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View Code? Open in Web Editor NEWEditorial venue for ML Reproducibility Challenge Accepted papers
Home Page: https://openreview.net/group?id=ML_Reproducibility_Challenge
Editorial venue for ML Reproducibility Challenge Accepted papers
Home Page: https://openreview.net/group?id=ML_Reproducibility_Challenge
Hello,
We are attempting to compile the camera ready version of our paper but we have encountered a few errors (see https://pastebin.com/7anJ8MKR). Our code can be found in #18.
The citations are missing in the compiled pdf and tex does not seem to find the .bib file.
We have changed the path in .yaml and tried both ../openreview/bibliography.bib and bibliography.bib
but neither seem to work
Thank you
Hi , I just finished a first round of reformatting.
Some questions:
Hi, we are going through the process of preparing our pull requests. Some questions:
Thanks
Referring to our code in PR #5.
When trying to run the command make
from the journal
folder, we get errors due to pdflatex not being able to find the included files. For example, the line \input{intro.tex}
in the file openreview/content.tex
will not work:
Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41.
Rule 'pdflatex': Rules & subrules not known to be previously run:
pdflatex
Rule 'pdflatex': The following rules & subrules became out-of-date:
'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'xelatex -interaction=nonstopmode -recorder "article.tex"'
------------
Latexmk: References changed.
Latexmk: Non-existent bbl file 'article.bbl'
No file article.bbl.
Latexmk: Missing input file: 'intro.tex' from line
'! LaTeX Error: File `intro.tex' not found.'
Latexmk: Log file says output to 'article.pdf'
Latexmk: List of undefined refs and citations:
Citation `beta-vae' on page 2 undefined on input line 34
Citation `geco' on page 2 undefined on input line 33
Citation `pytorch' on page 1 undefined on input line 10
------------
Running 'make "article.bbl"'
------------
make[1]: *** No rule to make target 'article.bbl'. Stop.
------------
Running 'make "intro.tex"'
------------
make[1]: *** No rule to make target 'intro.tex'. Stop.
Latexmk: Summary of warnings:
Latex failed to resolve 3 citation(s)
Collected error summary (may duplicate other messages):
pdflatex: Command for 'pdflatex' gave return code 256
Latexmk: Use the -f option to force complete processing,
unless error was exceeding maximum runs of latex/pdflatex.
make: *** [article.pdf] Error 12
The compiler cannot find the intro.tex
file.
However, if we modify the include statement as \input{../openreview/content.tex}
it will work, and return an error to the next \input
statement whose path is not relative to the journal
folder. This happens also for included images, so to fix it we would need to add ../openreview
to all the figures and inputs.
Here is the link to the full output of make
.
I opened the issue because to me this looks related to some issue in the makefiles and it might be helpful to others.
alg1' on page 8 undefined on input line 440 Reference
fig3' on page 7 undefined on input line 348fig4' on page 7 undefined on input line 348 Reference
fig5' on page 7 undefined on input line 391table1' on page 5 undefined on input line 121 Reference
table1' on page 5 undefined on input line 189table1' on page 7 undefined on input line 391 Reference
table5' on page 7 undefined on input line 391make[1]: Entering directory '/home/stark/Projects/MLRC2020/openreview/last_attempt/RC-2020/garg2021re/journal'
make[1]: *** No rule to make target 'article.bbl'. Stop.
make[1]: Leaving directory '/home/stark/Projects/MLRC2020/openreview/last_attempt/RC-2020/garg2021re/journal'
Latexmk: Summary of warnings:
Latex failed to resolve 8 reference(s)
Latex failed to resolve 16 citation(s)
Latexmk: Errors, so I did not complete making targets
Collected error summary (may duplicate other messages):
pdflatex: Command for 'pdflatex' gave return code 256
Latexmk: Use the -f option to force complete processing,
unless error was exceeding maximum runs of latex/pdflatex.
Makefile:30: recipe for target 'article.pdf' failed
make: *** [article.pdf] Error 12
PR: #103
lenovo@lenovo-Lenovo-ideapad-330-15IKB:~/MLRC/2021$ ./build_all.sh
Building ahmed2022re/
/home/lenovo/MLRC/2021/ahmed2022re/journal
Latexmk: This is Latexmk, John Collins, 26 Dec. 2019, version: 4.67.
Latexmk: This is Latexmk, John Collins, 26 Dec. 2019, version: 4.67.
Rule 'pdflatex': The following rules & subrules became out-of-date:
'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'xelatex -interaction=nonstopmode -recorder "article.tex"'
------------
Latexmk: References changed.
Latexmk: Non-existent bbl file 'article.bbl'
No file article.bbl.
Latexmk: Missing input file: 'Capture.png' from line
'LaTeX Warning: File `Capture.png' not found on input line 99.'
Latexmk: Missing input file: 'Capture.png' from line
'! Unable to load picture or PDF file 'Capture.png'.'
Latexmk: Missing input file: 'graph_1.png' from line
'LaTeX Warning: File `graph_1.png' not found on input line 311.'
Latexmk: Missing input file: 'graph_1.png' from line
'! Unable to load picture or PDF file 'graph_1.png'.'
Latexmk: References changed.
Latexmk: References changed.
Latexmk: Log file says output to 'article.pdf'
Latexmk: List of undefined refs and citations:
Citation 'hartley2020dtoolai' on page 3 undefined on input line 34
Citation 'he2016deep' on page 3 undefined on input line 44
Citation 'he2016deep' on page 5 undefined on input line 67
Citation 'he2016deep' on page 5 undefined on input line 69
Citation 'heumos2021mlf' on page 3 undefined on input line 34
Citation 'kornblith2019similarity' on page 7 undefined on input line 129
Citation 'krizhevsky2009learning' on page 3 undefined on input line 44
Citation 'loshchilov2016sgdr' on page 6 undefined on input line 122
Citation 'paszke2019pytorch' on page 5 undefined on input line 67
Citation 'renard2020variability' on page 3 undefined on input line 34
Citation 'summers2021nondeterminism' on page 1 undefined on input line 3
Citation 'summers2021nondeterminism' on page 1 undefined on input line 8
Citation 'summers2021nondeterminism' on page 11 undefined on input line 342
Citation 'summers2021nondeterminism' on page 9 undefined on input line 170
Citation 'summers2021nondeterminism' on page 9 undefined on input line 177
Citation 'szegedy2015going' on page 1 undefined on input line 3
Citation 'wen2020batchensemble' on page 1 undefined on input line 3
Citation 'zhuang2021randomness' on page 3 undefined on input line 34
Citation 'zhuang2021randomness' on page 3 undefined on input line 47
Reference `fig:pic0' on page 5 undefined on input line 69
Reference `fig:pic1' on page 11 undefined on input line 276
Reference `sec:AdditionalResults' on page 5 undefined on input line 58
Reference `sec:Results' on page 12 undefined on input line 363
Reference `table:table1' on page 5 undefined on input line 69
Reference `table:table10' on page 11 undefined on input line 342
Reference `table:table2' on page 5 undefined on input line 106
Reference `table:table3' on page 7 undefined on input line 143
Reference `table:table4' on page 9 undefined on input line 177
Reference `table:table5' on page 9 undefined on input line 200
Reference `table:table6' on page 10 undefined on input line 217
Reference `table:table7' on page 10 undefined on input line 217
Reference `table:table7' on page 10 undefined on input line 219
Reference `table:table8' on page 11 undefined on input line 276
Reference `table:table9' on page 11 undefined on input line 316
------------
Running 'make "Capture.png"'
------------
make[1]: *** No rule to make target 'Capture.png'. Stop.
------------
Running 'make "article.bbl"'
------------
make[1]: *** No rule to make target 'article.bbl'. Stop.
------------
Running 'make "graph_1.png"'
------------
make[1]: *** No rule to make target 'graph_1.png'. Stop.
Latexmk: Summary of warnings from last run of (pdf)latex:
Latex failed to resolve 21 reference(s)
Latex failed to resolve 23 citation(s)
Collected error summary (may duplicate other messages):
pdflatex: Command for 'pdflatex' gave return code 1
Refer to 'article.log' for details
Latexmk: Use the -f option to force complete processing,
unless error was exceeding maximum runs, or warnings treated as errors.
make: *** [Makefile:30: article.pdf] Error 12
Build complete
rm: cannot remove 'article.bbl': No such file or directory
rm: cannot remove 'article.blg': No such file or directory
Building editorial/
/home/lenovo/MLRC/2021/editorial/journal
Latexmk: This is Latexmk, John Collins, 26 Dec. 2019, version: 4.67.
Latexmk: This is Latexmk, John Collins, 26 Dec. 2019, version: 4.67.
Rule 'pdflatex': The following rules & subrules became out-of-date:
'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'xelatex -interaction=nonstopmode -recorder "article.tex"'
------------
Latexmk: References changed.
Latexmk: Non-existent bbl file 'article.bbl'
No file article.bbl.
Latexmk: References changed.
Latexmk: References changed.
Latexmk: Log file says output to 'article.pdf'
Latexmk: List of undefined refs and citations:
Citation 'Roboto:2011' on page 2 undefined on input line 74
Citation 'Rougier:2017' on page 1 undefined on input line 12
Citation 'Rougier:2017' on page 1 undefined on input line 26
Citation 'Rougier:2018' on page 1 undefined on input line 13
Citation 'Science:2018' on page 1 undefined on input line 11
Citation 'SourceCodePro:2012' on page 2 undefined on input line 74
Citation 'SourceSerifPro:2014' on page 2 undefined on input line 74
Citation 'Topalidou:2015' on page 1 undefined on input line 4
------------
Running 'make "article.bbl"'
------------
make[1]: *** No rule to make target 'article.bbl'. Stop.
Rule 'biber article': File changes, etc:
Changed files, or newly in use since previous run(s):
'article.bcf'
------------
Run number 1 of rule 'biber article'
------------
------------
Running 'biber "article"'
------------
Latexmk: Found biber source file(s) [article.bcf bibliography.bib]
Rule 'pdflatex': File changes, etc:
Changed files, or newly in use since previous run(s):
'article.aux'
'article.bbl'
'article.out'
------------
Run number 2 of rule 'pdflatex'
------------
------------
Running 'xelatex -interaction=nonstopmode -recorder "article.tex"'
------------
Latexmk: Found input bbl file 'article.bbl'
Latexmk: Log file says output to 'article.pdf'
Latexmk: Found biber source file(s) [article.bcf bibliography.bib]
Rule 'pdflatex': File changes, etc:
Changed files, or newly in use since previous run(s):
'article.aux'
'article.run.xml'
------------
Run number 3 of rule 'pdflatex'
------------
------------
Running 'xelatex -interaction=nonstopmode -recorder "article.tex"'
------------
Latexmk: Found input bbl file 'article.bbl'
Latexmk: Log file says output to 'article.pdf'
Latexmk: Found biber source file(s) [article.bcf bibliography.bib]
Rule 'pdflatex': File changes, etc:
Changed files, or newly in use since previous run(s):
'article.aux'
'article.run.xml'
------------
Run number 4 of rule 'pdflatex'
------------
------------
Running 'xelatex -interaction=nonstopmode -recorder "article.tex"'
------------
Latexmk: Found input bbl file 'article.bbl'
Latexmk: Log file says output to 'article.pdf'
Latexmk: Found biber source file(s) [article.bcf bibliography.bib]
Build complete
Following is the message shown after cloning
Please make sure you have the correct access rights and the repository exists.
fatal: clone of '[email protected]:ReScience/template.git' into submodule path 'D:/ MLRC Submission/Camera Ready/RC-2020/template' failed Failed to clone 'template'. Retry scheduled Cloning into 'D:/MLRC Submission/Camera Ready/RC-2020/template'...
[email protected]: Permission denied (publickey).
fatal: Could not read from remote repository.
Please make sure you have the correct access rights and the repository exists.
fatal: clone of '[email protected]:ReScience/template.git' into submodule path 'D:/ MLRC Submission/Camera Ready/RC2020/template' failed
Failed to clone 'template' a second time, aborting
Since i am lacking in basics, and this is my first ever paper. i would like someone to guide me through the process as written guidelines bit confusing to me. i am really looking forward to get your help in order to timely submission of camera ready version.
regards
Waqas Ahmed
following file has some bug in it or what? i cant clone it untill i delet this file.
Waqas Ahmed@DESKTOP-4APMTJQ MINGW64 ~/Divya
$ git clone --recursive https://github.com/Divyasha02/MLRC.git
Cloning into 'MLRC'...
remote: Enumerating objects: 6689, done.
remote: Total 6689 (delta 0), reused 0 (delta 0), pack-reused 6689
Receiving objects: 100% (6689/6689), 151.20 MiB | 2.47 MiB/s, done.
Resolving deltas: 100% (2692/2692), done.
error: invalid path '2020/sundar2021reproducibility/journal/Icon?'
fatal: unable to checkout working tree
warning: Clone succeeded, but checkout failed.
You can inspect what was checked out with 'git status'
and retry with 'git restore --source=HEAD :/'
Hi,
Our paper got accepted but we failed to reproduce the results.
As suggested in the metadata.yaml we now have the following title:
"[¬Re] Reproducing 'Fair Selective Classification via Sufficiency'"
However, the check_yaml.py won't accept this as a correct title.
The check_title function only passes for "[Re] " but does not consider our case.
Could I suggest changing the code to:
def check_title(meta): check_ne(meta, "title", "Metadata") assert meta["title"].startswith( "[Re] " ) or meta["title"].startswith( "[¬Re] " ), "title in metadata should start with '[Re]' or '[¬Re]'"
Or is [Re] correct in our situation?
Thanks
When trying to run the command make from the journal folder, we are having some trouble.
Here a list of the issues I can see from the make-build.log
and article.log
:
(from article.log
)
I was assuming the Makefile automatically also runs bibtex, but according to the logs it does not. Do we manually have to run the Latex compile / bibtex pipeline before we run make
?
ackage biblatex Info: XeTeX detected.
(biblatex) Assuming input encoding 'utf8'.
Package biblatex Info: Automatic encoding selection.
(biblatex) Assuming data encoding 'utf8'.
Package biblatex Info: Document encoding is UTF8 ....
Package biblatex Info: ... and expl3
(biblatex) 2021-02-18 L3 programming layer (loader)
(biblatex) is new enough (at least 2020/04/06),
(biblatex) setting 'casechanger=expl3'.
(/usr/local/texlive/2021/texmf-dist/tex/latex/biblatex/blx-case-expl3.sty
Package: blx-case-expl3 2020/12/31 v3.16 expl3 case changing code for biblatex
)
\openout6 = `article.bcf'.
Package biblatex Info: Trying to load bibliographic data...
Package biblatex Info: ... file 'article.bbl' not found.
No file article.bbl.
Package biblatex Info: Reference section=0 on input line 5.
Package biblatex Info: Reference segment=0 on input line 5.
(./header.tex
I am unaware why this might be happening.
LaTeX Warning: Reference `tab:classification results' on page 7 undefined on in
put line 328.
[7] [8]
LaTeX Warning: Reference `tab:Authors seq-to-seq synth results' on page 9 undef
ined on input line 331.
...
LaTeX Warning: There were undefined references.
I also added the currently compiled article.pdf
to the repo, so that you can also have a look at the visual issues. Thanks for your help.
I have completed all my files editing but i am struggling with this issue. what might be the possible issue? metadata.tex is not foung or generated.
Rc files read:
NONE
Latexmk: This is Latexmk, John Collins, 17 Mar. 2022. Version 4.77, version: 4.77.
No specific requests made, so using default for latexmk.
Latexmk: Doing main (small) clean up for 'article.tex'
Latexmk: Doing extra clean up (of final output files) for 'article.tex'
Latexmk: Doing main (small) clean up for 'content.tex'
Latexmk: Doing extra clean up (of final output files) for 'content.tex'
Latexmk: Doing main (small) clean up for 'header.tex'
Latexmk: Doing extra clean up (of final output files) for 'header.tex'
rm: cannot remove 'metadata.tex': No such file or directory
C:\Users\Waqas Ahmed\AppData\Local\Microsoft\WindowsApps\python3.exe: can't open file 'C:\Users\Waqas': [Errno 2] No such file or directory
make: *** [Makefile:18: metadata.tex] Error 2
Build complete
rm: cannot remove 'article.aux': No such file or directory
rm: cannot remove 'article.bbl': No such file or directory
rm: cannot remove 'article.blg': No such file or directory
rm: cannot remove 'article.fdb_latexmk': No such file or directory
rm: cannot remove 'article.fls': No such file or directory
rm: cannot remove 'article.out': No such file or directory
rm: cannot remove 'article.log': No such file or directory
rm: cannot remove 'article.run.xml': No such file or directory
rm: cannot remove 'article.bcf': No such file or directory
Building editorial/
/c/Users/Waqas Ahmed/MLRC_2/MLRC/2021/editorial/journal
Makefile:1: *** missing separator. Stop.
rm: cannot remove 'metadata.tex': No such file or directory
Makefile:1: *** missing separator. Stop.
Build complete
rm: cannot remove 'article.aux': No such file or directory
rm: cannot remove 'article.bbl': No such file or directory
rm: cannot remove 'article.blg': No such file or directory
rm: cannot remove 'article.fdb_latexmk': No such file or directory
rm: cannot remove 'article.fls': No such file or directory
rm: cannot remove 'article.out': No such file or directory
rm: cannot remove 'article.log': No such file or directory
rm: cannot remove 'article.run.xml': No such file or directory
rm: cannot remove 'article.bcf': No such file or directory
Hi, I am running build_all.sh after successfully passing the check_yaml.py test suite and organizing my content. I am getting the following output:
Building editorial/
/Users/thesofakillers/repos/MLRC/2021/editorial/journal
Rc files read:
NONE
Latexmk: This is Latexmk, John Collins, 17 Mar. 2022. Version 4.77, version: 4.77.
No specific requests made, so using default for latexmk.
Latexmk: Doing main (small) clean up for 'article.tex'
Latexmk: Doing extra clean up (of final output files) for 'article.tex'
Latexmk: Doing main (small) clean up for 'content.tex'
Latexmk: Doing extra clean up (of final output files) for 'content.tex'
Latexmk: Doing main (small) clean up for 'header.tex'
Latexmk: Doing extra clean up (of final output files) for 'header.tex'
Latexmk: Doing main (small) clean up for 'metadata.tex'
Latexmk: Doing extra clean up (of final output files) for 'metadata.tex'
Latexmk: Missing bbl file 'article.bbl' in following:
No file article.bbl.
make[1]: *** No rule to make target `article.bbl'. Stop.
Build complete
Building togt2022badder/
/Users/thesofakillers/repos/MLRC/2021/togt2022badder/journal
Rc files read:
NONE
Latexmk: This is Latexmk, John Collins, 17 Mar. 2022. Version 4.77, version: 4.77.
No specific requests made, so using default for latexmk.
Latexmk: Doing main (small) clean up for 'article.tex'
Latexmk: Doing extra clean up (of final output files) for 'article.tex'
Latexmk: Doing main (small) clean up for 'content.tex'
Latexmk: Doing extra clean up (of final output files) for 'content.tex'
Latexmk: Doing main (small) clean up for 'header.tex'
Latexmk: Doing extra clean up (of final output files) for 'header.tex'
rm: metadata.tex: No such file or directory
Traceback (most recent call last):
File "/Users/thesofakillers/repos/MLRC/2021/togt2022badder/journal/./yaml-to-latex.py", line 93, in <module>
content = generate_latex_metadata(filename_in, article)
File "/Users/thesofakillers/repos/MLRC/2021/togt2022badder/journal/./yaml-to-latex.py", line 10, in generate_latex_metadata
"% DO NOT EDIT - automatically generated from {filename}\n\n"
IndexError: list index out of range
make: *** [metadata.tex] Error 1
Build complete
rm: article.aux: No such file or directory
rm: article.bbl: No such file or directory
rm: article.blg: No such file or directory
rm: article.fdb_latexmk: No such file or directory
rm: article.fls: No such file or directory
rm: article.out: No such file or directory
rm: article.log: No such file or directory
rm: article.run.xml: No such file or directory
rm: article.bcf: No such file or directory
I am not sure what I should do about the missing article.bbl
and the metadata.tex IndexError. Please let me know how I should debug this. Thank you
Hi, while running the make command, I am getting the following error. What could possibly be the reason?
/yaml-to-latex.py -i metadata.yaml -o metadata.tex Traceback (most recent call last): File "./yaml-to-latex.py", line 93, in <module> content = generate_latex_metadata(filename_in, article) File "./yaml-to-latex.py", line 50, in generate_latex_metadata "".format(filename=filename, _=article, abstract=abstract)) AttributeError: 'str' object has no attribute 'name' Makefile:18: recipe for target 'metadata.tex' failed make: *** [metadata.tex] Error 1
Hi, we're having trouble with loading our references. We tried many ways to do this, but are unable to find where the problem lies. Can you please help us?
Below you can find the .log file that is created on the latest run of 'make'.
article.log
All the files in our directory can be find under PR #24
The header which contains "Edited by..." is overlapping with the reproducibility summary and the citations are getting boldened and not recognized.
We are facing the following issues:
We see errors the following errors during build:
LaTeX Warning: Citation 'zhuang_adabelief_2020' on page 3 undefined on input li
ne 62.
LaTeX Warning: Citation 'SGD' on page 3 undefined on input line 73.
LaTeX Warning: Citation 'Momentum' on page 3 undefined on input line 73.
LaTeX Warning: Citation 'NAG' on page 3 undefined on input line 73.
LaTeX Warning: Citation 'Adam' on page 3 undefined on input line 73.
LaTeX Warning: Citation 'liu_variance_2020' on page 3 undefined on input line 7
3.
Whatever is referred using \ref
command appears as ??
in the pdf
Thanks for your help.
Hi,
This is a small detail but brew cask
doesn't work anymore. The command to install mactex is
brew install --cask mactex
I submitted a pull request #90 that has build issue - undefined refs and citations and article.bbl file is not found.
Log when errors begin:
Running 'xelatex -interaction=nonstopmode -recorder "article.tex"'
------------
Latexmk: Found input bbl file 'article.bbl'
Latexmk: Log file says output to 'article.pdf'
Latexmk: Found biber source file(s) [article.bcf bibliography.bib]
Build complete
Building zrimsek2022learning/
/home/andraz/MLRC/2021/zrimsek2022learning/journal
Latexmk: This is Latexmk, John Collins, 26 Dec. 2019, version: 4.67.
Latexmk: This is Latexmk, John Collins, 26 Dec. 2019, version: 4.67.
Rule 'pdflatex': The following rules & subrules became out-of-date:
'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'xelatex -interaction=nonstopmode -recorder "article.tex"'
------------
Latexmk: References changed.
Latexmk: Non-existent bbl file 'article.bbl'
No file article.bbl.
Latexmk: References changed.
Latexmk: References changed.
Latexmk: Log file says output to 'article.pdf'
Latexmk: List of undefined refs and citations:
Citation 'chen2019pipr' on page 1 undefined on input line 9
Citation 'chen2019pipr' on page 3 undefined on input line 50
Citation 'gui2019dnn' on page 3 undefined on input line 50
Citation 'hashemifar2018predicting' on page 3 undefined on input line 50
Citation 'lv2021learning' on page 1 undefined on input line 3
Reference `generalize' on page 7 undefined on input line 184
Reference `graph' on page 7 undefined on input line 205
Reference `graph' on page 9 undefined on input line 240
Reference `subsets' on page 5 undefined on input line 104
Reference `subsets' on page 6 undefined on input line 140
Reference `subsets' on page 8 undefined on input line 231
Reference `times' on page 6 undefined on input line 115
------------
Running 'make "article.bbl"'
------------
make[1]: *** No rule to make target 'article.bbl'. Stop.
Latexmk: Summary of warnings from last run of (pdf)latex:
Latex failed to resolve 7 reference(s)
Latex failed to resolve 5 citation(s)
Collected error summary (may duplicate other messages):
pdflatex: Command for 'pdflatex' gave return code 1
Refer to 'article.log' for details
Latexmk: Use the -f option to force complete processing,
unless error was exceeding maximum runs, or warnings treated as errors.
make: *** [Makefile:30: article.pdf] Error 12
Build complete
rm: cannot remove 'article.bbl': No such file or directory
rm: cannot remove 'article.blg': No such file or directory
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