Thanks Herve! Cheers, Vlad
On Wed, Nov 29, 2017 at 6:38 PM Hervé Pagès <hpa...@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 <hpa...@fredhutch.org > > <mailto:hpa...@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 > > P.O. Box 19024 > > Seattle, WA 98109-1024 > > > > E-mail: hpa...@fredhutch.org <mailto:hpa...@fredhutch.org> > > Phone: (206) 667-5791 > > Fax: (206) 667-1319 > > > > -- > > http://genat.uk > > < > 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: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > -- http://genat.uk [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
