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BioC 3.4: CHECK report for EBcoexpress on morelia

This page was generated on 2017-04-15 16:24:06 -0400 (Sat, 15 Apr 2017).

Package 358/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBcoexpress 1.18.0
John A. Dawson
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/EBcoexpress
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: EBcoexpress
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EBcoexpress_1.18.0.tar.gz
StartedAt: 2017-04-15 01:23:32 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 01:24:14 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 41.9 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 EBcoexpress_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/EBcoexpress.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.18.0’
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'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'
bwmc: no visible binding for global variable ‘median’
bwmc: no visible binding for global variable ‘mad’
ebCoexpressFullTCAECM: no visible global function definition for
  ‘bobyqa’
ebCoexpressOneStep: no visible global function definition for ‘bobyqa’
initializeHP : getMclustHPests : devHelper: no visible global function
  definition for ‘density’
initializeHP : getMclustHPests : devHelper : fundDev: no visible global
  function definition for ‘dnorm’
initializeHP : getMclustHPests: no visible global function definition
  for ‘Mclust’
initializeHP : getMclustHPests : checkMyData : funa: no visible global
  function definition for ‘dnorm’
initializeHP : getMclustHPests : checkMyData: no visible global
  function definition for ‘density’
initializeHP : getMclustHPests : checkMyData: no visible global
  function definition for ‘plot’
initializeHP : getMclustHPests : checkMyData: no visible global
  function definition for ‘lines’
initializeHP: no visible global function definition for ‘par’
makeMyD: no visible global function definition for ‘cor’
priorDiagnostic : funa: no visible global function definition for
  ‘dnorm’
priorDiagnostic: no visible global function definition for ‘density’
priorDiagnostic: no visible global function definition for ‘plot’
priorDiagnostic: no visible global function definition for ‘lines’
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’
showNetwork: no visible global function definition for ‘plot’
showPair: no visible global function definition for ‘palette’
showPair : getUsed: no visible global function definition for ‘median’
showPair : getUsed: no visible global function definition for ‘mad’
showPair: no visible binding for global variable ‘plot’
showPair: no visible global function definition for ‘box’
showPair: no visible global function definition for ‘lm’
showPair: no visible binding for global variable ‘segments’
Undefined global functions or variables:
  Mclust RGB bobyqa box cor density dnorm graph.full hex layout.circle
  lines lm mad median palette par plot segments
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "box", "lines", "par", "plot", "segments")
  importFrom("stats", "cor", "density", "dnorm", "lm", "mad", "median")
to your NAMESPACE file.
* 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 ... 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

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-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-3.4-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
ebCoexpressMeta1.1640.0121.196
ebCoexpressSeries0.5050.0030.508
fiftyGenes0.0030.0010.004
initializeHP0.4370.0030.440
makeMyD0.0370.0020.038
priorDiagnostic0.7480.0060.756
rankMyGenes0.5580.0030.562
showNetwork0.8070.0140.940
showPair0.0380.0030.042
utilities0.0040.0010.005