Problems with RSQLite compilation
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conkline • 0
@conkline-12167
Last seen 4.7 years ago

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
rsqlite bioconductor bioclite rcpp.h • 2.9k views
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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.

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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...

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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.

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@martin-morgan-1513
Last seen 9 weeks ago
United States

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")
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