CRAN Package Check Results for Package tmod

Last updated on 2018-02-20 13:50:16 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	0.31	5.19	93.95	99.14	WARN
r-devel-linux-x86_64-debian-gcc	0.31	4.37	70.63	75.00	WARN
r-devel-linux-x86_64-fedora-clang	0.31			70.06	ERROR
r-devel-linux-x86_64-fedora-gcc	0.31			66.72	ERROR
r-devel-windows-ix86+x86_64	0.31	8.00	96.00	104.00	WARN
r-patched-linux-x86_64	0.31	3.17	115.54	118.71	WARN
r-patched-solaris-x86	0.31			184.00	WARN
r-release-linux-x86_64	0.31	3.11	113.94	117.05	WARN
r-release-windows-ix86+x86_64	0.31	13.00	142.00	155.00	WARN
r-release-osx-x86_64	0.31				ERROR
r-oldrel-windows-ix86+x86_64	0.31	9.00	139.00	148.00	WARN
r-oldrel-osx-x86_64	0.31				OK

Check Details

Version: 0.31
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
    Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols, :
     not using pch[2..] since pch[1L] has multiple chars
    Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols, :
     not using pch[2..] since pch[1L] has multiple chars
    Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols, :
     not using pch[2..] since pch[1L] has multiple chars
    trying URL ‘http://www.wikipathways.org//wpi/batchDownload.php?species=Homo%20sapiens&fileType=txt’
    downloaded 11 KB

    Quitting from lines 1170-1178 (tmod.rmd)
    Error: processing vignette ‘tmod.rmd’ failed with diagnostics:
    zip file ‘/tmp/RtmprEM032/file4d3c17d63a3c’ cannot be opened
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.31
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
    Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols, :
     not using pch[2..] since pch[1L] has multiple chars
    Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols, :
     not using pch[2..] since pch[1L] has multiple chars
    Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols, :
     not using pch[2..] since pch[1L] has multiple chars
    trying URL ‘http://www.wikipathways.org//wpi/batchDownload.php?species=Homo%20sapiens&fileType=txt’
    downloaded 11 KB

    Quitting from lines 1170-1178 (tmod.rmd)
    Error: processing vignette ‘tmod.rmd’ failed with diagnostics:
    zip file ‘/tmp/RtmpI0GUfh/file36274c8d314d’ cannot be opened
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.31
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: ‘limma’ ‘org.Hs.eg.db’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-osx-x86_64

Version: 0.31
Check: examples
Result: ERROR
    Running examples in ‘tmod-Ex.R’ failed
    The error most likely occurred in:

    > ### Name: tmodLimmaTest
    > ### Title: Run tmod enrichment tests directly on a limma object
    > ### Aliases: tmodLimmaTest
    >
    > ### ** Examples
    >
    > library(limma)
    Error in library(limma) : there is no package called ‘limma’
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-osx-x86_64

Version: 0.31
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
    Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols, :
     not using pch[2..] since pch[1L] has multiple chars
    Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols, :
     not using pch[2..] since pch[1L] has multiple chars
    Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols, :
     not using pch[2..] since pch[1L] has multiple chars
    trying URL 'http://www.wikipathways.org//wpi/batchDownload.php?species=Homo%20sapiens&fileType=txt'
    Warning in download.file("http://www.wikipathways.org//wpi/batchDownload.php?species=Homo%20sapiens&fileType=txt", :
     InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
    Quitting from lines 1170-1178 (tmod.rmd)
    Error: processing vignette 'tmod.rmd' failed with diagnostics:
    cannot open URL 'http://www.wikipathways.org//wpi/batchDownload.php?species=Homo%20sapiens&fileType=txt'
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 0.31
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols, :
     not using pch[2..] since pch[1L] has multiple chars
    Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols, :
     not using pch[2..] since pch[1L] has multiple chars
    Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols, :
     not using pch[2..] since pch[1L] has multiple chars
    trying URL ‘http://www.wikipathways.org//wpi/batchDownload.php?species=Homo%20sapiens&fileType=txt’
    downloaded 11 KB

    Quitting from lines 1170-1178 (tmod.rmd)
    Error: processing vignette ‘tmod.rmd’ failed with diagnostics:
    zip file ‘/tmp/RtmpPCYSSq/file339f7b4d946’ cannot be opened
    Execution halted
Flavor: r-patched-linux-x86_64

Version: 0.31
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols, :
     not using pch[2..] since pch[1L] has multiple chars
    Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols, :
     not using pch[2..] since pch[1L] has multiple chars
    Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols, :
     not using pch[2..] since pch[1L] has multiple chars
    trying URL 'http://www.wikipathways.org//wpi/batchDownload.php?species=Homo%20sapiens&fileType=txt'
    downloaded 11 KB

    Quitting from lines 1170-1178 (tmod.rmd)
    Error: processing vignette 'tmod.rmd' failed with diagnostics:
    zip file '/tmp/Rtmpo4aW3h/filefbe7de63624' cannot be opened
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.31
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols, :
     not using pch[2..] since pch[1L] has multiple chars
    Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols, :
     not using pch[2..] since pch[1L] has multiple chars
    Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols, :
     not using pch[2..] since pch[1L] has multiple chars
    trying URL ‘http://www.wikipathways.org//wpi/batchDownload.php?species=Homo%20sapiens&fileType=txt’
    downloaded 11 KB

    Quitting from lines 1170-1178 (tmod.rmd)
    Error: processing vignette ‘tmod.rmd’ failed with diagnostics:
    zip file ‘/tmp/Rtmpkulje6/file50897c09bf07’ cannot be opened
    Execution halted
Flavor: r-release-linux-x86_64

Version: 0.31
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols, :
     not using pch[2..] since pch[1L] has multiple chars
    Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols, :
     not using pch[2..] since pch[1L] has multiple chars
    Warning in legend("topleft", as.character(l$groups), pch = l$shapes, col = cols, :
     not using pch[2..] since pch[1L] has multiple chars
    trying URL 'http://www.wikipathways.org//wpi/batchDownload.php?species=Homo%20sapiens&fileType=txt'
    Warning in download.file("http://www.wikipathways.org//wpi/batchDownload.php?species=Homo%20sapiens&fileType=txt", :
     InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
    Quitting from lines 1170-1178 (tmod.rmd)
    Error: processing vignette 'tmod.rmd' failed with diagnostics:
    cannot open URL 'http://www.wikipathways.org//wpi/batchDownload.php?species=Homo%20sapiens&fileType=txt'
    Execution halted
Flavors: r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64