[Bioc-devel] Installing RSQLite
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