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BioC 2.13: CHECK report for EBcoexpress on zin1

This page was generated on 2014-04-05 09:48:17 -0700 (Sat, 05 Apr 2014).

Package 221/750HostnameOS / ArchBUILDCHECKBUILD BIN
EBcoexpress 1.6.0
John A. Dawson
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/EBcoexpress
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: EBcoexpress
Version: 1.6.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings EBcoexpress_1.6.0.tar.gz
StartedAt: 2014-04-05 00:55:19 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:56:03 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 44.6 seconds
RetCode: 0
Status:  OK 
CheckDir: EBcoexpress.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/EBcoexpress.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.6.0’
* 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 ... [4s/4s] 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 dependencies in R code ... NOTE
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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘EBcoexpressVignette.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* 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

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/EBcoexpress.Rcheck/00check.log’
for details.

EBcoexpress.Rcheck/00install.out:

* installing *source* package ‘EBcoexpress’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c EBcoexpress.c -o EBcoexpress.o
EBcoexpress.c: In function ‘bwmcCworker’:
EBcoexpress.c:74:7: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
gcc -std=gnu99 -shared -L/usr/local/lib -o EBcoexpress.so EBcoexpress.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-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
ebCoexpressMeta1.7240.0001.729
ebCoexpressSeries0.9640.0000.966
fiftyGenes0.0040.0000.005
initializeHP0.7360.0000.738
makeMyD0.0360.0040.038
priorDiagnostic1.1960.0041.199
rankMyGenes0.8960.0000.897
showNetwork1.0360.0121.051
showPair0.0400.0040.044
utilities0.0080.0040.010