[Bioc-devel] Pandoc issues
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 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 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) 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" 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
Herv? Pag?s 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