[Bioc-devel] Pandoc issues

Wed Nov 29 19:38:58 CET 2017

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
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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