Re: [Bioc-devel] Issue importing bigwig files with rtracklayer from Amazon Cloud Drive

I checked in something that tries to find openssl automatically on the Mac. It looks like AWS is for some reason returning 404 for the HEAD command that the UCSC library uses the get info about the file like the content size. Same thing happens when I play around in Firefox's developer tools. The

Re: [Bioc-devel] Issue importing bigwig files with rtracklayer from Amazon Cloud Drive

Hi Michael, I forgot about pkg-util (just did a fresh BioC 3.3 install). I assumed the OS X binary would work out of the box. Anyhow, I installed rtracklayer (release) manually and got another error (slightly different message now). $ svn co https://hedgehog.fhcrc.org/bioconductor/branches/R

Re: [Bioc-devel] Issue importing bigwig files with rtracklayer from Amazon Cloud Drive

The URL redirection is something I can try to add. For the other error, you need to get openssl installed and made visible to pkg-config, so that rtracklayer finds it during its build process. Michael On Thu, May 5, 2016 at 2:01 PM, Leonardo Collado Torres wrote: > Hi Michael, > > I have a use

[Bioc-devel] Issue importing bigwig files with rtracklayer from Amazon Cloud Drive

Hi Michael, I have a use case that is similar to https://support.bioconductor.org/p/81267/#82142 and looks to me like it might need some changes in rtracklayer to work. That's why I'm posting it here this time. Basically, I'm trying to use rtracklayer to import a bigwig file over the web which is

Re: [Bioc-devel] error message - package GSAR

This is an issue that was reported 3 years ago (http://thr3ads.net/r-devel/2013/04/2193760-Failed-to-locate-the-texi2pdf-output-file) and has not been fixed, probably because it is extremely hard to reproduce. It tends to happen on random packages from one day to the next. In fact, in today's b

Re: [Bioc-devel] error message - package GSAR

Thank you Dan for clarification. I guess I had bad luck in the last build. Yasir -Original Message- From: Dan Tenenbaum [mailto:dtene...@fredhutch.org] Sent: Thursday, May 05, 2016 3:26 PM To: Rahmatallah, Yasir Cc: bioc-devel Subject: Re: [Bioc-devel] error message - package GSAR This

Re: [Bioc-devel] R CMD check error related to data docs in a new package

Awesome, thanks Martin! You make it look easy! On Thu, May 5, 2016 at 6:08 AM, Martin Morgan wrote: > > > On 05/05/2016 02:05 AM, Leonardo Collado Torres wrote: >> >> Hi, >> >> I need some help with a new package I'm coding (which we plan to >> submit to BioC). I keep getting a warning in R CMD

[Bioc-devel] error message - package GSAR

Hi, I'm the maintainer of package GSAR. Last Tuesday's build produced the following error message for the Windows platform only Warning: running command '"C:\Users\BIOCBU?1\AppData\Local\Programs\MIKTEX?1.9\miktex\bin\texify.exe" --quiet --pdf "GSAR.tex" --max-iterations=20 -I "E:/biocbld/bbs

Re: [Bioc-devel] downloads number status shields for packages

Hi, The download report is actually about to change. See: https://bioconductor.org/packages/new-stats/bioc/Biobase/ for how the new stats are going to look. This is work in progress (ETA is next week) but an important change is that you'll be able to get the numbers from tabulated files (e.g.

Re: [Bioc-devel] downloads number status shields for packages

Hi Marcin, Here is a link to how Bioconductor creates it's badges: https://github.com/Bioconductor/bioconductor.org/blob/master/Rakefile#L648 If you would like to create a badge for raw counts the following might be of use to you. Please also see help on XML Path Language: https://www.w3.org/TR/x

[Bioc-devel] [Announcement] RTCGA - Factory of R Packages is Released

Hi all bioc-developers, I have just finished work with RTCGA package and released, on Bioconductor, the *RTCGA Factory of R Packages*. Read this quick guide to find out more about this R Toolkit for Biostatisti

Re: [Bioc-devel] R CMD check error related to data docs in a new package

On 05/05/2016 02:05 AM, Leonardo Collado Torres wrote: Hi, I need some help with a new package I'm coding (which we plan to submit to BioC). I keep getting a warning in R CMD check that I haven't been able to figure out what is wrong. I'm guessing that it's something fairly straightforward, I'