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lefko3 log file (check_x86_64_linux)

Sat Oct 15 07:57:33 2022: Checking package lefko3 (SVN revision 103) ...
* using log directory ‘/srv/rf/building/build_2022-10-15-07-51/RF_PKG_CHECK/PKGS/lefko3.Rcheck’
* using R version 4.2.1 Patched (2022-10-13 r83098)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘lefko3/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lefko3’ version ‘5.5.0.9000’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Richard P. Shefferson ’

Version contains large components (5.5.0.9000)

Found the following (possibly) invalid URLs:
  URL: https://doi.org/10.1002/ece3.1037
    From: inst/doc/Chapter1.html
          inst/doc/Chapter2.html
    Status: 503
    Message: Service Unavailable
  URL: https://doi.org/10.1002/ecm.1447
    From: inst/doc/Chapter1.html
          inst/doc/Chapter6.html
          inst/doc/Chapter8.html
    Status: 503
    Message: Service Unavailable
  URL: https://doi.org/10.1034/j.1600-0706.2002.980212.x
    From: inst/doc/Chapter2.html
          inst/doc/Chapter6.html
          inst/doc/Chapter8.html
    Status: 503
    Message: Service Unavailable
  URL: https://doi.org/10.1046/j.1365-2745.2001.00546.x
    From: inst/doc/Chapter2.html
          inst/doc/Chapter6.html
          inst/doc/Chapter8.html
    Status: 503
    Message: Service Unavailable
  URL: https://doi.org/10.1111/1365-2745.12281
    From: inst/doc/Chapter1.html
          inst/doc/Chapter2.html
          inst/doc/Chapter5.html
    Status: 503
    Message: Service Unavailable
  URL: https://doi.org/10.1111/1541-0420.00006
    From: inst/doc/Chapter1.html
          inst/doc/Chapter2.html
    Status: 503
    Message: Service Unavailable
  URL: https://doi.org/10.1111/2041-210X.13526
    From: inst/CITATION
          inst/doc/Chapter1.html
    Status: 503
    Message: Service Unavailable
  URL: https://doi.org/10.1111/ele.12940
    From: inst/doc/Chapter1.html
          inst/doc/Chapter2.html
    Status: 503
    Message: Service Unavailable
  URL: https://doi.org/10.1111/j.1365-2745.2009.01611.x
    From: inst/doc/Chapter1.html
          inst/doc/Chapter9.html
    Status: 503
    Message: Service Unavailable
  URL: https://doi.org/10.1111/j.1365-2745.2009.01616.x
    From: inst/doc/Chapter1.html
    Status: 503
    Message: Service Unavailable
  URL: https://doi.org/10.1111/j.2041-210X.2012.00222.x
    From: inst/doc/Chapter1.html
    Status: 503
    Message: Service Unavailable
  URL: https://doi.org/10.1890/0012-9658(1998)079%5B2539:AGTATD%5D2.0.CO;2
    From: inst/doc/Chapter1.html
    Status: 503
    Message: Service Unavailable
  URL: https://doi.org/10.1890/0012-9658(2000)081%5B0694:SSSAAN%5D2.0.CO;2
    From: inst/doc/Chapter1.html
    Status: 503
    Message: Service Unavailable
  URL: https://doi.org/10.1890/0012-9658(2000)081%5B1675:TDOPPD%5D2.0.CO;2
    From: inst/doc/Chapter1.html
          inst/doc/Chapter2.html
          inst/doc/Chapter5.html
          inst/doc/Chapter6.html
          inst/doc/Chapter8.html
    Status: 503
    Message: Service Unavailable
  URL: https://doi.org/10.1890/0012-9658(2001)082%5B0145:EDASOA%5D2.0.CO;2
    From: inst/doc/Chapter1.html
          inst/doc/Chapter5.html
    Status: 503
    Message: Service Unavailable
  URL: https://doi.org/10.1890/09-0423.1
    From: inst/doc/Chapter2.html
    Status: 503
    Message: Service Unavailable

Found the following (possibly) invalid DOIs:
  DOI: 10.1111/2041-210X.13526
    From: inst/CITATION
    Status: Service Unavailable
    Message: 503
* 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 ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘lefko3’ can be installed ... [318s/318s] OK
* checking installed package size ... NOTE
  installed size is 74.7Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  70.6Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘doc’
* 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [29s/29s] 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [34s/34s] OK
* checking examples with --run-donttest ... [18m/18m] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* skipping checking HTML version of manual: no command ‘tidy’ found
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 3 NOTEs
See
  ‘/srv/rf/building/build_2022-10-15-07-51/RF_PKG_CHECK/PKGS/lefko3.Rcheck/00check.log’
for details.


Run time: 1574.51 seconds.

Additional Logs:   00install.out
Thanks to:
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