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

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?


NOTICE
Please consider the environment before printing this email. This message and any attachments are intended for the addressee named and may contain legally privileged/confidential/copyright information. If you are not the intended recipient, you should not read, use, disclose, copy or distribute this communication. If you have received this message in error please notify us at once by return email and then delete both messages. We accept no liability for the distribution of viruses or similar in electronic communications. This notice should not be removed.

        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel


NOTICE
Please consider the environment before printing this email. This message and any attachments are intended for the addressee named and may contain legally privileged/confidential/copyright information. If you are not the intended recipient, you should not read, use, disclose, copy or distribute this communication. If you have received this message in error please notify us at once by return email and then delete both messages. We accept no liability for the distribution of viruses or similar in electronic communications. This notice should not be removed.

	[[alternative HTML version deleted]]

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

This email message may contain legally privileged and/or...{{dropped:2}}

Hello,

That contradicts the instructions on the sleuth Download page. It contains the R commands

biocLite("rhdf5")
and
devtools::install_github("pachterlab/sleuth")

You may have read the instructions too quickly and mixed the arguments up.

Bioconductor requires lots of function documentation with runnable examples and a vignette. Sleuth isn't currently at the R package quality level necessary for Bioconductor.

--------------------------------------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia