1): partial argument
  match of 'const' to 'constant'
showPair : getUsed: warning in mad(aY, const = 1): partial argument
  match of 'const' to 'constant'
* 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' ... NOTE
The following files should probably not be installed:
  'biom.bst'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [15s/16s] 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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/EBcoexpress.Rcheck/00check.log'
for details.

EBcoexpress.Rcheck/00install.out:

* installing *source* package 'EBcoexpress' ...
** 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 EBcoexpress.c -o EBcoexpress.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 -L/usr/local/lib -o EBcoexpress.so EBcoexpress.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/EBcoexpress.Rcheck/EBcoexpress/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (EBcoexpress)

EBcoexpress.Rcheck/EBcoexpress-Ex.timings:

nameusersystemelapsed
ebCoexpressMeta3.0710.0253.371
ebCoexpressSeries1.3600.0111.404
fiftyGenes0.0100.0000.011
initializeHP0.8840.0080.901
makeMyD0.0760.0020.078
priorDiagnostic2.1630.0172.603
rankMyGenes1.3380.0101.409
showNetwork2.2610.0472.491
showPair0.0840.0040.095
utilities0.0280.0020.032