[R-sig-Fedora] missing Rversion.h and Rconfig.h when installing RSQLite under FC8
Martyn Plummer
plummer at iarc.fr
Fri Oct 17 19:02:53 CEST 2008
Dear Han,
The short answer to your question is that you need to install the
R-devel package, which contains the header files. This question comes
up a lot. Most people ask on R-help so I have to thank you for asking
here as it gives us a chance to discuss this.
The good news is that R 2.8.0 will produce a sensible error message
suggesting that you have a missing R-devel RPM. But the real question is
why are we splitting off the header files into a separate RPM at all? It
certainly isn't to save disk space:
[martyn at seurat i386]$ ls -l R-2.7.2-1.fc9.i386.rpm R-devel-2.7.2-1.fc9.i386.rpm
-rw-r--r-- 1 martyn mock 26469726 2008-08-26 16:17 R-2.7.2-1.fc9.i386.rpm
-rw-r--r-- 1 martyn mock 92558 2008-08-26 16:17 R-devel-2.7.2-1.fc9.i386.rpm
Brian Ripley considers this to be a bug, and I have to say he has a
point.
I would very much prefer if the R-devel files were merged back into the
main R rpm. Would anyone from Fedora like to comment?
Martyn
On Fri, 2008-10-17 at 09:12 -0700, Vries, Han de wrote:
> Hello,
>
> I am having problems installing RSQLite under FC8. The error message
> seems to indicate Rversion.h and Rconfig.h are missing. To illustrate
> the problem, I have copied below the output shown when I first install R
> (binary distribution) and then try to install RSQLite. Because the
> problem does not occur when installing RSQLite with R under Windows I
> suspect the problem is perhaps due to my limited understanding about the
> correct way to install R under Fedora.
>
> Kind regards,
>
> Han de Vries
>
>
>
>
>
>
>
> [hdevries at models6-cambr R]$ sudo rpm -U
> ~/Desktop/R-2.7.2-1.fc8.x86_64.rpm
>
> warning: /home/hdevries/Desktop/R-2.7.2-1.fc8.x86_64.rpm: Header V3 DSA
> signature: NOKEY, key ID 97d3544e
>
>
>
> [hdevries at models6-cambr R]$ sudo R
>
>
>
> R version 2.7.2 (2008-08-25)
>
> Copyright (C) 2008 The R Foundation for Statistical Computing
>
> ISBN 3-900051-07-0
>
>
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
>
> You are welcome to redistribute it under certain conditions.
>
> Type 'license()' or 'licence()' for distribution details.
>
>
>
> Natural language support but running in an English locale
>
>
>
> R is a collaborative project with many contributors.
>
> Type 'contributors()' for more information and
>
> 'citation()' on how to cite R or R packages in publications.
>
>
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
>
> 'help.start()' for an HTML browser interface to help.
>
> Type 'q()' to quit R.
>
>
>
> > install.packages("RSQLite")
>
> Warning in install.packages("RSQLite") :
>
> argument 'lib' is missing: using '/usr/lib64/R/library'
>
> --- Please select a CRAN mirror for use in this session ---
>
> Loading Tcl/Tk interface ... done
>
> trying URL 'http://cran.stat.ucla.edu/src/contrib/RSQLite_0.7-0.tar.gz'
>
> Content type 'application/x-tar' length 975692 bytes (952 Kb)
>
> opened URL
>
> ==================================================
>
> downloaded 952 Kb
>
>
>
> * Installing *source* package 'RSQLite' ...
>
> checking for gcc... gcc -m64 -std=gnu99
>
> checking for C compiler default output file name... a.out
>
> checking whether the C compiler works... yes
>
> checking whether we are cross compiling... no
>
> checking for suffix of executables...
>
> checking for suffix of object files... o
>
> checking whether we are using the GNU C compiler... yes
>
> checking whether gcc -m64 -std=gnu99 accepts -g... yes
>
> checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
>
> checking how to run the C preprocessor... gcc -m64 -std=gnu99 -E
>
> checking for gcc... (cached) gcc -m64 -std=gnu99
>
> checking whether we are using the GNU C compiler... (cached) yes
>
> checking whether gcc -m64 -std=gnu99 accepts -g... (cached) yes
>
> checking for gcc -m64 -std=gnu99 option to accept ISO C89... (cached)
> none needed
>
> checking for library containing fdatasync... none required
>
> configure: creating ./config.status
>
> config.status: creating src/Makevars
>
> ** libs
>
> gcc -m64 -std=gnu99 -I/usr/include/R -DRSQLITE_USE_BUNDLED_SQLITE
> -DSQLITE_MAX_SQL_LENGTH=2000000 -DSQLITE_ENABLE_RTREE=1 -DTHREADSAFE=0
> -I/usr/local/include -fpic -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m64 -mtune=generic -c RS-DBI.c -o RS-DBI.o
>
> In file included from RS-DBI.h:32,
>
> from RS-DBI.c:19:
>
> Rhelpers.h:16:24: error: Rversion.h: No such file or directory
>
> In file included from /usr/include/R/Rdefines.h:26,
>
> from Rhelpers.h:18,
>
> from RS-DBI.h:32,
>
> from RS-DBI.c:19:
>
> /usr/include/R/R_ext/RS.h:27:54: error: Rconfig.h: No such file or
> directory
>
> In file included from RS-DBI.h:32,
>
> from RS-DBI.c:19:
>
> Rhelpers.h:75:49: error: missing binary operator before token "("
>
> Rhelpers.h:93:49: error: missing binary operator before token "("
>
> RS-DBI.c: In function 'RS_DBI_makeDataFrame':
>
> RS-DBI.c:396: warning: implicit declaration of function 'SET_CHR_EL'
>
> RS-DBI.c:399: warning: implicit declaration of function 'LST_EL'
>
> RS-DBI.c:399: warning: passing argument 1 of 'Rf_length' makes pointer
> from integer without a cast
>
> RS-DBI.c: In function 'RS_DBI_allocOutput':
>
> RS-DBI.c:426: warning: assignment makes pointer from integer without a
> cast
>
> RS-DBI.c: In function 'RS_DBI_copyfields':
>
> RS-DBI.c:627: warning: implicit declaration of function 'CHR_EL'
>
> RS-DBI.c:627: error: invalid lvalue in assignment
>
> RS-DBI.c:628: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:629: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:630: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:631: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:632: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:633: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:634: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c: In function 'RS_DBI_managerInfo':
>
> RS-DBI.c:926: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:928: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:929: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:930: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:931: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:932: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:933: error: invalid lvalue in assignment
>
> RS-DBI.c: In function 'RS_DBI_connectionInfo':
>
> RS-DBI.c:962: error: invalid lvalue in assignment
>
> RS-DBI.c:963: error: invalid lvalue in assignment
>
> RS-DBI.c:964: error: invalid lvalue in assignment
>
> RS-DBI.c:965: error: invalid lvalue in assignment
>
> RS-DBI.c:966: error: invalid lvalue in assignment
>
> RS-DBI.c:968: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:969: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:972: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c: In function 'RS_DBI_resultSetInfo':
>
> RS-DBI.c:996: error: invalid lvalue in assignment
>
> RS-DBI.c:997: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:998: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:999: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:1000: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:1001: warning: passing argument 1 of 'SET_VECTOR_ELT' makes
> pointer from integer without a cast
>
> RS-DBI.c: In function 'RS_DBI_getFieldDescriptions':
>
> RS-DBI.c:1026: error: invalid lvalue in assignment
>
> RS-DBI.c:1027: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:1028: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:1029: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:1030: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:1031: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> RS-DBI.c:1032: warning: passing argument 1 of 'INTEGER' makes pointer
> from integer without a cast
>
> make: *** [RS-DBI.o] Error 1
>
> chmod: cannot access `/usr/lib64/R/library/RSQLite/libs/*': No such file
> or directory
>
> ERROR: compilation failed for package 'RSQLite'
>
> ** Removing '/usr/lib64/R/library/RSQLite'
>
>
>
> The downloaded packages are in
>
> /tmp/RtmpsE6PGQ/downloaded_packages
>
> Updating HTML index of packages in '.Library'
>
> Warning message:
>
> In install.packages("RSQLite") :
>
> installation of package 'RSQLite' had non-zero exit status
>
> > sessionInfo()
>
> R version 2.7.2 (2008-08-25)
>
> x86_64-redhat-linux-gnu
>
>
>
> locale:
>
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.U
> TF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=
> C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATI
> ON=C
>
>
>
> attached base packages:
>
> [1] stats graphics grDevices utils datasets methods base
>
>
>
>
> loaded via a namespace (and not attached):
>
> [1] tcltk_2.7.2 tools_2.7.2
>
>
>
>
>
>
>
>
>
> -------------------------------------------------
>
> Han de Vries
>
> Senior Analyst
>
>
>
> RAND Europe
>
> Westbrook Centre, Milton Road
>
> Cambridge CB4 1YG
>
> United Kingdom
>
> Tel +44.1223.353.329
>
> Fax +44.1223.358.845
>
> Mob +44.7894.593.530
>
> www.rand.org
>
> -------------------------------------------------
>
>
>
>
> __________________________________________________________________________
>
> This email message is for the sole use of the intended...{{dropped:16}}
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