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BioC 3.4: CHECK report for weaver on moscato1

This page was generated on 2016-09-21 03:43:50 -0700 (Wed, 21 Sep 2016).

Package 1246/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
weaver 1.39.0
Seth Falcon
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/weaver
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: weaver
Version: 1.39.0
Command: rm -rf weaver.buildbin-libdir weaver.Rcheck && mkdir weaver.buildbin-libdir weaver.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=weaver.buildbin-libdir weaver_1.39.0.tar.gz >weaver.Rcheck\00install.out 2>&1 && cp weaver.Rcheck\00install.out weaver-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=weaver.buildbin-libdir --install="check:weaver-install.out" --force-multiarch --no-vignettes --timings weaver_1.39.0.tar.gz
StartedAt: 2016-09-20 18:17:56 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 18:18:22 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 26.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: weaver.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf weaver.buildbin-libdir weaver.Rcheck && mkdir weaver.buildbin-libdir weaver.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=weaver.buildbin-libdir weaver_1.39.0.tar.gz >weaver.Rcheck\00install.out 2>&1 && cp weaver.Rcheck\00install.out weaver-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=weaver.buildbin-libdir --install="check:weaver-install.out" --force-multiarch --no-vignettes --timings weaver_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/weaver.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'weaver/DESCRIPTION' ... OK
* this is package 'weaver' version '1.39.0'
* 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 whether package 'weaver' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'codetools'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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:
  'codetools' 'digest' 'tools'
  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
cache_expr: no visible binding for global variable 'DEPS'
eval_and_cache: no visible global function definition for 'sessionInfo'
findDeps: no visible global function definition for 'findGlobals'
findDeps: no visible global function definition for 'findLocals'
get_expr_hash: no visible global function definition for 'digest'
make_cache_expr : <local> : <anonymous>: no visible binding for global
  variable 'DEPS'
weaver: no visible binding for global variable 'RweaveLatexWritedoc'
weaver: no visible binding for global variable 'RweaveLatexOptions'
weaverLatexFinish: no visible global function definition for
  'RweaveLatexFinish'
weaverLatexSetup: no visible global function definition for
  'RweaveLatexSetup'
weaverLatexSetup: no visible global function definition for
  'RweaveLatexOptions'
Undefined global functions or variables:
  DEPS RweaveLatexFinish RweaveLatexOptions RweaveLatexSetup
  RweaveLatexWritedoc digest findGlobals findLocals sessionInfo
Consider adding
  importFrom("utils", "RweaveLatexFinish", "RweaveLatexOptions",
             "RweaveLatexSetup", "RweaveLatexWritedoc", "sessionInfo")
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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  inst/extdata/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section 'Writing portable packages' in
the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 1 WARNING, 3 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/weaver.Rcheck/00check.log'
for details.


weaver.Rcheck/00install.out:


install for i386

* installing *source* package 'weaver' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'weaver' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'weaver' as weaver_1.39.0.zip
* DONE (weaver)

weaver.Rcheck/examples_i386/weaver-Ex.timings:

nameusersystemelapsed
weaver000

weaver.Rcheck/examples_x64/weaver-Ex.timings:

nameusersystemelapsed
weaver000