Re: Trinityrnaseq status

On 08/22/2015 09:34 PM, Michael Crusoe wrote:

On Sat, Aug 22, 2015 at 6:49 AM Andreas Tille <andreas@an3as.eu> wrote:

Hi,

On Sat, Aug 22, 2015 at 12:57:20AM +0000, Michael Crusoe wrote:
>
> trinityrnaseq: waiting on libjung-free-java, rsem, express, and jaligner.
> Otherwise all the tests run successfully for me.

I really hope that jaligner will make it soon - no idea why several
packages later in the queue made it way faster.

On the upside it is now the second oldest package in queue so hopefully it will get some attention soon.

> libjung-free-java package: in NEW queue courtesy Olivier
> https://ftp-master.debian.org/new/libjung-free-java_2.0.1-1.html
>
> rsem: waiting for r-bioc-ebseq; needs manpages, patch descriptions, add new
> patches to add hardening flags

Usually it is related to CFLAGS/CXXFLAGS/ etc... not being "extended" but replaced in makefiles:

example:

CFLAGS = -O3

instead of

CFLAGS += -O3

and oflen LDFLAGS not being used at ld step

>
> r-bioc-ebseq: ready for sponsoring now that r-cran-blockmodeling is in the
> archive

Uploaded.

Thanks!

> Any and all assistance you and the group can provide for the above would be
> greatly appreciated!

Please be more verbose if you see tasks I could do to support this.

Do have experience in what incantations it takes to add the hardening build flags to recalcitrant packages?

--

Michael R. Crusoe: Programmer & Bioinformatician crusoe@ucdavis.edu
The lab for Data Intensive Biology; University of California, Davis
https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe
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