Devtools: Check Bioconductor dependencies when running install_github?
Hi,
I am trying to run install_github to install an R package hosted on Github. This package has a dependency package that is hosted on Bioconductor but not hosted on CRAN. It seems that install_github will not automatically detect the Bioconductor dependencies so the installation just fails because install_github can not find the denpendency package on CRAN. Now I have to install the Bioconductor package first and then install the Github package. This makes the installation process tedious and frustrated for other users. Is there a way that install_github can also detect the package dependencies on Bioconductor?
zji90
All 12 comments
This works fine for me; can you please provide a reproducible example of when it's not working for you?
Does the following work for you?
devtools::install_github('PeteHaitch/BioCpkgA')
It should install a toy package BioCpkgA whose only dependency is GenomicTuples, which is available via Bioconductor and not CRAN.
# My sesion info
devtools::session_info()
Session info ---------------------------------------------------------------------
setting value
version R version 3.1.2 (2014-10-31)
system x86_64, darwin10.8.0
ui RStudio (0.99.234)
language (EN)
collate en_AU.UTF-8
tz Australia/Melbourne
Packages -------------------------------------------------------------------------
package * version date source
Biobase * 2.26.0 2014-10-14 Bioconductor
BiocGenerics * 0.12.1 2014-11-14 Bioconductor
BioCpkgA 0.1 2015-03-02 Github (PeteHaitch/BioCpkgA@26d12ba)
bitops * 1.0-6 2013-08-17 CRAN (R 3.1.0)
devtools * 1.7.0 2015-01-17 CRAN (R 3.1.2)
GenomeInfoDb * 1.2.4 2014-12-19 Bioconductor
GenomicRanges * 1.18.4 2015-01-07 Bioconductor
GenomicTuples * 1.0.0 2014-10-14 Bioconductor
httr * 0.6.1 2015-01-01 CRAN (R 3.1.2)
IRanges * 2.0.1 2014-12-12 Bioconductor
packrat * 0.4.3 2015-01-29 CRAN (R 3.1.2)
Rcpp * 0.11.4 2015-01-24 CRAN (R 3.1.2)
RCurl * 1.95-4.5 2014-12-06 CRAN (R 3.1.2)
rstudioapi * 0.2 2014-12-31 CRAN (R 3.1.2)
S4Vectors * 0.4.0 2014-10-14 Bioconductor
stringr * 0.6.2 2012-12-06 CRAN (R 3.1.0)
XVector * 0.6.0 2014-10-14 Bioconductor
PeteHaitch
on 2 Mar 2015
This example does not work for me:
devtools::install_github('PeteHaitch/BioCpkgA')
Downloading github repo PeteHaitch/BioCpkgA@master
Installing BioCpkgA
Installing dependencies for BioCpkgA:
GenomicTuples
Installing package into ‘/home/nsheffield/R’
(as ‘lib’ is unspecified)
'/usr/lib/R/bin/R' --vanilla CMD INSTALL \
'/tmp/Rtmp6GpfdN/devtools194d288e6252/PeteHaitch-BioCpkgA-26d12ba' \
--library='/home/nsheffield/R' --install-tests
ERROR: dependency ‘GenomicTuples’ is not available for package ‘BioCpkgA’
* removing ‘/home/nsheffield/R/BioCpkgA’
If I first install GenomicTuples, then it works:
devtools::install_github('PeteHaitch/BioCpkgA')
Downloading github repo PeteHaitch/BioCpkgA@master
Installing BioCpkgA
'/usr/lib/R/bin/R' --vanilla CMD INSTALL \
'/tmp/Rtmp6GpfdN/devtools194d690d04ab/PeteHaitch-BioCpkgA-26d12ba' \
--library='/home/nsheffield/R' --install-tests
* installing *source* package ‘BioCpkgA’ ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (BioCpkgA)
Here is a package of mine with the same issue: https://github.com/sheffien/LOLA
It will not download and install IRanges, for example.
devtools::session_info()
Session info -------------------------------------------------------------------
setting value
version R version 3.2.0 (2015-04-16)
system x86_64, linux-gnu
ui X11
language en_US
collate en_US.UTF-8
tz <NA>
Packages -----------------------------------------------------------------------
package * version date source
BiocInstaller 1.19.3 2015-04-21 Bioconductor
bitops * 1.0-6 2013-08-17 CRAN (R 3.2.0)
devtools * 1.7.0 2015-01-17 CRAN (R 3.2.0)
httr * 0.6.1 2015-01-01 CRAN (R 3.2.0)
RCurl * 1.95-4.5 2014-12-28 CRAN (R 3.2.0)
rstudioapi * 0.3.1 2015-04-07 CRAN (R 3.2.0)
stringr * 0.6.2 2012-12-06 CRAN (R 3.2.0)
nsheff
on 21 Apr 2015
Hmm, yes there does seem to be a problem. I just tried on a fresh installation of R 3.2 and confirmed that devtools::install_github('PeteHaitch/BioCpkgA') doesn't work unless GenomicTuples is first installed via
source("http://bioconductor.org/biocLite.R")
biocLite("GenomicTuples")
or BiocInstaller::biocLite('GenomicTuples') (if BiocInstaller is already installed).
I thought this used to work (i.e., in R 3.1), but I may be mistaken.
I won't have time to look into this until next week at the earliest, possibly the following week.
# Session info with BioC release
> devtools::session_info()
Session info ---------------------------------------------------------------------
setting value
version R version 3.2.0 (2015-04-16)
system x86_64, darwin13.4.0
ui RStudio (0.99.235)
language (EN)
collate en_AU.UTF-8
tz Australia/Melbourne
Packages -------------------------------------------------------------------------
package * version date source
BiocInstaller 1.18.1 2015-04-17 Bioconductor
bitops * 1.0-6 2013-08-17 CRAN (R 3.2.0)
devtools * 1.7.0 2015-01-17 CRAN (R 3.2.0)
httr * 0.6.1 2015-01-01 CRAN (R 3.2.0)
RCurl * 1.95-4.5 2014-12-28 CRAN (R 3.2.0)
rstudioapi * 0.3.1 2015-04-07 CRAN (R 3.2.0)
stringr * 0.6.2 2012-12-06 CRAN (R 3.2.0)
# Session info with BioC devel, i.e., following BiocInstaller::useDevel(TRUE)
> devtools::session_info()
Session info ---------------------------------------------------------------------
setting value
version R version 3.2.0 (2015-04-16)
system x86_64, darwin13.4.0
ui RStudio (0.99.235)
language (EN)
collate en_AU.UTF-8
tz Australia/Melbourne
Packages -------------------------------------------------------------------------
package * version date source
BiocInstaller 1.19.3 2015-04-20 Bioconductor
bitops * 1.0-6 2013-08-17 CRAN (R 3.2.0)
devtools * 1.7.0 2015-01-17 CRAN (R 3.2.0)
httr * 0.6.1 2015-01-01 CRAN (R 3.2.0)
RCurl * 1.95-4.5 2014-12-28 CRAN (R 3.2.0)
rstudioapi * 0.3.1 2015-04-07 CRAN (R 3.2.0)
stringr * 0.6.2 2012-12-06 CRAN (R 3.2.0)
Unfortunately I think this is just the reality of relying on bioconductor packages. If anyone has bright ideas about how to make it a bit better, I'd be happy to review a PR.
hadley
on 21 Apr 2015
This is indeed a pity, now the installation instructions for a package of mine ("lamortenera/epicseg") have become more tedious and might scare users.
Maybe that's a very naive and stupid idea, but what argues against providing a flag for allowing installation from Bioconductor? Something like the bioc_required option provided by R-travis?
I guess this could be implemented by installing every dependency with
source("http://bioconductor.org/biocLite.R")
biocLite("pkgname")
instead of
install.packages("pkgname")
That said, devtools is still an awesome package and thanks so much for it.
lamortenera
on 15 Jun 2015
Or is it possible to add the list of bioconductor repos as a repos source in package_deps??
http://bioconductor.org/packages/release/bioc/
http://bioconductor.org/packages/release/data/annotation
http://bioconductor.org/packages/release/data/experiment
http://bioconductor.org/packages/release/extra
These will return the list of available packages using available_packages, just checked on R 3.2.0 and devtools 1.8.0
rmflight
on 15 Jun 2015
This is awesome! My bad that I didn't see it.
Thanks so much!
lamortenera
on 15 Jun 2015
But it looks like there would need to be a pull request to add these to the package_deps function before they would be useful in install_github??
rmflight
on 15 Jun 2015
Ah right, I celebrated too early. I thought that the ... in install_github were used in install, which has also some ... used in install.packages, which has option repos. But this is not working :(
lamortenera
on 15 Jun 2015
One way to make devtools install dependencies from Bioconductor is like this:
# Install a cool package
devtools::install_github(repo="Bioconductor-mirror/CoolPkg1")
# Human: Error: CoolPkg1 require SomePkgA version x.10.10 ; only SomePkgA version x.9.9 is installed.
# Machine: Look for SomePkgA on gitbub?
# Human: Yes
# Machine: From which github users?
# [1] Bioconductor-mirror
# [2] Bioconductor-mirror (use as default)
# Human: Answer: 2
# Machine: Ok, now I will try to install required dependencies from this github user: Bioconductor-mirror
# Machine: Just sit back and relax.
# Mahcine: But beware that you will get all the risk of using unstable versions of packages.
# Human: What?!!! Ok, could you please roll back?
# Machine: No, it's too late. Joking :-)
# Human: Phew!
# Machine: Rolling back ....
Continued...
# Machine: You know what, maybe you don't need this install_github() at all.
# Machine: To install Bioconductor development versions of packages
# Machine: Just run this:
source("http://bioconductor.org/biocLite.R")
BiocInstaller::useDevel()
biocLite("CoolPkg1")
# Human: Cool. What if things mess up so bad and I want to revert to stable version.
# Machine: No problem, do this:
# Quit current R session and open a new one
source("http://bioconductor.org/biocLite.R")
pkgs <- rownames(installed.packages())
BiocInstaller::useDevel(FALSE)
biocLite(pkgs) # this could take hours to finish.
biocyberman
on 6 Aug 2015
There is a trick for this: add biocViews: to the package's DESCRIPTION and R will know to search the bioconductor repository automatically for package requirements. This trick is not documented anywhere.
ck37
on 26 Jul 2016
This old issue has been automatically locked. If you believe you have found a related problem, please file a new issue (with reprex) and link to this issue. https://reprex.tidyverse.org/
![lock[bot] picture](https://avatars.githubusercontent.com/in/6672?v=4&s=40)
lock[bot]
on 18 Sep 2018
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Most helpful comment
There is a trick for this: add
biocViews:to the package's DESCRIPTION and R will know to search the bioconductor repository automatically for package requirements. This trick is not documented anywhere.