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bvieth / powsimR

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.
https://bvieth.github.io/powsimR/
Artistic License 2.0
103 stars 23 forks source link

Installing on macOS #13

Closed swvanderlaan closed 6 years ago

swvanderlaan commented 6 years ago

Hi,

Maybe this is not really an issue, rather a bug?

I've installed R via home-brew. And now I wanted to install the powsimR package. All in all, not an issue (on R-3.4.2), except for the PDF creation of the vignettes. Apparently one needs LaTeX for that. So to make it work I did this:

step 1

I made sure home-brew is up-to-date.

step 2

I installed a basic LaTeX package; following these instructions: https://tex.stackexchange.com/a/319572.

brew cask install basictex

step 3

I rebooted.

step 4

I updated tlmgr and after that install titling as root

sudo tlmgr update --self
sudo tlmgr install titling

step 5

It's recommended to also install the recommended font-collection.

sudo tlmgr install collection-fontsrecommended

step 6

I try to install powsimR:

devtools::install_github('bvieth/powsimR', build_vignettes = TRUE, dependencies = FALSE)

But now I get this message:

devtools::install_github('bvieth/powsimR', build_vignettes = TRUE, dependencies = FALSE)
Downloading GitHub repo bvieth/powsimR@master
from URL https://api.github.com/repos/bvieth/powsimR/zipball/master
Installing powsimR
'/usr/local/Cellar/r/3.4.3_1/lib/R/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD build  \
  '/private/var/folders/kh/0s66cjl5487fg_fhwgxqd2340000gn/T/RtmpIQ11b5/devtools5b223199244/bvieth-powsimR-0e31927'  \
  --no-resave-data --no-manual

* checking for file ‘/private/var/folders/kh/0s66cjl5487fg_fhwgxqd2340000gn/T/RtmpIQ11b5/devtools5b223199244/bvieth-powsimR-0e31927/DESCRIPTION’ ... OK
* preparing ‘powsimR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
  Running 'texi2dvi' on 'powsimR.tex' failed.
LaTeX errors:
! LaTeX Error: File `beramono.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Calls: <Anonymous> -> texi2pdf -> texi2dvi
Execution halted
Installation failed: Command failed (1)

Hope you have a solution? I know, building the vignettes is not strictly needed...nonetheless... :-)

Best,

Sander

cziegenhain commented 6 years ago

Hey Sander,

I'm using powsimR on my Mac but haven't tried building vignettes myself. It seems your basic Latex installation doesn't contain the right packages. Maybe you should give MacTex a go, as far as I know thats a pretty comprehensive Latex distribution.

Good luck,

Christoph