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

Marc Carlson mcarlson at fhcrc.org
Fri Jul 9 00:37:54 CEST 2010

Hi Auke,

The installer should place the contents of "inst/extdata" into "extdata"
of your installed library, but that is about it.  There *IS* a
dependency however that is logged in the DESCRIPTION file.  Each chip
package requires that an "org" package be installed in order for it to
work.  So for example, this package "zebrafish.db_2.4.1.tar.gz "
requires the "org.Dr.eg.db".  And the message below seems to be
complaining that the database in "org.Dr.eg.db" is not available.  It
does not need to write to this DB, but it does need to be able to read
it.  Did you install the org packages and other dependencies 1st?

Also is there a specific reason why is biocLite() is not your preferred
way to install bioconductor packages?  It handles all of these issues
for you and installs requested packages (and resolves dependencies).



On 07/08/2010 02:37 PM, Auke Booij wrote:
> 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

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