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BioC 3.0: CHECK report for EBcoexpress on oaxaca

This page was generated on 2015-04-10 10:06:00 -0700 (Fri, 10 Apr 2015).

Package 264/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBcoexpress 1.10.0
John A. Dawson
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/EBcoexpress
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: EBcoexpress
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch EBcoexpress_1.10.0.tar.gz
StartedAt: 2015-04-09 23:08:18 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:09:18 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 60.1 seconds
RetCode: 0
Status:  OK 
CheckDir: EBcoexpress.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch EBcoexpress_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/EBcoexpress.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EBcoexpress/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EBcoexpress’ 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 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 ... [5s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘colorspace’ ‘graph’ ‘igraph’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘EBarrays’ ‘mclust’ ‘minqa’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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'
ebCoexpressFullTCAECM: no visible global function definition for
  ‘bobyqa’
ebCoexpressOneStep: no visible global function definition for ‘bobyqa’
initializeHP : getMclustHPests: no visible global function definition
  for ‘Mclust’
showNetwork: no visible global function definition for ‘graph.full’
showNetwork: no visible global function definition for ‘hex’
showNetwork: no visible global function definition for ‘RGB’
showNetwork: no visible global function definition for ‘layout.circle’
* 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 compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/EBcoexpress.Rcheck/00check.log’
for details.

EBcoexpress.Rcheck/00install.out:

* installing *source* package ‘EBcoexpress’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c EBcoexpress.c -o EBcoexpress.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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-3.0-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
ebCoexpressMeta1.4530.0101.770
ebCoexpressSeries0.7060.0030.777
fiftyGenes0.0030.0010.003
initializeHP0.4630.0020.471
makeMyD0.0350.0000.037
priorDiagnostic1.0350.0051.049
rankMyGenes0.7080.0040.714
showNetwork1.2900.0251.343
showPair0.0530.0020.055
utilities0.0060.0010.007