ResolvePackageNotFound: - cairo 1.12.18 6 #5

bensworth · 2017-11-18T19:33:05Z

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?

The text was updated successfully, but these errors were encountered:

cnobles · 2017-11-22T19:35:28Z

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

bensworth · 2017-11-27T16:41:45Z

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 · 2017-11-27T17:12:50Z

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 · 2017-11-27T17:15:27Z

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 · 2017-11-27T17:19:44Z

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 · 2017-11-27T18:11:37Z

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 · 2017-11-27T18:53:56Z

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

helixscript · 2017-12-06T21:25:09Z

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 · 2017-12-15T20:09:53Z

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 · 2018-01-13T01:44:13Z

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 · 2018-03-13T16:17:52Z

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 · 2018-03-14T19:59:11Z

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 · 2018-03-14T20:45:45Z

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 · 2018-03-22T00:22:05Z

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 · 2018-03-22T00:29:00Z

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..

helixscript · 2018-03-22T00:32:57Z

What would be your preferred vehicle? Our group would prefer to support the Conda route since it is difficult to get a VM to parallelize well.

bensworth · 2018-03-22T00:59:06Z

Oh the conda would definitely be better. But most importantly, we just want to use INSPIIRED to look at data, and whatever the fastest way is to make that happen is best. We have the VM running, but maybe starting from the conda environment is a better route to get everything working.

helixscript · 2018-03-22T14:10:29Z

Fair enough - I will focus on version locking the Conda today and send an update shortly. Best, John

…

On Wed, Mar 21, 2018 at 8:59 PM, Ben Southworth ***@***.***> wrote: Oh the conda would definitely be better. But most importantly, we just want to use INSPIIRED to look at data, and whatever the fastest way is to make that happen is best. We have the VM running, but maybe starting from the conda environment is a better route to get everything working. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#5 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHSJQ4_ytZ24Wy7NMB4DacvUZ0Rv2SbIks5tgvdbgaJpZM4QjHrw> .

-- John K. Everett http://www.linkedin.com/in/JohnEverettPhD

helixscript · 2018-03-22T16:15:04Z

Hi Ben, I updated the deployment branch. https://github.com/BushmanLab/INSPIIRED/tree/INSPIIRED-deployment I locked down some more library versions so that Conda does not try to auto-update additional libraries which subsequently breaks the code base. I created a new INSPIIREDv2 environment and changed the install procedure which is documented in the Github readme. Please first remove the old INSPIIRED environment before attempting to install the new version. ie. %> cd INSPIIRED %> export INSPIIRED=$(pwd) %> ~/miniconda3/bin/conda remove --name INSPIIREDv2 --all %> ~/miniconda3/bin/conda update conda %> source ~/miniconda3/bin/activate INSPIIREDv2 %> Rscript bin/setupR.R %> Rscript bin/setupINSPIIRED.R I've tested this up to the point of uploading the identified sites to the provided sqlLite db. We have new report making software which I will release shortly. Are you working with a CPU cluster (bsub/qsub) or are you running the software in a single CPU? Best, John

…

On Thu, Mar 22, 2018 at 10:10 AM, John Everett ***@***.***> wrote: Fair enough - I will focus on version locking the Conda today and send an update shortly. Best, John On Wed, Mar 21, 2018 at 8:59 PM, Ben Southworth ***@***.***> wrote: > Oh the conda would definitely be better. But most importantly, we just > want to use INSPIIRED to look at data, and whatever the fastest way is to > make that happen is best. We have the VM running, but maybe starting from > the conda environment is a better route to get everything working. > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#5 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AHSJQ4_ytZ24Wy7NMB4DacvUZ0Rv2SbIks5tgvdbgaJpZM4QjHrw> > . > -- John K. Everett http://www.linkedin.com/in/JohnEverettPhD

-- John K. Everett http://www.linkedin.com/in/JohnEverettPhD

aluisascosta · 2020-01-23T15:06:27Z

Hi,
I am trying to create the INSPIIRED conda environment on a cluster (using the INSPIIRED-deployment branch) but I get the following error.

ResolvePackageNotFound:

icu==54.1=0
cffi==1.6.0=py27_0
curl==7.49.0=1
pyopenssl==0.16.0=py27_0
freetype==2.5.5=1
python==2.7.11=5
cryptography==1.4=py27_0
jpeg==9b=2
pcre==8.39=1
mkl==11.3.3=0
biopython==1.67=np111py27_0
qt==5.6.2=5
tk==8.5.18=0
readline==6.2=2
glib==2.50.2=1
cairo==1.14.8=0
harfbuzz==0.9.39=1
git==2.6.4=0
libpng==1.6.30=1
pycparser==2.14=py27_1
libxml2==2.9.2=0
numpy==1.11.0=py27_1

marencc · 2020-05-21T23:17:07Z

Did they answer

Hi,
I am trying to create the INSPIIRED conda environment on a cluster (using the INSPIIRED-deployment branch) but I get the following error.

ResolvePackageNotFound:

* icu==54.1=0

* cffi==1.6.0=py27_0

* curl==7.49.0=1

* pyopenssl==0.16.0=py27_0

* freetype==2.5.5=1

* python==2.7.11=5

* cryptography==1.4=py27_0

* jpeg==9b=2

* pcre==8.39=1

* mkl==11.3.3=0

* biopython==1.67=np111py27_0

* qt==5.6.2=5

* tk==8.5.18=0

* readline==6.2=2

* glib==2.50.2=1

* cairo==1.14.8=0

* harfbuzz==0.9.39=1

* git==2.6.4=0

* libpng==1.6.30=1

* pycparser==2.14=py27_1

* libxml2==2.9.2=0

* numpy==1.11.0=py27_1

Did they answer???

I've tried CONDA_RESTORE_FREE_CHANNEL=1 conda env create -f bin/INSPIIRED.conda.yml and it works nicely with that problem. But I can't make it work from Rscript bin/setupR.R onwards...

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

ResolvePackageNotFound: - cairo 1.12.18 6 #5

ResolvePackageNotFound: - cairo 1.12.18 6 #5

bensworth commented Nov 18, 2017

cnobles commented Nov 22, 2017

bensworth commented Nov 27, 2017

aubreybailey commented Nov 27, 2017

bensworth commented Nov 27, 2017 via email

aubreybailey commented Nov 27, 2017 •

edited

Loading

ressy commented Nov 27, 2017

aubreybailey commented Nov 27, 2017

helixscript commented Dec 6, 2017

helixscript commented Dec 15, 2017

bensworth commented Jan 13, 2018

bensworth commented Mar 13, 2018

cnobles commented Mar 14, 2018

bensworth commented Mar 14, 2018 •

edited

Loading

helixscript commented Mar 22, 2018

bensworth commented Mar 22, 2018 •

edited

Loading

helixscript commented Mar 22, 2018

bensworth commented Mar 22, 2018

helixscript commented Mar 22, 2018 via email

helixscript commented Mar 22, 2018 via email

aluisascosta commented Jan 23, 2020

marencc commented May 21, 2020 •

edited

Loading

ResolvePackageNotFound: - cairo 1.12.18 6 #5

ResolvePackageNotFound: - cairo 1.12.18 6 #5

Comments

bensworth commented Nov 18, 2017

cnobles commented Nov 22, 2017

bensworth commented Nov 27, 2017

aubreybailey commented Nov 27, 2017

bensworth commented Nov 27, 2017 via email

aubreybailey commented Nov 27, 2017 • edited Loading

ressy commented Nov 27, 2017

aubreybailey commented Nov 27, 2017

helixscript commented Dec 6, 2017

helixscript commented Dec 15, 2017

bensworth commented Jan 13, 2018

bensworth commented Mar 13, 2018

cnobles commented Mar 14, 2018

bensworth commented Mar 14, 2018 • edited Loading

helixscript commented Mar 22, 2018

bensworth commented Mar 22, 2018 • edited Loading

helixscript commented Mar 22, 2018

bensworth commented Mar 22, 2018

helixscript commented Mar 22, 2018 via email

helixscript commented Mar 22, 2018 via email

aluisascosta commented Jan 23, 2020

marencc commented May 21, 2020 • edited Loading

aubreybailey commented Nov 27, 2017 •

edited

Loading

bensworth commented Mar 14, 2018 •

edited

Loading

bensworth commented Mar 22, 2018 •

edited

Loading

marencc commented May 21, 2020 •

edited

Loading