Question: ERROR: compilation failed for package RSQLite

[gocougpullman]

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

---

this is dual posted - the bioconductor support page and your page. They asked me to contact you.
https://support.bioconductor.org/p/104533/

[gocougpullman]

Sorry for the formatting

[krlmlr]

Thanks for raising this. RSQLite is continuously tested on Ubuntu 16.04, I wonder if the problem you see is related to a particular detail in your system configuration. Can you try on a clean install of Ubuntu?

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