CRAN Package Check Results for Package biofiles

Last updated on 2019-09-20 01:47:40 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.0 49.58 126.53 176.11 OK
r-devel-linux-x86_64-debian-gcc 1.0.0 45.26 99.39 144.65 OK
r-devel-linux-x86_64-fedora-clang 1.0.0 240.22 WARN
r-devel-linux-x86_64-fedora-gcc 1.0.0 231.09 WARN
r-devel-windows-ix86+x86_64 1.0.0 143.00 195.00 338.00 OK
r-patched-linux-x86_64 1.0.0 50.45 120.68 171.13 OK
r-patched-solaris-x86 1.0.0 285.40 WARN
r-release-linux-x86_64 1.0.0 51.55 122.17 173.72 OK
r-release-windows-ix86+x86_64 1.0.0 99.00 198.00 297.00 OK
r-release-osx-x86_64 1.0.0 ERROR
r-oldrel-windows-ix86+x86_64 1.0.0 95.00 180.00 275.00 OK
r-oldrel-osx-x86_64 1.0.0 ERROR

Check Details

Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘IntroBiofiles.Rnw’ using knitr
    Error: processing vignette 'IntroBiofiles.Rnw' failed with diagnostics:
    Running 'texi2dvi' on 'IntroBiofiles.tex' failed.
    LaTeX errors:
    ! LaTeX Error: Missing \begin{document}.
    
    See the LaTeX manual or LaTeX Companion for explanation.
    Type H <return> for immediate help.
     ...
    ! Argument of \Hy@scantitle has an extra }.
    <inserted text>
     \par
    l.166 \renewcommand{\title}
     [1]{\def\@bioctitle{#1}\@oldtitle{#1}}
    ! Paragraph ended before \Hy@scantitle was complete.
    <to be read again>
     \par
    l.166 \renewcommand{\title}
     [1]{\def\@bioctitle{#1}\@oldtitle{#1}}
    ! LaTeX Error: Missing \begin{document}.
    
    See the LaTeX manual or LaTeX Companion for explanation.
    Type H <return> for immediate help.
     ...
    ! Illegal parameter number in definition of \@.
    <to be read again>
     1
    l.166 \renewcommand{\title}[1]{\def\@bioctitle{#1
     }\@oldtitle{#1}}
    ! Use of \@ doesn't match its definition.
    l.166 ...command{\title}[1]{\def\@bioctitle{#1}\@o
     ldtitle{#1}}
    If you say, e.g., `\def\a1{...}', then you must always
    put `1' after `\a', since control sequence names are
    ! You can't use `macro parameter character #' in horizontal mode.
    l.166 ...title}[1]{\def\@bioctitle{#1}\@oldtitle{#
     1}}
    Sorry, but I'm not programmed to handle this case;
    I'll just pretend that you didn't ask for it.
    ! LaTeX Error: Missing \begin{document}.
    
    See the LaTeX manual or LaTeX Companion for explanation.
    Type H <return> for immediate help.
     ...
    ! Argument of \etb@resrvda has an extra }.
    <inserted text>
     \par
    l.210 \patchcmd{\PN@parnote@real}{\thinspace}{}
     {}{}
    ! Paragraph ended before \etb@resrvda was complete.
    <to be read again>
     \par
    l.210 \patchcmd{\PN@parnote@real}{\thinspace}{}
     {}{}
    ! LaTeX Error: Missing \begin{document}.
    
    See the LaTeX manual or LaTeX Companion for explanation.
    Type H <return> for immediate help.
     ...
    ! Undefined control sequence.
    \\etb@patchcmd ...etb@resrvda \let #2\etb@resrvda
     \undef \etb@resrvda \@firs...
    l.210 \patchcmd{\PN@parnote@real}{\thinspace}{}
     {}{}
    ! Argument of \@firstoftwo has an extra }.
    <inserted text>
     \par
    l.210 \patchcmd{\PN@parnote@real}{\thinspace}{}
     {}{}
    ! Paragraph ended before \@firstoftwo was complete.
    <to be read again>
     \par
    l.210 \patchcmd{\PN@parnote@real}{\thinspace}{}
     {}{}
    ! Argument of \@secondoftwo has an extra }.
    <inserted text>
     \par
    l.210 \patchcmd{\PN@parnote@real}{\thinspace}{}
     {}{}
    ! Paragraph ended before \@secondoftwo was complete.
    <to be read again>
     \par
    l.210 \patchcmd{\PN@parnote@real}{\thinspace}{}
     {}{}
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.71 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.71 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.71 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.71 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Undefined control sequence.
    <argument> ... \hsize -\width \@totalleftmargin\z
     @ \linewidth \hsize \advan...
    l.71 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.75 \end{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.75 \end{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.75 \end{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.75 \end{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.75 \end{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.75 \end{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.75 \end{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.75 \end{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.82 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.82 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.82 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.82 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Undefined control sequence.
    <argument> ... \hsize -\width \@totalleftmargin\z
     @ \linewidth \hsize \advan...
    l.82 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.87 \end{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.87 \end{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.87 \end{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.87 \end{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.87 \end{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.87 \end{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.87 \end{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.87 \end{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.91 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.91 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.91 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.91 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Undefined control sequence.
    <argument> ... \hsize -\width \@totalleftmargin\z
     @ \linewidth \hsize \advan...
    l.91 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Missing number, treated as zero.
    <to
    --- failed re-building ‘IntroBiofiles.Rnw’
    
    SUMMARY: processing the following file failed:
     ‘IntroBiofiles.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘IntroBiofiles.Rnw’ using knitr
    Error: processing vignette 'IntroBiofiles.Rnw' failed with diagnostics:
    Running 'texi2dvi' on 'IntroBiofiles.tex' failed.
    LaTeX errors:
    ! LaTeX Error: Missing \begin{document}.
    
    See the LaTeX manual or LaTeX Companion for explanation.
    Type H <return> for immediate help.
     ...
    ! Argument of \Hy@scantitle has an extra }.
    <inserted text>
     \par
    l.166 \renewcommand{\title}
     [1]{\def\@bioctitle{#1}\@oldtitle{#1}}
    ! Paragraph ended before \Hy@scantitle was complete.
    <to be read again>
     \par
    l.166 \renewcommand{\title}
     [1]{\def\@bioctitle{#1}\@oldtitle{#1}}
    ! LaTeX Error: Missing \begin{document}.
    
    See the LaTeX manual or LaTeX Companion for explanation.
    Type H <return> for immediate help.
     ...
    ! Illegal parameter number in definition of \@.
    <to be read again>
     1
    l.166 \renewcommand{\title}[1]{\def\@bioctitle{#1
     }\@oldtitle{#1}}
    ! Use of \@ doesn't match its definition.
    l.166 ...command{\title}[1]{\def\@bioctitle{#1}\@o
     ldtitle{#1}}
    If you say, e.g., `\def\a1{...}', then you must always
    put `1' after `\a', since control sequence names are
    ! You can't use `macro parameter character #' in horizontal mode.
    l.166 ...title}[1]{\def\@bioctitle{#1}\@oldtitle{#
     1}}
    Sorry, but I'm not programmed to handle this case;
    I'll just pretend that you didn't ask for it.
    ! LaTeX Error: Missing \begin{document}.
    
    See the LaTeX manual or LaTeX Companion for explanation.
    Type H <return> for immediate help.
     ...
    ! Argument of \etb@resrvda has an extra }.
    <inserted text>
     \par
    l.210 \patchcmd{\PN@parnote@real}{\thinspace}{}
     {}{}
    ! Paragraph ended before \etb@resrvda was complete.
    <to be read again>
     \par
    l.210 \patchcmd{\PN@parnote@real}{\thinspace}{}
     {}{}
    ! LaTeX Error: Missing \begin{document}.
    
    See the LaTeX manual or LaTeX Companion for explanation.
    Type H <return> for immediate help.
     ...
    ! Undefined control sequence.
    \\etb@patchcmd ...etb@resrvda \let #2\etb@resrvda
     \undef \etb@resrvda \@firs...
    l.210 \patchcmd{\PN@parnote@real}{\thinspace}{}
     {}{}
    ! Argument of \@firstoftwo has an extra }.
    <inserted text>
     \par
    l.210 \patchcmd{\PN@parnote@real}{\thinspace}{}
     {}{}
    ! Paragraph ended before \@firstoftwo was complete.
    <to be read again>
     \par
    l.210 \patchcmd{\PN@parnote@real}{\thinspace}{}
     {}{}
    ! Argument of \@secondoftwo has an extra }.
    <inserted text>
     \par
    l.210 \patchcmd{\PN@parnote@real}{\thinspace}{}
     {}{}
    ! Paragraph ended before \@secondoftwo was complete.
    <to be read again>
     \par
    l.210 \patchcmd{\PN@parnote@real}{\thinspace}{}
     {}{}
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.71 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.71 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.71 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.71 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Undefined control sequence.
    <argument> ... \hsize -\width \@totalleftmargin\z
     @ \linewidth \hsize \advan...
    l.71 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.75 \end{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.75 \end{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.75 \end{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.75 \end{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.75 \end{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.75 \end{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.75 \end{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.75 \end{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.82 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.82 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.82 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.82 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Undefined control sequence.
    <argument> ... \hsize -\width \@totalleftmargin\z
     @ \linewidth \hsize \advan...
    l.82 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.87 \end{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.87 \end{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.87 \end{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.87 \end{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.87 \end{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.87 \end{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.87 \end{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.87 \end{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.91 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.91 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Missing number, treated as zero.
    <to be read again>
     \@
    l.91 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Illegal unit of measure (pt inserted).
    <to be read again>
     \@
    l.91 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Undefined control sequence.
    <argument> ... \hsize -\width \@totalleftmargin\z
     @ \linewidth \hsize \advan...
    l.91 ...0.941, 0.941}\color{fgcolor}\begin{kframe}
    
    ! Missing number, treated as zero.
    <to
    --- failed re-building ‘IntroBiofiles.Rnw’
    
    SUMMARY: processing the following file failed:
     ‘IntroBiofiles.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.0.0
Check: package dependencies
Result: ERROR
    Packages required but not available:
     'BiocGenerics', 'Biostrings', 'GenomeInfoDb', 'GenomicRanges',
     'IRanges', 'S4Vectors', 'XVector'
    
    Package suggested but not available for checking: ‘BiocStyle’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64

Version: 1.0.0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘BiocStyle’
Flavor: r-oldrel-osx-x86_64

Version: 1.0.0
Check: tests
Result: ERROR
     Running ‘test-all.R’ [9s/13s]
    Running the tests in ‘tests/test-all.R’ failed.
    Last 13 lines of output:
     ── 5. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#17)
     `gbLocation("123^125")` threw an error with unexpected message.
     Expected match: "Inadmissible range"
     Actual message: "c++ exception (unknown reason)"
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 267 SKIPPED: 1 FAILED: 5
     1. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#6)
     2. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#9)
     3. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#13)
     4. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#14)
     5. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#17)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-oldrel-osx-x86_64

Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Quitting from lines 10-11 (IntroBiofiles.Rnw)
    Error: processing vignette 'IntroBiofiles.Rnw' failed with diagnostics:
    there is no package called 'BiocStyle'
    Execution halted
Flavor: r-oldrel-osx-x86_64