Vries, Han de
2008-Oct-17 16:12 UTC
[R-sig-Fedora] missing Rversion.h and Rconfig.h when installing RSQLite under FC8
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@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@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_NAMEC;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 r...{{dropped:9}}
Martyn Plummer
2008-Oct-17 17:02 UTC
[R-sig-Fedora] missing Rversion.h and Rconfig.h when installing RSQLite under FC8
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}}