[Bioc-devel] Pandoc issues

Hervé Pagès hpages at fredhutch.org
Tue Nov 28 19:11:45 CET 2017

Hi Vladimir,

mmh... scmap::getSankey() used to work (and still works in the release
version of scmap) so I wonder what could have changed in the devel
version or in one of its dependencies to cause it to fail now...

Anyway we'll look into updating pandoc to the latest version (currently
at version 1.19.1 on the Linux build machines).

As for rmarkdown, it's a CRAN package and is currently at version 1.8


That's the version installed on the build machines. Note that we only
install packages from CRAN or Bioconductor on these machines.

If you think you found a bug in rmarkdown 1.8, or if you need a
feature that is only available in the devel version of rmarkdown,
I would suggest that you contact the rmarkdown developers by opening
an issue on GitHub:


If the devel version of rmarkdown requires a higher version of pandoc
in order to work properly, then maybe you could suggest them to update
the SystemRequirements field, which is currently:

   SystemRequirements: pandoc (>= 1.12.3) - http://pandoc.org

(in both, rmarkdown 1.8 and 1.8.3)


On 11/28/2017 07:12 AM, Vladimir Kiselev wrote:
> Hi,
> I am not able to plot Sankey diagrams using `googleVis` in the vignette of
> my package (scmap). Here is error message:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_scmap_malbec2-2Dbuildsrc.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=jLWOiNFAZa84KbrplYwm7kRMOroZY12KiSd0p8IqVZ8&s=I7TrevPM1GFPs-rgSeoLGPYGY_sLAm6Yy6rlTqoxHd0&e=
> It says:
> pandoc: Could not fetch
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.google.com_jsapi-3Fcallback-3DdisplayChartSankeyID6c664210b0e5&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=jLWOiNFAZa84KbrplYwm7kRMOroZY12KiSd0p8IqVZ8&s=N63pYR8w9-MrUrDc90piBokiczL4gh556OQLJvpuGD4&e=
> TlsExceptionHostPort (HandshakeFailed Error_EOF) "www.google.com" 443
> I had the same problem on my local machine before but updating pandoc to
> the latest version and also installing the development version of
> `rmarkdown` package solved the problem.
> So at the moment most of the things from `googleVis` (
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_web_packages_googleVis_vignettes_googleVis-5Fexamples.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=jLWOiNFAZa84KbrplYwm7kRMOroZY12KiSd0p8IqVZ8&s=oUML7QXSM8n4Y7_7rTi5JMPxnHoTxQlHhW10HV4SOeI&e=)
> fail if built in the package vignette.
> Would it be possible to address this issue?
> Many thanks,
> Vlad

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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