[Bioc-devel] Installation process for affymetrix databases (*.db packages)

[Auke Booij]

On Thu, Jul 8, 2010 at 10:21 PM, Marc Carlson <mcarlson at fhcrc.org> wrote:
> Why is it that you think these packages are writing to these SQLite
> databases?  They should not be doing so.  Their purpose is only to be
> annotation packages and they make use of a relational database simply to
> represent biological data.

Hm, perhaps it's not really writing, but requesting write permissions
nonetheless? I'm searching through the code to figure out what's
happening, but it seems at some point the R CMD INSTALL I'm starting
as part of the sandboxed install process tries to load some libraries
which try to write to sqlite libraries... partial output below. Does
any of this ring a bell?


R CMD INSTALL --build /usr/portage/distfiles/zebrafish.db_2.4.1.tar.gz
-l /var/tmp/paludis/dev-R-zebrafishdb-2.4.1/work/tmp_install
* installing *source* package 'zebrafish.db' ...
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: DBI
ACCESS DENIED  open_wr:
/usr/lib64/R/library/org.Dr.eg.db/extdata/org.Dr.eg.sqlite
ISE:write_logfile unable to append logfile
ISE open_wr(/usr/lib64/R/library/org.Dr.eg.db/extdata/org.Dr.eg.sqlite):
Permission denied
	abs_path: /usr/lib64/R/library/org.Dr.eg.db/extdata/org.Dr.eg.sqlite
	res_path: /usr/lib64/R/library/org.Dr.eg.db/extdata/org.Dr.eg.sqlite
/usr/lib/libsandbox.so(+0x3709)[0x7ffdc4cf5709]
/usr/lib/libsandbox.so(+0x379b)[0x7ffdc4cf579b]
/usr/lib/libsandbox.so(+0x4bd1)[0x7ffdc4cf6bd1]
/usr/lib/libsandbox.so(open64+0xc7)[0x7ffdc4cfa687]
/usr/lib64/R/library/RSQLite/libs/RSQLite.so(+0x427e6)[0x7ffdbf8797e6]
/usr/lib64/R/library/RSQLite/libs/RSQLite.so(+0x43850)[0x7ffdbf87a850]
/usr/lib64/R/library/RSQLite/libs/RSQLite.so(+0x44257)[0x7ffdbf87b257]
/usr/lib64/R/library/RSQLite/libs/RSQLite.so(RS_SQLite_newConnection+0x109)[0x7ffdbf8482a5]
/usr/lib64/R/lib/libR.so(+0x95763)[0x7ffdc488f763]
/usr/lib64/R/lib/libR.so(Rf_eval+0x76e)[0x7ffdc48b6585]
/proc/12572/cmdline: /usr/lib64/R/bin/exec/R --no-restore --slave
--args nextArg--buildnextArg/usr/portage/distfiles/zebrafish.db_2.4.1.tar.gznextArg-lnextArg/var/tmp/paludis/dev-R-zebrafishdb-2.4.1/work/tmp_install