Am 15.10.2015 um 13:20 schrieb Christian Brenninkmeijer:
> Regarding package dependency.
> Assume there packages A, B and C
> B depends on A and C on A and B
> At the Start there is
> A0, B0 and C0
> B0 depends on A0 and C0 on A0 and B0
> Now if A is updated there is a A1
> But B0 still depends on A0 and C0 still on A0 and B0
> Now if C is updated you have C1
> C1 detects the latest versions of A and B so depends on A1 and B0
> But B0 still depends on A0
> The result is that C1 directly depends on A1 and indirectly (via B0) on A0
> Could the tool shed detect this double dependency and refuse to load C1 
> unless it specifically references A0 and B0

As far as I know (@Dave, please correct me if I'm wrong) A0 does not
exists for Galaxy as soon as you have A1 installed.
Galaxy should see during runtime that A is a "package", a special
repository only containing tool dependencies, and should only take the
most recent version. Imho a different behaviour is a bug. And I actually
don't know why A0 is not deleted as soon as A1 is installed successfully.

Revisions as Sarah has described in her mail do not exist for
tool-dependency packages, afaik.

> ===
> Regard R 
> I agree that as a wrapper it Galaxy is highly dependent on what the 
> underlying tools report.
> And if they change what they report that is a disaster.
> What I do in my testing is after all the R is loaded try to run an R script 
> which loads the packages as a test.
> Something like:
> library(Cairo)
> args<-commandArgs(TRUE)
> writeLines(capture.output(sessionInfo()), args[1])
> sessionInfo()
> But even then the tool goes green with an R error,
> Christian
> ________________________________________
> From: Björn Grüning []
> Sent: Thursday, October 15, 2015 10:48 AM
> To: Christian Brenninkmeijer; Sarah DIEHL;
> Subject: Re: [galaxy-dev] recurring issues with revisions of packages from 
> toolshed
> Am 15.10.2015 um 11:43 schrieb Christian Brenninkmeijer:
>> Note these are personal views of another admin not official Galaxy views.
>> The version issues is a hard one to solve, as automatically updating 
>> upstream project is also dangerous as that leaves them in a state that has 
>> not be verified by the developer.
>> Best solution could be for the toolshed to warn if a tool upload would pull 
>> in multiple versions.
> Can you elaborate there a little bit more?
>> As for the R install issue.
>> 1. I too find it extremely frustrating how often Galaxy just silently fails.
> We are working on this.
> But it is really hard to convince R to provide us with a real error
> code. I spend several days, but different R versions, fail differently
> or not at all ..
> I will keep you posted on this and hopefully the latest idea from us
> works out.
> Sorry for any inconvenience,
> Bjoern
>> 2. It could be due to a missing R package.
>> The galaxy tool to determine required R packages appears to miss ones only 
>> listed as linked in.
>> For example I had one which depends on lme4.
>> This failed to build because RcppEigen was missing
>> Yet it RccpEigen is only listed as "LinkingTo:"
>> Christian
>> ________________________________
>> From: galaxy-dev [] on behalf of 
>> Sarah DIEHL []
>> Sent: Wednesday, October 14, 2015 2:05 PM
>> To:
>> Subject: [galaxy-dev] recurring issues with revisions of packages from 
>> toolshed
>> Dear all,
>> I continuously have several issues with tool dependency packages from the 
>> toolshed and their revisions. It looks like the tools I install have 
>> requirements for different revisions of the same package_xy repository. What 
>> I end up with quite often is having the same package installed in multiple 
>> revisions (see attached "galaxytools_multiple_revisions.jpg" screenshot). 
>> When I then update the older revision, it's still listet twice and 
>> additionally the tool that had the older one as a dependency now says it's 
>> missing a repository dependency.
>> Although this is already quite annoying and creates a mess within the tool 
>> list, I could live with it. However, sometimes it completely messes up 
>> revisions. In the second attached screenshot (numpy_revision_issue.jpg) you 
>> can see that this numpy repository thinks it is revision "300877695495", but 
>> it's actual location has revision "8b3a5c7061d8". This causes tools that 
>> depend on revision "300877695495" to think it's there, but when the 
>> dependency is resolved at runtime of the tool, numpy is not found (since 
>> it's location is in a different revision's folder) and the run fails. As you 
>> can also see from the screenshot, resetting the metadata doesn't do anything 
>> about this. Also reinstalling doesn't work, since the database keeps the 
>> faulty record and uses it upon reinstallation.
>> I think it's a problem that when I install tools that have outdated 
>> revisions of a package repository as a dependency, they don't recognize that 
>> a newer version is available (and already installed), but instead insist on 
>> installing the older revision, too. I don't understand why they even have 
>> this strict requirement on a specific version of a package repo, and not 
>> just the version of the tool inside.
>> Btw. I also noticed that the installation of R packages (e.g. in 
>> package_dexseq_1_14) silently fails. Some of the requirements and also the 
>> dexseq R package itself failed the installation, but Galaxy didn't recognize 
>> any error and it still showed up as "Installed".
>> Best regards,
>> Sarah
>> ----
>> Sarah Diehl
>> HPC System Administrator
>> Campus Belval | Biotech II
>> 6, avenue du Swing
>> L-4371 Belvaux
>> T +352 46 66 44 5360
>> -----
>> This message is confidential and may contain privileged information. It is 
>> intended for the named recipient only. If you receive it in error please 
>> notify me and permanently delete the original message and any copies.
>> -----
>> ___________________________________________________________
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