Open eschen42 opened 2 years ago
Thanks for reopening. I will start looking into this soon. I believe we have a lot of issues that we ought to address in this feedstock, including missing perl files and stuff :(
i may also be tempted to build a fuller version of latex to deal with this...
@ngam Thank you for your help! Perhaps this is a duplicate of issue 19 except that I do not get the final line reported there:
I can't find the format file `latex.fmt'!
If it is a duplicate, then I am fine with it being closed.
For the moment I can work around this by knitting to HTML rather than PDF. Not ideal, but sufficient for the interim.
My workaround for this was not to use texlive-core
but rather use conda-forge/r-tinytex
, which requires running:
library(tinytex)
tinytex::install_tinytex()
before calling rmarkdown::render
.
That isn't exactly a "fix", but it got me un-blocked vis à vis creating a PDF.
Hi @ngam, any chance this bug will get a fix soon?
@Adamtaranto unfortunately, no. I tried pretty hard to fix this and I couldn't 😢
I saw your comments in the other issue. What's your use case? It seems the bioconda maintainers removed jcvi's dependency on this https://github.com/bioconda/bioconda-recipes/blob/f36f2790baaa4d895b59b000227c4954b6f1b82b/recipes/jcvi/meta.yaml#LL48-L50C20.
@ngam - I'm using the jcvi.graphics.synteny module to plot some figures, the issue seems to be that matplotlib insists on calling latex at some point and this can't be turned off. Many people seem to be running into this problem in #19
I've figured out that at least some of the missing scripts that are causing the issue are present in MacTex / other versions of Tex-Live but not the conda version.
"TeXLive/TLUtils.pm" is here in tlpkg
and mktexlsr.pl is in MacTex at /usr/local/texlive/2022/texmf-dist/scripts/texlive/mktexlsr.pl
Can you please include the missing files in the conda recipe for texlive-core?
Issue:
Can't locate mktexlsr.pl in @INC
In issue 42, @ngam indicated that this is a separate issue from that issue. That issue shows that my efforts to resolve my issue have come to naught.
Context:
Rscript cmd_anova.R
Snippet from
cmd_anova.R
:Tail of output:
Environment (
conda list
):Details about
conda
and system (conda info
):