CRAN Package Check Results for Package rentrez

Last updated on 2015-07-06 10:47:16.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.4.2 1.12 42.62 43.74 OK --no-tests
r-devel-linux-x86_64-debian-gcc 0.4.2 1.18 45.64 46.82 NOTE --no-tests
r-devel-linux-x86_64-fedora-clang 0.4.2 21.35 ERROR
r-devel-linux-x86_64-fedora-gcc 0.4.2 32.42 ERROR
r-devel-osx-x86_64-clang 0.4.2 87.46 ERROR
r-devel-windows-ix86+x86_64 0.4.2 7.00 57.00 64.00 OK
r-patched-linux-x86_64 0.4.2 1.03 68.13 69.16 ERROR
r-patched-solaris-sparc 0.4.2 194.20 OK
r-patched-solaris-x86 0.4.2 49.90 ERROR
r-release-linux-x86_64 0.4.2 0.98 53.12 54.10 OK
r-release-osx-x86_64-mavericks 0.4.2 OK
r-release-windows-ix86+x86_64 0.4.2 6.00 60.00 66.00 OK
r-oldrel-windows-ix86+x86_64 0.4.2 5.00 56.00 61.00 ERROR

Check Details

Version: 0.4.2
Flags: --no-tests
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Loading required package: XML
    
    Attaching package: 'XML'
    
    The following object is masked from 'package:tools':
    
     toHTML
    
    Quitting from lines 102-105 (rentrez_tutorial.Rmd)
    Error: processing vignette ‘rentrez_tutorial.Rmd’ failed with diagnostics:
    subscript out of bounds
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.4.2
Check: tests
Result: ERROR
    Running the tests in ‘tests/test-all.R’ failed.
    Last 13 lines of output:
     > library("testthat")
     > test_check("rentrez")
     Loading required package: rentrez
     Loading required package: XML
     1. Failure (at test_link.r#9): The record-linking funcitons work ---------------
     length(elinks$pubmed_nuccore) > 0 isn't true
    
     testthat results ================================================================
     OK: 64 SKIPPED: 0 FAILED: 1
     1. Failure (at test_link.r#9): The record-linking funcitons work
    
     Error: testthat unit tests failed
     Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-x86

Version: 0.4.2
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Loading required package: XML
    
    Attaching package: 'XML'
    
    The following object is masked from 'package:tools':
    
     toHTML
    
    Quitting from lines 102-105 (rentrez_tutorial.Rmd)
    Error: processing vignette 'rentrez_tutorial.Rmd' failed with diagnostics:
    subscript out of bounds
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86

Version: 0.4.2
Check: examples
Result: ERROR
    Running examples in 'rentrez-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: parse_pubmed_xml
    > ### Title: Summarise an XML record from pubmed.
    > ### Aliases: parse_pubmed_xml
    >
    > ### ** Examples
    >
    > hox_paper <- entrez_search(db="pubmed", term="10.1038/nature08789[doi]")
    > hox_rel <- entrez_link(db="pubmed", dbfrom="pubmed", id=hox_paper$ids)
    Error in make_entrez_query("elink", db = db, dbfrom = dbfrom, config = config, :
     server error: (502) Bad Gateway
    Calls: entrez_link -> make_entrez_query -> <Anonymous>
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64