Package: weaver

Version: 1.46.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:weaver.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings weaver_1.46.0.tar.gz

StartedAt: 2018-10-17 05:25:54 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 05:26:21 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 27.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: weaver.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:weaver.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings weaver_1.46.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/weaver.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.46.0'
* 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 include directives in Makefiles ... 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
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/weaver.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/weaver_1.46.0.tar.gz && rm -rf weaver.buildbin-libdir && mkdir weaver.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=weaver.buildbin-libdir weaver_1.46.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL weaver_1.46.0.zip && rm weaver_1.46.0.tar.gz weaver_1.46.0.zip
###
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install for i386

* installing *source* package 'weaver' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'weaver'
    finding HTML links ... done
    internal                                html  
    weaver                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'weaver' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'weaver' as weaver_1.46.0.zip
* DONE (weaver)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'weaver' successfully unpacked and MD5 sums checked
In R CMD INSTALL