CRAN Package Check Results for Package rentrez

Last updated on 2016-08-27 10:48:06.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.2 1.06 40.79 41.85 OK
r-devel-linux-x86_64-debian-gcc 1.0.2 1.44 54.04 55.47 WARN
r-devel-linux-x86_64-fedora-clang 1.0.2 35.95 OK
r-devel-linux-x86_64-fedora-gcc 1.0.2 33.76 OK
r-devel-osx-x86_64-clang 1.0.2 30.58 OK
r-devel-windows-ix86+x86_64 1.0.2 6.00 37.00 43.00 OK --no-vignettes
r-patched-linux-x86_64 1.0.2 1.07 40.77 41.84 OK
r-patched-solaris-sparc 1.0.2 211.40 OK
r-patched-solaris-x86 1.0.2 47.60 OK
r-release-linux-x86_64 1.0.2 0.99 66.13 67.13 ERROR
r-release-osx-x86_64-mavericks 1.0.2 OK
r-release-windows-ix86+x86_64 1.0.2 5.00 37.00 42.00 OK --no-vignettes
r-oldrel-windows-ix86+x86_64 1.0.2 4.00 48.00 52.00 OK --no-vignettes

Check Details

Version: 1.0.2
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Quitting from lines 209-218 (rentrez_tutorial.Rmd)
    Error: processing vignette ‘rentrez_tutorial.Rmd’ failed with diagnostics:
    subscript out of bounds
    Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-release-linux-x86_64

Version: 1.0.2
Check: examples
Result: ERROR
    Running examples in ‘rentrez-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: parse_pubmed_xml
    > ### Title: Summarize 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)
    Warning in check_xml_errors(x) :
     NCBI C++ Exception:
     Error: TXCLIENT(CException::eUnknown) "/pubmed_gen/rbuild/version/20160802/entrez/2.13.1/src/internal/txclient/TxClient.cpp", line 1036: ncbi::CTxRawClientImpl::readAll() --- Read failed: EOF (the other side has unexpectedly closed connection), peer: 130.14.22.15:8064
    
    Error in res[[1]] : subscript out of bounds
    Calls: entrez_link -> parse_elink
    Execution halted
Flavor: r-release-linux-x86_64