<div dir="ltr"><div><div><div><div>Hi Andreas,<br></div>First of thank you for all your hard work! No disrespect was meant in my short original mail.<br><br></div>I don't know much about sra-toolkit either, I hope I'll have some time over the next month to look at this....<br></div>Thanks again,<br></div><div>Eli<br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Oct 20, 2017 at 1:27 AM, Andreas Tille <span dir="ltr"><<a href="mailto:andreas@fam-tille.de" target="_blank">andreas@fam-tille.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Eliyahu,<br>
<br>
thanks for using the packages provided by the Debian Med team.<br>
<span class=""><br>
On Thu, Oct 19, 2017 at 10:06:25PM +0300, E.S. Rosenberg wrote:<br>
> Are there any plans to update the deb to 2.8.2?<br>
<br>
</span>I admit there is no real "plan" to update any specific software. A<br>
small team of enthusiasts is struggling very hard to keep way more than<br>
500 packages in the field of bioinformatics up to date. While you did<br>
perfectly right to ask for a certain package which definitely raises<br>
our motivation to pick this before other targets I have the following<br>
recommendations.<br>
<br>
  1. Follow the "official" way to ask for new versions which is done<br>
   via the bug tracking system:<br>
<br>
     reportbug sra-toolkit<br>
     Bug-Title: New version available<br>
     Severity: wishlist<br>
<br>
   May be you add some extra information about the new features of<br>
   this new version.<br>
<br>
  2. You clone the packaging git as described in Debian Med policy[1]<br>
   and try to do the needed stuff in Git. If you manage to do this<br>
   we'll grant you commit permissions so you can contribute directly<br>
   to our project. This will enhance your chances that the package<br>
   becomes available sooner drastically.<br>
<br>
Besides these hints I had a look at the packaging. The sra-toolkit (and<br>
its Build-Depends ncbi-vdb) have manually crafted build systems and I<br>
never ever observed a smooth upgrade. While I managed to build ncbi-vdb<br>
2.8.2-2 after some patching (its just uploading right now) I was ending<br>
up to a point with sra-toolkit when it says:<br>
<br>
...<br>
make[3]: Entering directory '/build/sra-sdk-2.8.2-3+dfsg/<wbr>test/vdb-config'<br>
Testing exit code vdb-config of vdb-config... 2017-10-19T22:11:57 vdb-config.2.8.2 err: libs/kfs/unix/sysdir.c:2158:<wbr>KSysDirOpenDirRead_v1: condition violated while updating node - Warning: normally this application should not be run as root/superuser<br>
vdb-config exited with 3 at ./<a href="http://test-vdb-config.pl" rel="noreferrer" target="_blank">test-vdb-config.pl</a> line 12.<br>
Makefile:33: recipe for target 'test-vdb-config' failed<br>
make[3]: *** [test-vdb-config] Error 3<br>
make[3]: Leaving directory '/build/sra-sdk-2.8.2-3+dfsg/<wbr>test/vdb-config'<br>
/build/sra-sdk-2.8.2-3+dfsg/<wbr>build/Makefile.targets:90: recipe for target 'vdb-config_runtests' failed<br>
make[2]: *** [vdb-config_runtests] Error 2<br>
...<br>
<br>
I have no idea what to do next and may be I need some sleep now. Every<br>
reader, may be you or somebody else is kindly invited to try fixing the<br>
build system. I admit that I'm pretty bored by this and I really wonder<br>
what might make these two toolkits so special that none of the well<br>
established build systems should fit their needs. :-(<br>
<br>
Kind regards<br>
<br>
    Andreas.<br>
<br>
<br>
[1] <a href="https://debian-med.alioth.debian.org/docs/policy.html#source" rel="noreferrer" target="_blank">https://debian-med.alioth.<wbr>debian.org/docs/policy.html#<wbr>source</a><br>
<span class="HOEnZb"><font color="#888888"><br>
--<br>
<a href="http://fam-tille.de" rel="noreferrer" target="_blank">http://fam-tille.de</a><br>
</font></span></blockquote></div><br></div>