[Bioc-devel] Pandoc issues

Vladimir Kiselev vladimir.yu.kiselev at gmail.com
Sun Dec 10 22:54:57 CET 2017 

Thanks Herve!

Cheers,
Vlad

On Wed, Nov 29, 2017 at 6:38 PM Hervé Pagès <hpages at fredhutch.org> wrote:

> Hi Vladimir,
>
> On 11/28/2017 01:25 PM, Vladimir Kiselev wrote:
> > Hi Herve,
> >
> > Thanks for your reply! scmap::getSankey() didn't really work in the
> > release, so I switched it off quite long ago by setting `eval = FALSE`.
> >
> > Regarding rmarkdown: I remember when I updated Pandoc I got a different
> > error from rmarkdown, then I googled it and found that it was related to
> > the changes in the new version of Pandoc (I can't find the link
> > now....). The rmarkdown maintainer said he'd fixed it in the latest
> > version which is not the release version it. I have installed rmarkdown
> > from github (at the moment I have 1.8.3) and there was no error. They
> > probably forgot to update SystemRequirements.
>
> Wouldn't hurt to remind them about this.
>
> >
> > So, I suppose updating Pandoc on your side won't solve the problem
> > completely and we will need to wait until the new version of rmarkdown
> > is pushed to CRAN. At the moment I can probably switch Sankey diagrams
> > off in my vignette. The problem is I have just significantly updated it
> > and these diagrams are quite important now.
>
> Probably worth asking the rmarkdown folks whether they're planning
> to upload version 1.8.3 to CRAN soon, and to decide whether to switch
> off the diagrams or not based on what they say. Once rmarkdown 1.8.3
> (or higher) is on CRAN, I suggest that you update your Depends
> field to depend on rmarkdown >= 1.8.3. This will ensure that your
> users can also use scmap::getSankey(), not just our build machines.
>
> Note that if these diagrams are important, then you will probably need
> to consider porting your fixes to release. Your regular users use
> release, not devel.
>
> Best,
> H.
>
> >
> > Cheers,
> > Vlad
> >
> > On Tue, Nov 28, 2017 at 6:11 PM Hervé Pagès <hpages at fredhutch.org
> > <mailto:hpages at fredhutch.org>> wrote:
> >
> >     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
> >     there:
> >
> >     https://cran.r-project.org/web/packages/rmarkdown/index.html
> >     <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_web_packages_rmarkdown_index.html&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=o06dg2fAJGC3Eb8JQuR9_acNxX2qvLudAJFMzZVaYTY&s=f7tzfxUzfieYY_eZcLQOwHRy2zo5gG7OykARY3AJ1uw&e=
> >
> >
> >     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:
> >
> >     https://github.com/rstudio/rmarkdown/issues
> >     <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_rstudio_rmarkdown_issues&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=o06dg2fAJGC3Eb8JQuR9_acNxX2qvLudAJFMzZVaYTY&s=m5Nj-tCYC2oES9jqql7akRGNlCzSBf8qtWU-TL5l0qA&e=
> >
> >
> >     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
> >     <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__pandoc.org&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=o06dg2fAJGC3Eb8JQuR9_acNxX2qvLudAJFMzZVaYTY&s=0kGjllslkO0BS6iCNW4TIf2Qu4KjhpR2ZH939fc_o7Y&e=
> >
> >
> >     (in both, rmarkdown 1.8 and 1.8.3)
> >
> >     Best,
> >     H.
> >
> >
> >     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
> >     <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.google.com&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=o06dg2fAJGC3Eb8JQuR9_acNxX2qvLudAJFMzZVaYTY&s=-Oi8dMc775d0Mp1-PVOWZpNIdACYnnyZ8hJVT6B7Ct8&e=
> >"
> >     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 Res
> >     <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__maps.google.com_-3Fq-3Dutchinson-2BCancer-2BRes-26entry-3Dgmail-26source-3Dg&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=o06dg2fAJGC3Eb8JQuR9_acNxX2qvLudAJFMzZVaYTY&s=InTy029KGXXjuzR0RsWuk4oK3yhhqUz0kIHIK16IbiI&e=
> >earch
> >     Center
> >     1100 Fairview Ave. N, M1-B514
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> >
> >     E-mail: hpages at fredhutch.org <mailto:hpages at fredhutch.org>
> >     Phone:  (206) 667-5791
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> >
> > --
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> > <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__genat.uk&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=o06dg2fAJGC3Eb8JQuR9_acNxX2qvLudAJFMzZVaYTY&s=EodiUl8l10wK2g8hAlNuVL_vPEelNLQVBz0yGA-eQnY&e=
> >
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
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http://genat.uk

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