swap `BiocInstaller` with `BiocManager`

[Arun Seetharam]

Looks like package BiocInstaller is not available (for R version 3.5.0) and it is superseded by BiocManager. Can this be changed so that the installer finds BiocManager and does not complain?

> install_github("arendsee/phylostratr")
Downloading GitHub repo arendsee/phylostratr@master
from URL https://api.github.com/repos/arendsee/phylostratr/zipball/master
Installing phylostratr
‘BiocInstaller’ must be installed for this functionality.
Would you like to install it?

1: Yes
2: No

Selection: 1
Installing package into ‘/opt/rit/spack-app/linux-rhel7-x86_64/gcc-4.8.5/r-rsqlite-2.0-zew7f5pkhdh6gk4qdv6hown4uf4zszsb/rlib/R/library’
(as ‘lib’ is unspecified)
Warning in install.packages(pkg) :
  'lib = "/opt/rit/spack-app/linux-rhel7-x86_64/gcc-4.8.5/r-rsqlite-2.0-zew7f5pkhdh6gk4qdv6hown4uf4zszsb/rlib/R/library"' is not writable
Would you like to use a personal library instead? (yes/No/cancel) yes
Error in loadNamespace(name) : there is no package called ‘BiocInstaller’
In addition: Warning message:
package ‘BiocInstaller’ is not available (for R version 3.5.0)

Thanks,

[Zebulun Arendsee]

This is actually an issue in devtools. You can get around it by manually installing Biostrings (the one Bioconductor package phylostratr uses).

install.packages("BiocManager")
BiocManager::install("Biostrings")

[Arun Seetharam]

No, that doesn't work for me. I installed it and loaded it, but it still goes through the same steps asking me to install BiocInstaller Not sure what to do.

[Zebulun Arendsee]

Is your devtools package up-to-date?

[Arun Seetharam]

Hi Zeb,

Here is my session info:

Packages -----------------------------------------------------------------------
 package      * version date       source
 BiocGenerics * 0.28.0  2018-10-30 Bioconductor
 BiocManager    1.30.4  2018-11-13 CRAN (R 3.5.0)
 Biostrings   * 2.50.2  2019-01-03 Bioconductor
 curl           3.0     2017-10-06 CRAN (R 3.5.0)
 devtools     * 1.12.0  2016-12-05 CRAN (R 3.5.0)
 digest         0.6.12  2017-01-27 CRAN (R 3.5.0)
 git2r          0.18.0  2017-01-01 CRAN (R 3.5.0)
 httr           1.3.1   2017-08-20 CRAN (R 3.5.0)
 IRanges      * 2.16.0  2018-10-30 Bioconductor
 memoise        1.1.0   2017-04-21 CRAN (R 3.5.0)
 R6             2.2.2   2017-06-17 CRAN (R 3.5.0)
 S4Vectors    * 0.20.1  2018-11-09 Bioconductor
 withr          1.0.2   2016-06-20 CRAN (R 3.5.0)
 XVector      * 0.22.0  2018-10-30 Bioconductor
 zlibbioc       1.28.0  2018-10-30 Bioconductor

Thanks,

[Zebulun Arendsee]

Yeah, that is pretty old, you might want to upgrade it. The current devtools package should be using the up-to-date function. I'm using version 2.0.1.

[Arun Seetharam]

Thanks, that helped! I'll close this issue now.
BTW, the taxizedb have additional dependencies and are really pain to install them on a cluster (sqlite/postgresql).

[Zebulun Arendsee]

Ah yeah, true about the taxizedb dependencies. sqlite is needed to hand the SQL database. But the other tricky dependencies are not. The taxizedb dependencies could probably be made optional. I'll see what I can do.

[Zebulun Arendsee]

@aseetharam Actually, I ran into the same dependency problem earlier. I solved it by modifying the taxizedb package, removing the need for the missing dependencies -- specifically RMariaDB and RPostgreSQL. You can install that version from arendsee/taxizedb. This is not a good long-term solution, though, since I am not maintaining that package.