Hi,

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:

>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'

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:

>x = "--with-sqlite-dir=~/src/sftwre/sqlite_bld/"
>install.packages ("RSQLite", type="source", configure.args = x)

trying URL ' http://cran.fhcrc.org/src/contrib/RSQLite_0.4-19.tar.gz'
Content type 'application/x-gzip' length 3064252 bytes
opened URL
==================================================
downloaded 2992Kb

* Installing *source* package 'RSQLite' ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for gcc... (cached) gcc -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -std=gnu99 accepts -g... (cached) yes
checking for gcc -std=gnu99 option to accept ANSI C... (cached) none needed
configure: error: dir ~/src/sftwre/sqlite_bld/ does not exist


Now I know that the directory exists, but I am obviously entering it
incorrectly. Is there any suggestions? I tried reading all the documentation
but they don't seem to elucidate the situation for me.

> sessionInfo()
R version 2.5.0 Under development (unstable) (2007-02-07 r40669)
i386-apple-darwin8.8.2

locale:
C

attached base packages:
[1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"
[7] "base"


Thanks,
--Tony

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