ResolvePackageNotFound: - cairo 1.12.18 6

[bensworth]

I am trying to configure INSPIRED on a Mac, but get the above error on the Cairo package when I call conda env create -f bin/INSPIIRED.conda.yml. I then installed the Cairo package via: conda install -c anaconda cairo without luck. This installed version 1.14.10, so I tried installing specifically 1.12.18: conda install -c richlewis cairo, but also without luck. Where does Cairo need to be installed to set up INSPIRED?

[cnobles]

Thanks, we weren't aware of the issue. We'll look into it and get the software updated as soon as we can.

[bensworth]

Update: I tried to install on a cluster running Debian GNU/Linux and was stopped with a similar error, this time ResolvePackageNotFound: - glib 2.43.0 2. Do I need to manually install the dependencies for the INSPIIRED library, or is something going wrong and they are not being installed in the setup?

[aubreybailey]

Hi Ben
could you run the following command on your cluster and report the result here for us?
ldd --version
It should return something like:
ldd (GNU libc) 2.19

[bensworth]

Yep, ldd (Debian GLIBC 2.24-17) 2.24

…

On 11/27/17 9:12 AM, aubreybailey wrote: Hi Ben could you run the following command on your cluster and report the result here for us? |ldd --version| It should return something like: |ldd (GNU libc) 2.19| — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#5 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AIPhhAJe3Ml3U6KjnRYYGTobNsA2IeeNks5s6u2SgaJpZM4QjHrw>.

[aubreybailey]

Yeah, that's definitely a bug on our side. @ressy can you please check the anaconda deps and see why it is pinned that high? Even our development machine 120 is only on 2.23, and it should be running downstream ubuntu. I bet we can pin something reasonable like 2.19 in our conda files.
Thanks for reporting, Ben!

[ressy]

Thanks Aubrey. I haven't been working on INSPIIRED myself (yet) but I'll check with @everettJK about the context on this -- looks like the specific versions for glib and cairo and a bunch of things were added last year in 58d173c. If that was just to pin things down to an explicit state from the start, then maybe it'll be as simple as adjusting the version numbers like you said.

[aubreybailey]

whoops. Sorry I guessed wrong! should have grabbed John instead. fingers crossed for explicit down-pinning

[helixscript]

Hi Everyone --
Apologies for the late reply.
I am creating a new Conda environment and install script and will be in touch shortly once I update the repository.
J

[helixscript]

Hi Everyone --
In addition to the Cairo issue, newer versions of dplyr were causing issues with database queries.
I created a new INSPIIRED branch (INSPIIRED-deployment) with a new Conda environment recipe which appears to resolve the issues on our side. The new recipe locks library versions and an updated install script uses devtools to install specific versions of R libraries not available through Conda.
J

[bensworth]

Seems to make it past Cairo, but I tried on a MacBook pro and iMac and get the same error:

`Fetching package metadata .................

ResolvePackageNotFound:

• r-magrittr 1.5 r3.3.1_0`

[bensworth]

HI guys, any update on either of the open issues? We still cannot install the package outside of the virtual machine, nor get the expected behavior applied to non-example data in the virtual machine.

[cnobles]

Hey Ben, any chance you were able to download the deployment-branch of the pipeline and try that?

John had put in some work to restrict the package versions to create a more stable build. Do you still get the error? It didn't come up when I tried the build.

[bensworth]

Yep, see above. Interestingly, tried again today and got a slightly different error:
conda env create -f bin/INSPIIRED.conda.yml

Fetching package metadata .................

ResolvePackageNotFound: 
  - r-getopt 1.20.0 r3.3.1_0

Still the same package problems though. What kind of system are you installing on? Have tried two different macs without success.

---

Update: I built a docker container on a linux cluster and tried to install INSPIIRED there. I use the Conda docker container here: https://hub.docker.com/r/continuumio/miniconda/, and made sure condo was up to date. In the master branch, I get errors

Solving environment: failed

ResolvePackageNotFound: 
  - ncurses==5.9=4
  - wkhtmltopdf==0.12.3=0
  - blat==35=1
  - libxml2==2.9.3=0
  - glib==2.43.0=2
  - r-getopt==1.20.0=r3.2.2_0

On the INSPIIRED-deployment branch, there is only one package that cannot be found:

Solving environment: failed

ResolvePackageNotFound: 
  - r-getopt==1.20.0=r3.3.1_0

[helixscript]

Hi Ben,
Apologies for the delayed response.
I discussed the issue with Chris earlier this week.
Apparently we have not version locked enough of the packages.
I will work on this deployment issue tomorrow and send an update before the end of the week.
J

[bensworth]

Thanks! I would like to say that insight into the other problems we are experiencing trying to run in the virtual machine is definitely higher priority. We've been wanting to analyze some data for several months now with INSPIIRED, but haven't had any success. This is more to bring to your guys' attention, and so maybe outside the virtual machine it will be easier to dig into the code and debug if necessary..