Question: Problems with RSQLite compilation
gravatar for conkline
19 months ago by
conkline0 wrote:


attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:

[1] BiocInstaller_1.24.0

loaded via a namespace (and not attached):

[1] tools_3.3.2


Hello - I'm new to Bioconductor and am having issues getting BiocLite up and running; every time I try I get a "fatal error" telling me I'm missing a header file for RSQlite. Any thoughts? I'm running Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31). biocValid() returns [1] TRUE. 


> biocLite("RSQLite")


Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).

Installing package(s) ‘RSQLite’

trying URL ''

Content type 'application/x-gzip' length 2108699 bytes (2.0 MB)


downloaded 2.0 MB

* installing *source* package ‘RSQLite’ ...

** package ‘RSQLite’ successfully unpacked and MD5 sums checked

** libs

Makevars:21: Makevars.local: No such file or directory

touch "Makevars.local"

clang++ -I/usr/local/Cellar/r/3.3.2/R.framework/Resources/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_SOUNDEX -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -I"/usr/local/lib/R/3.3/site-library/Rcpp/include" -I"/usr/local/lib/R/3.3/site-library/BH/include" -I"/usr/local/lib/R/3.3/site-library/plogr/include"   -fPIC  -g -O2  -c RcppExports.cpp -o RcppExports.o

In file included from RcppExports.cpp:4:

In file included from ./RSQLite_types.h:4:

./RSQLite.h:9:12: fatal error: 'Rcpp.h' file not found

  #include <Rcpp.h>


1 error generated.

make: *** [RcppExports.o] Error 1

ERROR: compilation failed for package ‘RSQLite’

* removing ‘/usr/local/lib/R/3.3/site-library/RSQLite’

The downloaded source packages are in


Warning message:

In install.packages(pkgs = doing, lib = lib, ...) :

  installation of package ‘RSQLite’ had non-zero exit status
ADD COMMENTlink modified 19 months ago by Martin Morgan ♦♦ 22k • written 19 months ago by conkline0

RSQLite is not in Bioconductor, so you don't need to use BiocLite, to install it. The problem installing RSQLite doesn't seem to be due to BiocLite.

ADD REPLYlink written 19 months ago by Lluís R370

I disagree with Lluis, it is standard practice to install all packages with biocLite() -- it does no harm in general, and is essential for Bioconductor packages. It's true that RSQLite isn't a Bioconductor package, and that the problem is not technically 'ours', but I guess you're trying to install RSQLite as a part of some project related to Bioconductor, and certainly many Bioconductor packages depend on RSQLite, so we should probably help if possible...

ADD REPLYlink modified 19 months ago • written 19 months ago by Martin Morgan ♦♦ 22k

My apologies Martin, I didn't understood the error message. I couldn't provide further help than pointing that it wasn't an error due to BiocLite.

ADD REPLYlink written 19 months ago by Lluís R370
gravatar for Martin Morgan
19 months ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

It's not really clear why Rcpp is not being found (it is a dependency of RSQLite, and R would have installed it if it were not already installed). You could try re-installing it first

ADD COMMENTlink written 19 months ago by Martin Morgan ♦♦ 22k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 351 users visited in the last hour