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statnet / networkDynamic

Dynamic Extensions for Network Objects
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GH R CMD check trips on Rnw vignette #20

Closed mbojan closed 11 months ago

mbojan commented 1 year ago

The GH workflow checking the package needs to be modified to process Rnw vignette as it now trips because of missing LaTeX packages (supposedly).

martinamorris commented 1 year ago

thx for working on this @mbojan

skyebend commented 11 months ago 
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘.../DESCRIPTION’ ... OK
* preparing ‘networkDynamic’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
Error: --- re-building ‘networkDynamic.Rnw’ using Sweave
Loading required package: network
‘network’ 1.18.1 (2023-01-24), part of the Statnet Project
* ‘news(package="network")’ for changes since last version
* ‘citation("network")’ for citation information
* ‘[https://statnet.org’](https://statnet.xn--org-to0a/) for help, support, and other information
‘networkDynamic’ 0.11.3 (2023-02-15), part of the Statnet Project
* ‘news(package="networkDynamic")’ for changes since last version
* ‘citation("networkDynamic")’ for citation information
* ‘[https://statnet.org’](https://statnet.xn--org-to0a/) for help, support, and other information
trying URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/esna/Sampson.zip'
Content type 'application/zip' length 2182 bytes
==================================================
downloaded 2182 bytes
Warning in get.vertex.attribute.active(net, "happiness", onset = 2.5, terminus = 4.5) :
  Multiple attribute values matched query spell for attribute happiness.active on some vertices. Only earliest value used
Error: Error: processing vignette 'networkDynamic.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'networkDynamic.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *> 

l.6 \usepackage
               {color}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘networkDynamic.Rnw’
SUMMARY: processing the following file failed:
  ‘networkDynamic.Rnw’
Error: Error: Vignette re-building failed.
Execution halted
Error: Error in proc$get_built_file() : Build process failed
Calls: <Anonymous> ... build_package -> with_envvar -> force -> <Anonymous>
Execution halted
Error: Process completed with exit code 1.
mbojan commented 11 months ago

While we're at it, does it actually make sense to convert the vignette to Rmd in HTML rather than fix the workflow? I think HTMLs are quicker to process and also viewable/browsable within RStudio. If so, I'll save these here for reference:

martinamorris commented 11 months ago

While we're at it, does it actually make sense to convert the vignette to Rmd in HTML rather than fix the workflow? I think HTMLs are quicker to process and also viewable/browsable within RStudio.

I would support this (and be happy to help work on it if it's a big chore)

On Tue, Dec 5, 2023 at 11:12 AM Michał Bojanowski @.***> wrote:

While we're at it, does it actually make sense to convert the vignette to Rmd in HTML rather than fix the workflow? I think HTMLs are quicker to process and also viewable/browsable within RStudio.

— Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/statnet/networkDynamic/issues/20*issuecomment-1841461646__;Iw!!K-Hz7m0Vt54!hNv2UZFF99Vc3Y95hO36JAOySoJuKB-cs5Q6MydEjouIBc8ZgRQwNZzaom2HYtxW9csc4gKYWPQLtmjitgARBG0$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AB6QTYXZPXOUL7KT7PWZ6WDYH5WYPAVCNFSM6AAAAAA7O6JNVWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBRGQ3DCNRUGY__;!!K-Hz7m0Vt54!hNv2UZFF99Vc3Y95hO36JAOySoJuKB-cs5Q6MydEjouIBc8ZgRQwNZzaom2HYtxW9csc4gKYWPQLtmjipaupbV8$ . You are receiving this because you commented.Message ID: @.***>

krivit commented 11 months ago

I use a custom R-CMD-check that tries to take care of those things. Let me try it in a branch.

krivit commented 11 months ago

Seems to work; and also provide code coverage as a bonus.

krivit commented 11 months ago

I.e., https://app.codecov.io/github/statnet/networkDynamic/tree/R-CMD-check-test .

martinamorris commented 11 months ago

Neato! Thx Pavel :)

On Wed, Dec 6, 2023 at 4:02 PM Pavel N. Krivitsky @.***> wrote:

I.e., https://app.codecov.io/github/statnet/networkDynamic/tree/R-CMD-check-test https://urldefense.com/v3/__https://app.codecov.io/github/statnet/networkDynamic/tree/R-CMD-check-test__;!!K-Hz7m0Vt54!kC1vdXFlNzbGl9iWZN3YXeXqdJGxYzg9EDDXbcFREQf2fmsGUlKU1Sm31HKco8E7i8zy-XVILO-uPWrcMMGuviQ$ .

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