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glmmADMB log file (check_x86_64_linux)

Fri Feb 23 19:05:22 2018: Checking package glmmADMB (SVN revision 289) ...
* using log directory ‘/srv/rf/building/build_2018-02-23-19-04/RF_PKG_CHECK/PKGS/glmmADMB.Rcheck’
* using R version 3.4.3 Patched (2018-02-21 r74284)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘glmmADMB/DESCRIPTION’ ... OK
* this is package ‘glmmADMB’ version ‘0.8.3.4’
* checking CRAN incoming feasibility ... WARNING
Maintainer: ‘Ben Bolker ’

New submission

FOSS licence with BuildVignettes: false

Unknown, possibly mis-spelled, fields in DESCRIPTION:
  ‘BuildVignette’

Package has a VignetteBuilder field but no prebuilt vignette index.

Found the following (possibly) invalid URLs:
  URL: http://admb-project.org/documentation/manuals/admb-user-manuals (moved to http://www.admb-project.org/documentation/manuals/admb-user-manuals)
    From: man/admbControl.Rd
    Status: 404
    Message: Not Found
  URL: http://www.highstat.com/Book2/ZuurDataMixedModelling.zip
    From: man/Owls.Rd
    Status: 404
    Message: Not Found

Size of tarball: 8587532 bytes
* 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 executable files ... WARNING
Found the following executable files:
  inst/bin/linux32/glmmadmb
  inst/bin/linux64/glmmadmb
  inst/bin/macos32/glmmadmb
  inst/bin/macos64/glmmadmb
  inst/bin/windows32/glmmadmb.exe
  inst/bin/windows64/glmmadmb.exe
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘glmmADMB’ can be installed ... [4s/4s] OK
* checking installed package size ... NOTE
  installed size is 19.0Mb
  sub-directories of 1Mb or more:
    bin       16.8Mb
    testdata   1.5Mb
* checking package 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 loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
VarCorr:
  function(x, sigma, ...)
VarCorr.glmmadmb:
  function(x, sigma, rdig)

VarCorr:
  function(x, sigma, ...)
VarCorr.summary.glmmadmb:
  function(x, sigma, rdig)

VarCorr:
  function(x, sigma, ...)
VarCorr.glmmadmb:
  function(x, sigma, rdig)

VarCorr:
  function(x, sigma, ...)
VarCorr.summary.glmmadmb:
  function(x, sigma, rdig)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [10s/10s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘Makefile’, ‘OwlModel.rda’, ‘glmmADMB.Rnw’, ‘glmmadmb.bib’,
    ‘lineno.sty’, ‘owls_mcmcbatch.R’, ‘owls_mcmcbatch.RData’
* checking examples ... [6s/6s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
Package vignette without corresponding PDF/HTML:
   ‘glmmADMB.Rnw’

* checking re-building of vignette outputs ... [159s/159s] WARNING
Error in re-building vignettes:
  ...
Loading required package: MASS

Attaching package: 'glmmADMB'

The following object is masked from 'package:MASS':

    stepAIC

The following object is masked from 'package:stats':

    step

make: *** No rule to make target 'glmmADMB.pdf', needed by 'all'.  Stop.
Error in buildVignettes(dir = "/srv/rf/building/build_2018-02-23-19-04/RF_PKG_CHECK/PKGS/glmmADMB.Rcheck/vign_test/glmmADMB") : 
  running 'make' failed
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 6 WARNINGs, 1 NOTE
See
  ‘/srv/rf/building/build_2018-02-23-19-04/RF_PKG_CHECK/PKGS/glmmADMB.Rcheck/00check.log’
for details.


Run time: 230.38 seconds.

Additional Logs:   00install.out
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