Hi Dan,
thanks a lot for your prompt response!
Do you have any idea how I could possibly trace down the memory issue on
Ubuntu?
I commented the sessionInfo() chunk at the end of the workflow and now I
get on "master"
> Error: pandoc document conversion failed with error 127
and
> system call
Hi,
I would like to transform a directed graph with cycles, e.g. a gene
regulatory network, into a DAG. In particular, I would like to do that by
removing a minimal set of edges.
This problem is known to be NP-hard
https://en.wikipedia.org/wiki/Feedback_arc_set
but, apparently, several approxim
Dear Martin and List,
I have a problem with linking to Rhtslib on Mac OSX when my R installation
directory differs from the package installation directory. Trying to load csaw
(Bioc release version) gives me:
> require(csaw)
# ... whole lot of dependencies...
Loading required package: csaw
Erro
I can confirm that I am experiencing similar problems on OSX with several other
packages at the moment (openssl and git2r), I know that Xcode just updated and
am not sure if this is causing some of the problems (potentially some update
with their command line tools?)...
install.packages('openss
- Original Message -
> From: "Aaron Lun"
> To: "bioc-devel"
> Sent: Tuesday, May 24, 2016 8:06:13 AM
> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX
> Dear Martin and List,
>
> I have a problem with linking to Rhtslib on Mac OSX when my R installation
> directory di
- Original Message -
> From: "Dan Tenenbaum"
> To: "Aaron Lun"
> Cc: "bioc-devel"
> Sent: Tuesday, May 24, 2016 8:51:30 AM
> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX
> - Original Message -
>> From: "Aaron Lun"
>> To: "bioc-devel"
>> Sent: Tuesday, May
- Original Message -
> From: "Dan Tenenbaum"
> To: "Aaron Lun"
> Cc: "bioc-devel"
> Sent: Tuesday, May 24, 2016 9:38:01 AM
> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX
> - Original Message -
>> From: "Dan Tenenbaum"
>> To: "Aaron Lun"
>> Cc: "bioc-devel
- Original Message -
> From: "Jason Serviss"
> To: "Aaron Lun"
> Cc: "bioc-devel"
> Sent: Tuesday, May 24, 2016 8:20:18 AM
> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX
> I can confirm that I am experiencing similar problems on OSX with several
> other
> packages
Yep, works on my machine as well. Seems like it would be a pain to have
to do it manually every time csaw (or deepSNV, or diffHic) gets
re-installed, though.
I should stress that I didn't do anything special to my R installation
to get it to install packages in a different place. As far as I k
Dan,
Thanks for the input. Yes, maybe it is a different problem altogether. If it is
more convenient I can start another “thread” to keep the issues separated…
Due to the fact that I am running R-devel, as far as I am aware, all (?)
packages need to be installed from source. I have carefully f
[renamed the thread]
- Original Message -
> From: "Jason Serviss"
> To: "Dan Tenenbaum"
> Cc: "Aaron Lun" , "bioc-devel"
> Sent: Tuesday, May 24, 2016 11:32:17 AM
> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX
> Dan,
>
> Thanks for the input. Yes, maybe it is a dif
Dan,
Alright, I guess for the time being the most practical solution is to work in
the R-release version and, potentially, deal with this problem at a later date.
Thanks again!
Jason
> On 24 May 2016, at 20:46, Dan Tenenbaum wrote:
>
> [renamed the thread]
>
> - Original Message -
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