[Bioc-devel] Why sleuth is not in Bioconductor?

[Martin Morgan]

On 09/14/2016 06:54 AM, Ted Wong wrote:
> Thanks Vincent,
>
> I tried to install it with Bioconductor (described on their Github) before starting the question, but it was broken (at least for me). The command I tried was:
>
> biocLite("pachterlab/sleuth")

This is not a question about package development, so should be posted to 
the support site https://support.bioconductor.org. Nonetheless, 
biocLite() will recognize this as a github repository and will use 
devtools::install_github(). If you are having problems, then it is 
necessary to provide information about what your problem is, e.g., by 
copying and pasting the result of running biocLite() into your email, 
along with information about your R installation. I have

 > biocLite("pachterlab/sleuth")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.23.9), R 3.3.1 Patched (2016-09-07
   r71225).
Installing github package(s) 'pachterlab/sleuth'
Downloading GitHub repo pachterlab/sleuth at master
from URL https://api.github.com/repos/pachterlab/sleuth/zipball/master
Installing sleuth
'/home/mtmorgan/bin/R-3-3-branch/bin/R' --no-site-file --no-environ 
--no-save  \
   --no-restore --quiet CMD INSTALL  \
   '/tmp/RtmpxvzkWy/devtools284d59360fae/pachterlab-sleuth-048f055'  \
   --library='/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.3-Bioc-3.4'  \
   --install-tests

* installing *source* package ‘sleuth’ ...
** R
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
    ‘intro.Rmd’ using ‘UTF-8’
** testing if installed package can be loaded
* DONE (sleuth)
 > sessionInfo()
R version 3.3.1 Patched (2016-09-07 r71225)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BiocInstaller_1.23.9

loaded via a namespace (and not attached):
  [1] httr_1.2.1      R6_2.1.3        tools_3.3.1     withr_1.0.2
  [5] curl_1.2        memoise_1.0.0   knitr_1.14      git2r_0.15.0
  [9] digest_0.6.10   devtools_1.12.0


>
> I'll try to install directly from Github.
>
>
>
>
>
>
>
> On Wed, Sep 14, 2016 at 8:37 PM, Vincent Carey <stvjc at channing.harvard.edu<mailto:stvjc at channing.harvard.edu>> wrote:
> http://pachterlab.github.io/sleuth/download
>
>
>
> On Wed, Sep 14, 2016 at 6:20 AM, Ted Wong <t.wong at garvan.org.au<mailto:t.wong at garvan.org.au>> wrote:
> Dear all,
>
> I thought Sleuth (https://github.com/pachterlab/sleuth) is part of the Bioconductor. But I'm not able to find it anywhere.
>
> What's the status of the package?
>
>
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