Search
Question: Problems with RSQLite compilation
0
gravatar for conkline
10 months ago by
conkline0
conkline0 wrote:

sessionInfo():

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")

BioC_mirror: https://bioconductor.org

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

Installing package(s) ‘RSQLite’

trying URL 'https://cran.rstudio.com/src/contrib/RSQLite_1.1-2.tar.gz'

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

    ‘/private/var/folders/bx/3dm73lf15_q8jb9bg6y4fdc00000gn/T/RtmpkXxz16/downloaded_packages’

Warning message:

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

  installation of package ‘RSQLite’ had non-zero exit status
ADD COMMENTlink modified 10 months ago by Martin Morgan ♦♦ 20k • written 10 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 10 months ago by Lluís R300

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 10 months ago • written 10 months ago by Martin Morgan ♦♦ 20k

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 10 months ago by Lluís R300
0
gravatar for Martin Morgan
10 months ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k 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

biocLite("Rcpp")
biocLite("RSQLite")
ADD COMMENTlink written 10 months ago by Martin Morgan ♦♦ 20k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 241 users visited in the last hour