install fails: conda packages no longer available

[d-cameron]

It appears that a cHIVa cannot be created as the conda-forge packages no longer exist. Is there a way to fix this?

$ ./install.sh -v
2021-07-28 11:23:59 [     info] Starting cHIVa installation...
2021-07-28 11:23:59 [     info]     Conda path:  /home/user/miniconda3
2021-07-28 11:23:59 [     info]     cHIVa src :  /home/user/chiva
2021-07-28 11:23:59 [     info]     cHIVa env :  'chiva'
2021-07-28 11:23:59 [    debug] Components detected:
2021-07-28 11:23:59 [    debug]     Conda:         true
2021-07-28 11:23:59 [    debug]     Environment:   false
2021-07-28 11:23:59 [    debug]     R-package:     false
2021-07-28 11:24:00 [    debug]     Library:       false
2021-07-28 11:24:00 [     info] Conda already installed.
2021-07-28 11:24:00 [     info] Creating cHIVa environment...
2021-07-28 11:24:00 [     info]     Building from: etc/build.b0.2.0.txt

CondaHTTPError: HTTP 404 NOT FOUND for url <https://conda.anaconda.org/conda-forge/linux-64/gcc_impl_linux-64-7.3.0-habb00fd_1.tar.bz2>
Elapsed: 00:00.210475
CF-RAY: 675a4e38ccc03771-MEL

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

CondaHTTPError: HTTP 404 NOT FOUND for url <https://conda.anaconda.org/conda-forge/linux-64/gxx_impl_linux-64-7.3.0-hdf63c60_1.tar.bz2>
Elapsed: 00:00.448666
CF-RAY: 675a4e3a294517cc-MEL

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.


2021-07-28 11:24:02 [    error] Error in /home/user/chiva/install.sh in function conda on line 100
2021-07-28 11:24:02 [    debug]
2021-07-28 11:24:02 [    error] Environment creation failed!
****

INSPIIRED has a similar issue:

$ conda env create -f bin/INSPIIRED.conda.yml
Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound:
  - jpeg==8d=0
  - libtiff==4.0.6=2
  - readline==6.2=2
  - curl==7.49.0=0
  - pcre==8.31=0
  - libpng==1.6.17=0
  - python==2.7.11=0
  - r-getopt==1.20.0=r3.2.2_0
  - freetype==2.5.5=1
  - cffi==1.6.0=py27_0
  - cryptography==1.4=py27_0
  - biopython==1.67=np111py27_0
  - pycparser==2.14=py27_1
  - pyopenssl==0.16.0=py27_0
  - glib==2.43.0=2
  - pango==1.39.0=0
  - libxml2==2.9.3=0
  - tk==8.5.18=0
  - git==2.6.4=0
  - numpy==1.11.0=py27_1
  - mkl==11.3.3=0
  - cairo==1.12.18=6
  - harfbuzz==0.9.39=0

Is this a reproducability issue, or a conda configuration issue?

[cnobles]

Hey, glad you are interested in the pipeline. This issue is definitely due to outdated packages. There was a great deal of similarity in how I developed this repo and the iGUIDE repo, you may want to see if you can just switch out the two environments build files. I’m currently on a vacation, but could look at it maybe later this week, if time is not pressing. I honestly still felt like I had a lot of work that I could add to this repo, but never got to it while at UPenn. Let me know if you would like anymore clarification on the above.

[cnobles]

Just did a quick check of the code base, try doing the install with the ‘-r’ option. This will install from the requirements rather than the current build. Unfortunately I expect that this will take some time to solve the environmental conditions or the build, expect hours to over night in my experience. This is why I had the default as a build, which bypasses this solve step. This should resolve your issue for the install, as it will find the latest packages. If that doesn’t work, you may want to edit the R version in the etc / requirements.yml to update which version of R the environment will use. Some packages my no longer be hosted by cobra for the current version. Not sure at this point.