[R] Updating RSQLite fails

[Milan Bouchet-Valat]

Le vendredi 11 octobre 2013 à 18:49 +0200, Thibault Helleputte a écrit :
> Hello,
> 
> Working on an ubuntu 13.04 with a sessionInfo() specified below, I try to
> update my packages, and RSQLite update consistently fails like this:
> 
> > update.packages(checkBuilt=TRUE, ask=FALSE)
> Warning: package 'RUnit' in library '/usr/lib/R/site-library' will not be
> updated
> trying URL 'http://cran.rstudio.com/src/contrib/RSQLite_0.11.4.tar.gz'
> Content type 'application/x-gzip' length 1599919 bytes (1.5 Mb)
> opened URL
> ==================================================
> downloaded 1.5 Mb
> 
> * installing *source* package RSQLite ...
> ** package RSQLite successfully unpacked and MD5 sums checked
> 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 ISO C89... 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 ISO C89... (cached) none needed
> checking for library containing fdatasync... none required
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DRSQLITE_USE_BUNDLED_SQLITE
> -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS
> -DSQLITE_SOUNDEX -DSQLITE_MAX_VARIABLE_NUMBER=40000
> -DSQLITE_MAX_COLUMN=30000 -DTHREADSAFE=0     -fpic  -O3 -pipe  -g  -c
> RS-DBI.c -o RS-DBI.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DRSQLITE_USE_BUNDLED_SQLITE
> -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS
> -DSQLITE_SOUNDEX -DSQLITE_MAX_VARIABLE_NUMBER=40000
> -DSQLITE_MAX_COLUMN=30000 -DTHREADSAFE=0     -fpic  -O3 -pipe  -g  -c
> RS-SQLite.c -o RS-SQLite.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DRSQLITE_USE_BUNDLED_SQLITE
> -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS
> -DSQLITE_SOUNDEX -DSQLITE_MAX_VARIABLE_NUMBER=40000
> -DSQLITE_MAX_COLUMN=30000 -DTHREADSAFE=0     -fpic  -O3 -pipe  -g  -c
> param_binding.c -o param_binding.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DRSQLITE_USE_BUNDLED_SQLITE
> -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS
> -DSQLITE_SOUNDEX -DSQLITE_MAX_VARIABLE_NUMBER=40000
> -DSQLITE_MAX_COLUMN=30000 -DTHREADSAFE=0     -fpic  -O3 -pipe  -g  -c
> sqlite-all.c -o sqlite-all.o
> sqlite-all.c:1:35: warning: extra tokens at end of #ifdef directive
> [enabled by default]
> gcc: internal compiler error: Killed (program cc1)
> Please submit a full bug report,
> with preprocessed source if appropriate.
> See <file:///usr/share/doc/gcc-4.7/README.Bugs> for instructions.
I think you should do what the error message suggests: report this to
gcc developers, giving them a link to the package source and
instructions to reproduce the problem. This is clearly not a bug in R.

Now, if you want to work around this, maybe you should try to find a
newer or older version of gcc for your distribution. If you have enabled
testing updates repository, go back to the tested ones.


Regards

> make: *** [sqlite-all.o] Error 4
> ubuntu at ip-10-226-133-215:~$ ERROR: compilation failed for package RSQLite
> * removing /usr/lib/R/site-library/RSQLite
> * restoring previous /usr/lib/R/site-library/RSQLite
> 
> 
> SESSION INFO:
> 
> > sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-pc-linux-gnu (64-bit)
> 
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> 
> I tried also to install RSQLite via r-cran-rsqlite, but the it installs me
> the 0.11.1 instead of 0.11.4.
> 
> Any idea of how to get things right?
> 
> Thx
> 
> 
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