[Bioc-devel] Installing RSQLite

[Seth Falcon]

Hi Tony,

"Tony Chiang" <tchiang at fhcrc.org> writes:
> I am trying to install bioconductor on a new intel mac, but seem to be
> failing. I believe that a new
> package, RSQLite, now comes with the R-devel...cool. I try to use the
> command:

Eh?  Maybe you mean that Sqlite is included with the RSQLite package?

>>biocLite("RSQLite", source="type")
                      ^^^^^^^^^^^^^

                            ?


> to which I get the error:
>
> SQLite installation failed.
>
> INSTRUCTIONS:
>
>   1. You need to install SQLite manually.   For details,
>      consult the web site http://www.sqlite.org
>
>   2. After installing SQLite, re-run R CMD INSTALL, specifying
>      the location of the SQLite directories, e.g.,
>
>      R CMD INSTALL --configure-args=--with-sqlite-dir=<DIR> ...
>
>      or set PKG_LIBS and PKG_CPPFLAGS, as described in
>      R help(INSTALL).
>
> ERROR: configuration failed for package 'RSQLite'
> ** Removing '/Users/tonychiang/arch/i386/R-devel/library/RSQLite'

The real error might have been report above where you copy/pasted.  I
would be curious to see that because my experience has been that
RSQLite Just Works when installing from source.

> So I consult the website and install SQLite from source. Good. Now, the
> Error
> Instructions tell how to install this package using R CMD INSTALL with the
> --configure-args. There ain't nothing like that for biocLite. Okay, I recall
>
> Herve saying that biocLite is just a wrapper for install.packages (), so a
> look at the man page for install.packages shows that there is a
> configure.args parameter.  So I  do the following:

Nice :-)

>>x = "--with-sqlite-dir=~/src/sftwre/sqlite_bld/"

I suspect that the configure script does not do "~" expansion.  Using
an absolute path should help.

But RSQLite should have been ok to just build from source.
Can you try again with biocLite("RSQLite", type="source") and send me
(off list) the entire output.

+ seth