Publications not displaying correctly

I’ve built a site using the hugo-academic theme with blogdown.

The site is currently live at https://hopeful-hugle-603878.netlify.com/. When I build that site locally using blogdown::serve_site(), all 50+ publications appear as expected. However, when I deploy the site using netlify (having completed some edits between deploys), one or more recently a subset of the publications appears correctly, with the others showing up incorrectly. After some editrs, the re-deploy has been fine. I can’t find the variable that is determining success or failure of the re-deploys.

Both netlify and my local machine are using HUGO_VERSION 0.55.6.

I was interested in making my github repo public, but then I remembered that I have a google api key in there, and I realized that I might make an error in terms of what should be public / private, so I have elected to be cautious for now. If it is impossible to help troubleshoot, then I can try to figure out how to make the repo public without publicizing private data such as that.

Thank you so much in advance!

When you can’t share your repo, make a new one to share, and reproduce the error there, sans private info.

Half the time, just going through those steps solves the problem. :slight_smile:

1 Like

Thank you, @Maiki. I have now done as you have suggested so that the files can be seen here: https://github.com/byrdjb/troubleshooting_website.

That repo is not the one being deployed live at https://hopeful-hugle-603878.netlify.com/, but as of a few minutes ago, it was identical to it other than redaction of a few private key values.

Thanks in advance for any info you can share about why publications sometimes all display just fine and other times are filled with truncations and 0001 as the year.

Results of my latest netlify deploy, which didn’t produce proper output for the publications.

7:00:03 PM: Build ready to start
7:00:05 PM: build-image version: 9e0f207a27642d0115b1ca97cd5e8cebbe492f63
7:00:05 PM: build-image tag: v3.3.2
7:00:05 PM: buildbot version: ef8d0929ed0baabafd8bbb7d0b021e1fc24180c0
7:00:06 PM: Fetching cached dependencies
7:00:06 PM: Starting to download cache of 295.0MB
7:00:07 PM: Finished downloading cache in 1.807040942s
7:00:07 PM: Starting to extract cache
7:00:14 PM: Finished extracting cache in 6.700565362s
7:00:14 PM: Finished fetching cache in 8.749517842s
7:00:14 PM: Starting to prepare the repo for build
7:00:15 PM: Preparing Git Reference refs/heads/master
7:00:18 PM: Found netlify.toml. Overriding site configuration
7:00:18 PM: Starting build script
7:00:18 PM: Installing dependencies
7:00:19 PM: Started restoring cached node version
7:00:22 PM: Finished restoring cached node version
7:00:23 PM: v10.16.0 is already installed.
7:00:24 PM: Now using node v10.16.0 (npm v6.9.0)
7:00:25 PM: Attempting ruby version 2.6.2, read from environment
7:00:26 PM: Using ruby version 2.6.2
7:00:27 PM: Using PHP version 5.6
7:00:27 PM: Installing Hugo 0.55.6
7:00:27 PM: Hugo Static Site Generator v0.55.6-A5D4C82D2/extended linux/amd64 BuildDate: 2019-05-18T08:08:34Z
7:00:27 PM: Started restoring cached go cache
7:00:27 PM: Finished restoring cached go cache
7:00:27 PM: unset GOOS;
7:00:27 PM: unset GOARCH;
7:00:27 PM: export GOROOT=’/opt/buildhome/.gimme/versions/go1.12.linux.amd64’;
7:00:27 PM: export PATH="/opt/buildhome/.gimme/versions/go1.12.linux.amd64/bin:${PATH}";
7:00:27 PM: go version >&2;
7:00:27 PM: export GIMME_ENV=’/opt/buildhome/.gimme/env/go1.12.linux.amd64.env’;
7:00:27 PM: go version go1.12 linux/amd64
7:00:27 PM: Installing missing commands
7:00:27 PM: Verify run directory
7:00:27 PM: Executing user command: hugo
7:00:28 PM: Building sites …
7:00:32 PM: | EN
7:00:32 PM: +
7:00:32 PM: ------------------±----+
7:00:32 PM: Pages | 292
7:00:32 PM: Paginator pages | 7
7:00:32 PM: Non-page files | 81
7:00:32 PM: Static files | 27
7:00:32 PM: Processed images | 39
7:00:32 PM: Aliases | 39
7:00:32 PM: Sitemaps |
7:00:32 PM: 1
7:00:32 PM: Cleaned | 0
7:00:32 PM: Total in 4284 ms
7:00:32 PM: Skipping functions preparation step: no functions directory set
7:00:32 PM: Caching artifacts
7:00:32 PM: Started saving pip cache
7:00:32 PM: Finished saving pip cache
7:00:32 PM: Started saving emacs cask dependencies
7:00:32 PM: Finished saving emacs cask dependencies
7:00:32 PM: Started saving maven dependencies
7:00:32 PM: Finished saving maven dependencies
7:00:32 PM: Started saving boot dependencies
7:00:32 PM: Finished saving boot dependencies
7:00:32 PM: Started saving go dependencies
7:00:32 PM: Finished saving go dependencies
7:00:32 PM: Build script success
7:00:32 PM: Starting to deploy site from ‘public’
7:00:33 PM: Creating deploy tree asynchronously
7:00:37 PM: 127 new files to upload
7:00:37 PM: 0 new functions to upload
7:00:43 PM: Starting post processing
7:01:10 PM: Post processing done
7:01:11 PM: Site is live
7:01:18 PM: Finished processing build request in 1m13.11557069s

To see if I can stimulate some new thoughts on this problem, here is the Source for one of the publications that appears correctly and another one that does not. I am hoping this will help shed light on the nature of the problem.

Thanks!

Blockquote

</div>

</div>

<div class="grid-sizer col-lg-12 isotope-item pubtype-2 year-2010">

<div class="pub-list-item" style="margin-bottom: 1rem" itemscope itemtype="http://schema.org/CreativeWork">
<i class="far fa-file-alt pub-icon" aria-hidden="true"></i>

<span itemprop="author" class="article-metadata li-cite-author">

<span itemprop="author name" itemtype="http://schema.org/Person"><a href="[/authors/james-brian-byrd/](https://hopeful-hugle-603878.netlify.com/authors/james-brian-byrd/)">James Brian Byrd</a></span>, <span itemprop="author name" itemtype="http://schema.org/Person"><a href="[/authors/alencia-v.-woodard-grice/](https://hopeful-hugle-603878.netlify.com/authors/alencia-v.-woodard-grice/)">Alencia V. Woodard-Grice</a></span>, <span itemprop="author name" itemtype="http://schema.org/Person"><a href="[/authors/elizabeth-r.-stone/](https://hopeful-hugle-603878.netlify.com/authors/elizabeth-r.-stone/)">Elizabeth R. Stone</a></span>, <span itemprop="author name" itemtype="http://schema.org/Person"><a href="[/authors/amelia-c.-lucisano/](https://hopeful-hugle-603878.netlify.com/authors/amelia-c.-lucisano/)">Amelia C. Lucisano</a></span>, <span itemprop="author name" itemtype="http://schema.org/Person"><a href="[/authors/heidi-m.-schaefer/](https://hopeful-hugle-603878.netlify.com/authors/heidi-m.-schaefer/)">Heidi M. Schaefer</a></span>, <span itemprop="author name" itemtype="http://schema.org/Person"><a href="[/authors/chang-yu/](https://hopeful-hugle-603878.netlify.com/authors/chang-yu/)">Chang Yu</a></span>, <span itemprop="author name" itemtype="http://schema.org/Person"><a href="[/authors/anne-e.-eyler/](https://hopeful-hugle-603878.netlify.com/authors/anne-e.-eyler/)">Anne E. Eyler</a></span>, <span itemprop="author name" itemtype="http://schema.org/Person"><a href="[/authors/n.e.-salloum/](https://hopeful-hugle-603878.netlify.com/authors/n.e.-salloum/)">N.E. Salloum</a></span>, <span itemprop="author name" itemtype="http://schema.org/Person"><a href="[/authors/nancy-j.-brown/](https://hopeful-hugle-603878.netlify.com/authors/nancy-j.-brown/)">Nancy J. Brown</a></span>

</span>
(2010).
<a href="[/publication/allergy-2010/](https://hopeful-hugle-603878.netlify.com/publication/allergy-2010/)" itemprop="name">Association of angiotensin-converting enzyme inhibitor-associated angioedema with transplant and immunosuppressant use</a>.
<em>Allergy, 65</em>(11).

<p>

<a class="btn btn-outline-primary my-1 mr-1 btn-sm" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3305268/pdf/nihms-360692.pdf" target="_blank" rel="noopener">
PDF
</a>

<button type="button" class="btn btn-outline-primary my-1 mr-1 btn-sm js-cite-modal"
data-filename="/publication/allergy-2010/cite.bib">
Cite
</button>

<a class="btn btn-outline-primary my-1 mr-1 btn-sm" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3305268/" target="_blank" rel="noopener">
Source Document
</a>

<a class="btn btn-outline-primary my-1 mr-1 btn-sm" href="https://doi.org/10.1111/j.1398-9995.2010.02398.x" target="_blank" rel="noopener">
DOI
</a>

</p>

</div>

</div>

<div class="grid-sizer col-lg-12 isotope-item pubtype-0 year-0001">

<div class="pub-list-item" style="margin-bottom: 1rem" itemscope itemtype="http://schema.org/CreativeWork">
<i class="far fa-file-alt pub-icon" aria-hidden="true"></i>

<span itemprop="author" class="article-metadata li-cite-author">

</span>
(0001).
<a href="[/publication/misev-2018/](https://hopeful-hugle-603878.netlify.com/publication/misev-2018/)" itemprop="name"></a>.

<p>

<button type="button" class="btn btn-outline-primary my-1 mr-1 btn-sm js-cite-modal"
data-filename="/publication/misev-2018/cite.bib">
Cite
</button>

</p>

Blockquote

I just cloned your repo and checked that content folder and it has index.html in it, as well as index.md. Is that how Academic works? I’m not sure, but that stands out to me.

1 Like

Thank you. I also was surprised by that. Those seem to have been generated from the .md files by running Blogdown / Hugo.

I have not been able to find documentation to explain that facet of what I’m seeing.

I have been able to delete the index.html files that are in publications’ individual folders and still see intermittently successful deploys, so I have come to the tentative conclusion that they are not mission critical.

I’m almost sure they are in the way. When your site builds, it has to decide to copy over that index.html or generate one from your content file. Maybe. I noticed a lot of your content has those extra files. Definitely figure that out. :slight_smile:

1 Like

Ok–I will do some digging or see if Academic has its own support site that might be able to shine a light on the significance of those files.

Thank you!