Can't build main.pdf - Githubissues

aqw commented 5 years ago

$ make main.pdf
make -C img
make[1]: Entering directory '/home/aqw/git/paper-remodnav/img'
Rendering remodnav_algorithm.pdf
echo ./remodnav_algorithm.pdf
./remodnav_algorithm.pdf
make[1]: *** No rule to make target 'mainseq_lab_300dpi.png', needed by 'all'.  Stop.
make[1]: Leaving directory '/home/aqw/git/paper-remodnav/img'
make: *** [Makefile:10: figures] Error 2

mih commented 5 years ago

Makefile rules need tuning, you pretty much need to start with make -B (due to too much being present in the Git repo ATM). However, this does the entire analysis, so you need datalad, and the scientific python software stack installed. README (#2) will have to tell this story.

aqw commented 5 years ago

Thanks.

I'll whack at main.tex and leave it to you guys to make sure it still builds. ;-)

adswa commented 5 years ago

I've tried on a fresh repo with a virgin virtualenv and put my workflow into the README. There are two issues:

as noted in https://github.com/psychoinformatics-de/paper-remodnav/issues/1, the current remote for the studyforrest eyemovement label data needs to be turned into something anyone could pull from (current remote is still asims directory on medusa. alternative in scratch on medusa isn't any better for anyone not us)
when datalad installing recursively (I assume thats necessary to effortlessly get the input data as subdatasets, or am I mistaken, @mih?), there are errors (unrelated to this project and non-impeding, and probably to be evaded by setting a limit to the depth of recursiveness?)

Here's the traceback

```bash (remodnav_testing) ╭─adina@muninn ~/repos/testing ╰─➤ datalad install -r https://github.com/psychoinformatics-de/paper-remodnav.git [INFO ] Cloning https://github.com/psychoinformatics-de/paper-remodnav.git [1 other candidates] into '/home/adina/repos/testing/paper-remodnav' Username for 'https://github.com': adswa Password for 'https://adswa@github.com': [INFO ] Remote origin not usable by git-annex; setting annex-ignore install(ok): /home/adina/repos/testing/paper-remodnav (dataset) [INFO ] Installing recursively [INFO ] Cloning https://github.com/psychoinformatics-de/paper-remodnav.git/data/studyforrest-data-eyemovementlabels [2 other candidates] into '/home/adina/repos/testing/paper-remodnav/data/studyforrest-data-eyemovementlabels' [INFO ] Invalid command: 'git-annex-shell 'configlist' '/~/psychoinformatics-de/studyforrest-data-eyemovementlabels.git'' [INFO ] You appear to be using ssh to clone a git:// URL. [INFO ] Make sure your core.gitProxy config option and the [INFO ] GIT_PROXY_COMMAND environment variable are NOT set. [INFO ] Remote origin does not have git-annex installed; setting annex-ignore [INFO ] This could be a problem with the git-annex installation on the remote. Please make sure that git-annex-shell is available in PATH when you ssh into the remote. Once you have fixed the git-annex installation, run: git annex enableremote origin [INFO ] Cloning git@github.com:psychoinformatics-de/studyforrest-data-eyemovementlabels.git/code/remodnav [2 other candidates] into '/home/adina/repos/testing/paper-remodnav/data/studyforrest-data-eyemovementlabels/code/remodnav' [INFO ] Submodule HEAD got detached. Resetting branch master to point to 24136358. Original location was c9b86961 [INFO ] Cloning https://github.com/psychoinformatics-de/remodnav.git/remodnav/tests/data/anderson_etal [3 other candidates] into '/home/adina/repos/testing/paper-remodnav/data/studyforrest-data-eyemovementlabels/code/remodnav/remodnav/tests/data/anderson_etal' [INFO ] Submodule HEAD got detached. Resetting branch master to point to c6d02539. Original location was 0e6f8270 [INFO ] Cloning https://github.com/psychoinformatics-de/remodnav.git/remodnav/tests/data/studyforrest [3 other candidates] into '/home/adina/repos/testing/paper-remodnav/data/studyforrest-data-eyemovementlabels/code/remodnav/remodnav/tests/data/studyforrest' [INFO ] Remote origin not usable by git-annex; setting annex-ignore [INFO ] Cloning https://github.com/psychoinformatics-de/studyforrest-data-phase2.git/src/lab-eyetracking [2 other candidates] into '/home/adina/repos/testing/paper-remodnav/data/studyforrest-data-eyemovementlabels/code/remodnav/remodnav/tests/data/studyforrest/src/lab-eyetracking' [ERROR ] Failed to clone from any candidate source URL. Encountered errors per each url were: (OrderedDict([('https://github.com/psychoinformatics-de/studyforrest-data-phase2.git/src/lab-eyetracking', "Cmd('/usr/bin/git') failed due to: exit code(128)\n cmdline: /usr/bin/git clone --progress -v https://github.com/psychoinformatics-de/studyforrest-data-phase2.git/src/lab-eyetracking /home/adina/repos/testing/paper-remodnav/data/studyforrest-data-eyemovementlabels/code/remodnav/remodnav/tests/data/studyforrest/src/lab-eyetracking [cmd.py:wait:415]"), ('https://github.com/psychoinformatics-de/studyforrest-data-phase2.git/src/lab-eyetracking/.git', "Cmd('/usr/bin/git') failed due to: exit code(128)\n cmdline: /usr/bin/git clone --progress -v https://github.com/psychoinformatics-de/studyforrest-data-phase2.git/src/lab-eyetracking/.git /home/adina/repos/testing/paper-remodnav/data/studyforrest-data-eyemovementlabels/code/remodnav/remodnav/tests/data/studyforrest/src/lab-eyetracking [cmd.py:wait:415]"), ('/home/data/psyinf/forrest_gump/collection/fg_eyegaze_raw', "Cmd('/usr/bin/git') failed due to: exit code(128)\n cmdline: /usr/bin/git clone --progress -v /home/data/psyinf/forrest_gump/collection/fg_eyegaze_raw /home/adina/repos/testing/paper-remodnav/data/studyforrest-data-eyemovementlabels/code/remodnav/remodnav/tests/data/studyforrest/src/lab-eyetracking [cmd.py:wait:415]")]),) [install(/home/adina/repos/testing/paper-remodnav/data/studyforrest-data-eyemovementlabels/code/remodnav/remodnav/tests/data/studyforrest/src/lab-eyetracking)] [ERROR ] Installation of subdatasets failed with exception: InstallFailedError: Failed to install dataset from any of: ['https://github.com/psychoinformatics-de/studyforrest-data-phase2.git/src/lab-eyetracking', '/home/data/psyinf/forrest_gump/collection/fg_eyegaze_raw'] [get.py:_install_subds_from_flexible_source:184] [install(/home/adina/repos/testing/paper-remodnav/data/studyforrest-data-eyemovementlabels/code/remodnav/remodnav/tests/data/studyforrest/src/lab-eyetracking)] [INFO ] Cloning git@github.com:psychoinformatics-de/studyforrest-data-eyemovementlabels.git/inputs/raw_eyegaze [2 other candidates] into '/home/adina/repos/testing/paper-remodnav/data/studyforrest-data-eyemovementlabels/inputs/raw_eyegaze' [INFO ] Remote origin not usable by git-annex; setting annex-ignore [INFO ] Cloning https://github.com/psychoinformatics-de/studyforrest-data-phase2.git/src/lab-eyetracking [2 other candidates] into '/home/adina/repos/testing/paper-remodnav/data/studyforrest-data-eyemovementlabels/inputs/raw_eyegaze/src/lab-eyetracking' [ERROR ] Failed to clone from any candidate source URL. Encountered errors per each url were: (OrderedDict([('https://github.com/psychoinformatics-de/studyforrest-data-phase2.git/src/lab-eyetracking', "Cmd('/usr/bin/git') failed due to: exit code(128)\n cmdline: /usr/bin/git clone --progress -v https://github.com/psychoinformatics-de/studyforrest-data-phase2.git/src/lab-eyetracking /home/adina/repos/testing/paper-remodnav/data/studyforrest-data-eyemovementlabels/inputs/raw_eyegaze/src/lab-eyetracking [cmd.py:wait:415]"), ('https://github.com/psychoinformatics-de/studyforrest-data-phase2.git/src/lab-eyetracking/.git', "Cmd('/usr/bin/git') failed due to: exit code(128)\n cmdline: /usr/bin/git clone --progress -v https://github.com/psychoinformatics-de/studyforrest-data-phase2.git/src/lab-eyetracking/.git /home/adina/repos/testing/paper-remodnav/data/studyforrest-data-eyemovementlabels/inputs/raw_eyegaze/src/lab-eyetracking [cmd.py:wait:415]"), ('/home/data/psyinf/forrest_gump/collection/fg_eyegaze_raw', "Cmd('/usr/bin/git') failed due to: exit code(128)\n cmdline: /usr/bin/git clone --progress -v /home/data/psyinf/forrest_gump/collection/fg_eyegaze_raw /home/adina/repos/testing/paper-remodnav/data/studyforrest-data-eyemovementlabels/inputs/raw_eyegaze/src/lab-eyetracking [cmd.py:wait:415]")]),) [install(/home/adina/repos/testing/paper-remodnav/data/studyforrest-data-eyemovementlabels/inputs/raw_eyegaze/src/lab-eyetracking)] [ERROR ] Installation of subdatasets failed with exception: InstallFailedError: Failed to install dataset from any of: ['https://github.com/psychoinformatics-de/studyforrest-data-phase2.git/src/lab-eyetracking', '/home/data/psyinf/forrest_gump/collection/fg_eyegaze_raw'] [get.py:_install_subds_from_flexible_source:184] [install(/home/adina/repos/testing/paper-remodnav/data/studyforrest-data-eyemovementlabels/inputs/raw_eyegaze/src/lab-eyetracking)] [INFO ] Cloning https://github.com/psychoinformatics-de/paper-remodnav.git/remodnav [2 other candidates] into '/home/adina/repos/testing/paper-remodnav/remodnav' [INFO ] Submodule HEAD got detached. Resetting branch master to point to 113c1d82. Original location was c9b86961 [INFO ] Cloning git@github.com:psychoinformatics-de/remodnav.git/remodnav/tests/data/anderson_etal [2 other candidates] into '/home/adina/repos/testing/paper-remodnav/remodnav/remodnav/tests/data/anderson_etal' [INFO ] Submodule HEAD got detached. Resetting branch master to point to c6d02539. Original location was 0e6f8270 [INFO ] Cloning git@github.com:psychoinformatics-de/remodnav.git/remodnav/tests/data/studyforrest [2 other candidates] into '/home/adina/repos/testing/paper-remodnav/remodnav/remodnav/tests/data/studyforrest' [INFO ] Remote origin not usable by git-annex; setting annex-ignore [INFO ] Cloning https://github.com/psychoinformatics-de/studyforrest-data-phase2.git/src/lab-eyetracking [2 other candidates] into '/home/adina/repos/testing/paper-remodnav/remodnav/remodnav/tests/data/studyforrest/src/lab-eyetracking' [ERROR ] Failed to clone from any candidate source URL. Encountered errors per each url were: (OrderedDict([('https://github.com/psychoinformatics-de/studyforrest-data-phase2.git/src/lab-eyetracking', "Cmd('/usr/bin/git') failed due to: exit code(128)\n cmdline: /usr/bin/git clone --progress -v https://github.com/psychoinformatics-de/studyforrest-data-phase2.git/src/lab-eyetracking /home/adina/repos/testing/paper-remodnav/remodnav/remodnav/tests/data/studyforrest/src/lab-eyetracking [cmd.py:wait:415]"), ('https://github.com/psychoinformatics-de/studyforrest-data-phase2.git/src/lab-eyetracking/.git', "Cmd('/usr/bin/git') failed due to: exit code(128)\n cmdline: /usr/bin/git clone --progress -v https://github.com/psychoinformatics-de/studyforrest-data-phase2.git/src/lab-eyetracking/.git /home/adina/repos/testing/paper-remodnav/remodnav/remodnav/tests/data/studyforrest/src/lab-eyetracking [cmd.py:wait:415]"), ('/home/data/psyinf/forrest_gump/collection/fg_eyegaze_raw', "Cmd('/usr/bin/git') failed due to: exit code(128)\n cmdline: /usr/bin/git clone --progress -v /home/data/psyinf/forrest_gump/collection/fg_eyegaze_raw /home/adina/repos/testing/paper-remodnav/remodnav/remodnav/tests/data/studyforrest/src/lab-eyetracking [cmd.py:wait:415]")]),) [install(/home/adina/repos/testing/paper-remodnav/remodnav/remodnav/tests/data/studyforrest/src/lab-eyetracking)] [ERROR ] Installation of subdatasets failed with exception: InstallFailedError: Failed to install dataset from any of: ['https://github.com/psychoinformatics-de/studyforrest-data-phase2.git/src/lab-eyetracking', '/home/data/psyinf/forrest_gump/collection/fg_eyegaze_raw'] [get.py:_install_subds_from_flexible_source:184] [install(/home/adina/repos/testing/paper-remodnav/remodnav/remodnav/tests/data/studyforrest/src/lab-eyetracking)] action summary: install (error: 3, ok: 9) ```

mih commented 5 years ago

Please ignore this for now, there are a ton of changes coming, which will also fix this issue.

aqw commented 5 years ago

Pulled and gave it another whack today. A few comments:

Tkinter is required, which can't be installed through pip
I don't know if this is a known upstream issue, but datalad's error about needing git-annex-standalone is buried in a wave of output. Not terribly obvious for users. Any way there can be an explicit check and error?
the readme says pdflatex is needed but the build fails because latexmk is not found.

adswa commented 5 years ago

thx

mih commented 5 years ago

I can confirm that the following command provide me with a PDF of the paper (given an appropriate environment with all dependencies):

datalad install https://github.com/psychoinformatics-de/paper-remodnav.git
cd paper-remodnav
make

adswa commented 4 years ago

I think this is good to close.

psychoinformatics-de / paper-remodnav

Can't build main.pdf #4