Error building github version of phyloseq from source

[CarlyMuletzWolz]

When I try to update phyloseq to the github version (the version with all latest updates) I get an error. Here are my command lines:

source("http://bioconductor.org/biocLite.R")
biocLite("phyloseq")
install.packages("devtools")
library("devtools")
install_github("phyloseq", "joey711")

All work until I get to the install_github command. I get the error message below

install_github("phyloseq", "joey711")

Installing github repo(s) phyloseq/master from joey711
Installing phyloseq.zip from https://api.github.com/repos/joey711/phyloseq/zipball/master
Installing phyloseq
/Library/Frameworks/R.framework/Resources/bin/R --vanilla CMD build
'/private/var/folders/dg/clpwjnzx45v0b0t6r1v3ytsm0000gq/T/Rtmpr4n5et/joey711-phyloseq-e34e8aa'
--no-manual --no-resave-data

• checking for file '/private/var/folders/dg/clpwjnzx45v0b0t6r1v3ytsm0000gq/T/Rtmpr4n5et/joey711-phyloseq-e34e8aa/DESCRIPTION' ... OK
• preparing 'phyloseq':
• checking DESCRIPTION meta-information ... OK
• installing the package to re-build vignettes
• creating vignettes ... ERROR
  Loading required package: ade4

Attaching package: 'ade4'

The following object(s) are masked from 'package:base':

within

Loading required package: picante
Loading required package: ape
Loading required package: vegan
Loading required package: permute
This is vegan 2.0-5

Attaching package: 'vegan'

The following object(s) are masked from 'package:ade4':

cca

Loading required package: nlme
Warning: "legend" argument in scale_XXX is deprecated. Use guide="none" for suppress the guide display. (Deprecated; last used in version 0.8.9)
Warning: "legend" argument in scale_XXX is deprecated. Use guide="none" for suppress the guide display. (Deprecated; last used in version 0.8.9)
Warning: "legend" argument in scale_XXX is deprecated. Use guide="none" for suppress the guide display. (Deprecated; last used in version 0.8.9)
Loading required package: plyr

Attaching package: 'reshape'

The following object(s) are masked from 'package:plyr':

rename, round_any

Warning: "legend" argument in scale_XXX is deprecated. Use guide="none" for suppress the guide display. (Deprecated; last used in version 0.8.9)
Warning: Removed 1 rows containing missing values (geom_text).
Warning: Removed 1 rows containing missing values (geom_text).
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
Running 'texi2dvi' on 'phyloseq_analysis.tex' failed.
Calls: -> texi2pdf -> texi2dvi
Execution halted
Error: Command failed (1)

[CarlyMuletzWolz]

I posted this at the end of another issue and have added as a new issue upon recommendation from joey711.

Here was his response:

Looks like your system doesn't have a working version of latex, so it fails to rebuild the vignettes during installation. I'm not sure why R packages have to do that by default when building from source. The PDF files for the vignettes are already included, and it looks like your installation would otherwise work.

You have two clear options off the top of my head.

(1) One is to install LaTeX on your mac and try again. I think MacTeX is pretty easy for installation.

(2) Another is to use one of the more obscure options from the installation tutorial that I actually just posted yesterday, in which you attempt to install the mac binary version of the package form the development branch on Bioconductor, which I just updated yesterday so at the moment I pen this it is identical to the GitHub version, and the precise URL for the binary is still correct. You have already done the first part of these instructions: installing the dependencies by first installing the release version of phyloseq. Now just try the following lines of code. If it doesn't work then there is something wrong with the mac binary built by Bioconductor on the devel branch, and there's not much I can do about it.

temp <- tempfile()
macURL = "http://bioconductor.org/packages/devel/bioc/bin/macosx/leopard/contrib/2.16/phyloseq_1.3.11.tgz"
download.file(macURL, temp)
install.packages(temp, repos = NULL, type = "mac.binary.leopard")

(3) If the above two things don't work, post what happened, and I will build a binary on my mac and post it in the downloads section.

[CarlyMuletzWolz]

I installed MacTeX at http://tug.org/mactex/ and then the newest phyloseq was available to me!

[joey711]

Great! I will add to the installation tutorial how LaTeX is a necessary requirement for installing from source...

I'm glad that it is working for you! I will close this issue once I've added the additional notes to the installation tutorial.

[joey711]

This is now mentioned on the installation tutorial, so this issue is now closed.