ERROR: compilation failed for package RSQLite
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jsalsager ▴ 40
@jsalsager-14698
Last seen 14 months ago

Hi.

I have tried to install bioconductor and cummeRbund on my ubuntu 16.04 machine and I can't get anything to install. When I use

source("https://bioconductor.org/biocLite.R")
biocLite()

the installation fails because RSQLite won't install.

So I tried:

biocLite("RSQLite") and it won't install. 

I'll attach the error message below. Thanks in advance:

----------------------------------------------------------------------------------------------------

> biocLite("RSQLite")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).
Installing package(s) ‘RSQLite’
trying URL 'https://cran.rstudio.com/src/contrib/RSQLite_2.0.tar.gz'
Content type 'application/x-gzip' length 2269098 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

* installing *source* package ‘RSQLite’ ...
** package ‘RSQLite’ successfully unpacked and MD5 sums checked
** libs
g++  -I/usr/share/R/include -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -I"/home/simon/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -I"/home/simon/R/x86_64-pc-linux-gnu-library/3.4/BH/include" -I"/home/simon/R/x86_64-pc-linux-gnu-library/3.4/plogr/include"    -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ColumnStorage.cpp -o ColumnStorage.o
In file included from /usr/local/include/assert.h:5:0,
                 from /usr/include/c++/5/cassert:43,
                 from /home/simon/R/x86_64-pc-linux-gnu-library/3.4/plogr/include/plog/Util.h:2,
                 from /home/simon/R/x86_64-pc-linux-gnu-library/3.4/plogr/include/plog/Record.h:3,
                 from /home/simon/R/x86_64-pc-linux-gnu-library/3.4/plogr/include/plog/Log.h:7,
                 from /home/simon/R/x86_64-pc-linux-gnu-library/3.4/plogr/include/plogr.h:4,
                 from RSQLite.h:10,
                 from pch.h:1,
                 from ColumnStorage.cpp:1:
/usr/local/include/except.h:15:32: error: conflicting declaration ‘typedef struct Except_Frame_T* Except_Frame_T’
 typedef struct Except_Frame_T *Except_Frame_T;
                                ^
/usr/local/include/except.h:15:16: note: previous declaration as ‘struct Except_Frame_T’
 typedef struct Except_Frame_T *Except_Frame_T;
                ^
/usr/local/include/except.h:17:18: error: field ‘prev’ has incomplete type ‘Except_Frame_T’
   Except_Frame_T prev;
                  ^
/usr/local/include/except.h:16:8: note: definition of ‘struct Except_Frame_T’ is not complete until the closing brace
 struct Except_Frame_T {
        ^
/usr/lib/R/etc/Makeconf:168: recipe for target 'ColumnStorage.o' failed
make: *** [ColumnStorage.o] Error 1
ERROR: compilation failed for package ‘RSQLite’
* removing ‘/home/simon/R/x86_64-pc-linux-gnu-library/3.4/RSQLite’

The downloaded source packages are in
‘/tmp/RtmpBJOG0D/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RSQLite’ had non-zero exit status
> 

-------------------------------------------------------------------------------------------------------------
> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

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     

other attached packages:
[1] BiocInstaller_1.28.0

loaded via a namespace (and not attached):
[1] compiler_3.4.3 tools_3.4.3   

------------------------------------------------------------------------------------------------------------------------

traceback()
No traceback available 
ubuntu installation • 1.5k views
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Please update your question to contain the full output of the command biocLite("RSQLite").

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I updated my post. Thank you for the quick reply!

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@martin-morgan-1513
Last seen 3 months ago
United States

This is a problem with RSQLite, so should be reported at https://github.com/r-dbi/RSQLite/issues and / or to maintainer("RSQLite") or perhaps more likely with your own installation.

This output

In file included from /usr/local/include/assert.h:5:0,
                 from /usr/include/c++/5/cassert:43,

looks strange to me -- cassert in the 'system' install location finds assert.h in a local installation; maybe you've got two (incompatible) versions of a C compiler installed?

 

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