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CHECK report for weaver on tokay2

This page was generated on 2019-10-16 12:25:38 -0400 (Wed, 16 Oct 2019).

Package 1722/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
weaver 1.50.0
Seth Falcon
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/weaver
Branch: RELEASE_3_9
Last Commit: 73f3fec
Last Changed Date: 2019-05-02 11:53:29 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: weaver
Version: 1.50.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:weaver.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings weaver_1.50.0.tar.gz
StartedAt: 2019-10-16 07:51:48 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:52:12 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 24.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: weaver.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:weaver.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings weaver_1.50.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/weaver.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.50.0'
* 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 :  : : 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, .NOTPARALLEL 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-3.9-bioc/meat/weaver.Rcheck/00check.log'
for details.



Installation output

weaver.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/weaver_1.50.0.tar.gz && rm -rf weaver.buildbin-libdir && mkdir weaver.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=weaver.buildbin-libdir weaver_1.50.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL weaver_1.50.0.zip && rm weaver_1.50.0.tar.gz weaver_1.50.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 12127  100 12127    0     0   116k      0 --:--:-- --:--:-- --:--:--  124k

install for i386

* installing *source* package 'weaver' ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'weaver' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'weaver' as weaver_1.50.0.zip
* DONE (weaver)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'weaver' successfully unpacked and MD5 sums checked

Tests output


Example timings

weaver.Rcheck/examples_i386/weaver-Ex.timings

nameusersystemelapsed
weaver000

weaver.Rcheck/examples_x64/weaver-Ex.timings

nameusersystemelapsed
weaver000