Re: [Rd] Rgui crash under Windows
Dear Duncan, thank you very much for your reply, just for the sake of precision I missed a 'not' in my report, actually I intended: "the same does not happen under linux (SUSE 10.0), details follow" as I was not able to reproduce it under Linux, sorry for the inconvenience. Regards, Simone On 6/12/06, Duncan Murdoch <[EMAIL PROTECTED]> wrote: > On 6/11/2006 2:13 PM, Simone Giannerini wrote: > > Dear all, > > I found the following on R 2.3.1. for Windows XPpro SP2, tested on 2 PCs > > AMD 64 3700+, Ati 9700 > > AMD Athlon 2400+, Matrox G550 > > > > > > Do the following: > > > > x <- as.matrix(0); > > fix(x) > > > > pasting a big chunk of data, for instance the one below, into a cell > > of the editor will crash the RGui. > > Confirmed, and fixed. I'll commit the fixes to R-patched and R-devel soon. > > Duncan Murdoch > > > > > 33 > > 333 > > > > 333 > > > > 333 > > 333 > > > > platform i386-pc-mingw32 > > arch i386 > > os mingw32 > > system i386, mingw32 > > status > > major 2 > > minor 3.1 > > year 2006 > > month 06 > > day01 > > svn rev38247 > > language R > > version.string Version 2.3.1 (2006-06-01) > > * > > the same does happen under linux (SUSE 10.0), details follow > > > > platform x86_64-unknown-linux-gnu > > arch x86_64 > > os linux-gnu > > system x86_64, linux-gnu > > status > > major2 > > minor2.1 > > year 2005 > > month12 > > day 20 > > svn rev 36812 > > language R > > > > > > Regards, > > > > Simone > > > > > > __ > > > > Simone Giannerini > > Dipartimento di Scienze Statistiche "Paolo Fortunati" > > Universita' di Bologna > > Via delle belle arti 41 - 40126 Bologna, ITALY > > Tel: +39 051 2098248 Fax: +39 051 232153 > > > > __ > > R-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > -- __ Simone Giannerini Dipartimento di Scienze Statistiche "Paolo Fortunati" Universita' di Bologna Via delle belle arti 41 - 40126 Bologna, ITALY Tel: +39 051 2098248 Fax: +39 051 232153 __ [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Making a windows packages with zip
In the past I have been able to make windows packages (containing only R code) from my mac by simply zipping the installed package directory, eg. R CMD install asmrsim cd ~/Library/R/library/ zip -r9X asmrsim asmrsim (using code copied from this list, from Duncan Murdoch, I think) However, since 2.3.0, windows users now get the following error: Error in library(pkg, character.only = TRUE) : 'asmrsim' is not a valid package -- installed < 2.0.0? Obviously, the zip file was a hack in the first place, but is there any way to continue to make windows packages easily, or should I grit my teeth and install the cross compilation tool chain? Thanks, Hadley __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Making a windows packages with zip
hadley wickham wrote: > In the past I have been able to make windows packages (containing only > R code) from my mac by simply zipping the installed package directory, > eg. > > R CMD install asmrsim > cd ~/Library/R/library/ > zip -r9X asmrsim asmrsim > > (using code copied from this list, from Duncan Murdoch, I think) > > However, since 2.3.0, windows users now get the following error: > > Error in library(pkg, character.only = TRUE) : >'asmrsim' is not a valid package -- installed < 2.0.0? > > > Obviously, the zip file was a hack in the first place, but is there > any way to continue to make windows packages easily, or should I grit > my teeth and install the cross compilation tool chain? Either the latter or ask the Windows users to install the source package. Uwe Ligges > Thanks, > > Hadley > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Rgui crash under Windows
On 6/12/2006 4:52 AM, Simone Giannerini wrote: > Dear Duncan, > > thank you very much for your reply, just for the sake of precision > I missed a 'not' in my report, actually I intended: > > "the same does not happen under linux (SUSE 10.0), details follow" > > as I was not able to reproduce it under Linux, sorry for the inconvenience. No problem. I misread that in the original, and didn't think you had claimed a problem in Linux. Thanks for the report! Duncan Murdoch > > Regards, > > Simone > > > On 6/12/06, Duncan Murdoch <[EMAIL PROTECTED]> wrote: >> On 6/11/2006 2:13 PM, Simone Giannerini wrote: >>> Dear all, >>> I found the following on R 2.3.1. for Windows XPpro SP2, tested on 2 PCs >>> AMD 64 3700+, Ati 9700 >>> AMD Athlon 2400+, Matrox G550 >>> >>> >>> Do the following: >>> >>> x <- as.matrix(0); >>> fix(x) >>> >>> pasting a big chunk of data, for instance the one below, into a cell >>> of the editor will crash the RGui. >> Confirmed, and fixed. I'll commit the fixes to R-patched and R-devel > soon. >> Duncan Murdoch >> >>> 33 >>> 333 >>> >>> 333 >>> >>> 333 >>> 333 >>> >>> platform i386-pc-mingw32 >>> arch i386 >>> os mingw32 >>> system i386, mingw32 >>> status >>> major 2 >>> minor 3.1 >>> year 2006 >>> month 06 >>> day01 >>> svn rev38247 >>> language R >>> version.string Version 2.3.1 (2006-06-01) >>> * >>> the same does happen under linux (SUSE 10.0), details follow >>> >>> platform x86_64-unknown-linux-gnu >>> arch x86_64 >>> os linux-gnu >>> system x86_64, linux-gnu >>> status >>> major2 >>> minor2.1 >>> year 2005 >>> month12 >>> day 20 >>> svn rev 36812 >>> language R >>> >>> >>> Regards, >>> >>> Simone >>> >>> >>> __ >>> >>> Simone Giannerini >>> Dipartimento di Scienze Statistiche "Paolo Fortunati" >>> Universita' di Bologna >>> Via delle belle arti 41 - 40126 Bologna, ITALY >>> Tel: +39 051 2098248 Fax: +39 051 232153 >>> >>> __ >>> R-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-devel >> > > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Making a windows packages with zip
>
> Either the latter or ask the Windows users to install the source package.
>
Installing a source package doesn't seem to help:
> install.packages("classifly", repos="http://ggobi.org/r/";, type="source")
Warning message:
installation of package 'classifly' had non-zero exit status in:
install.packages("classifly", repos = "http://ggobi.org/r/";,
(Unfortunately I don't have access to a windows machine at present -
this is what a user reported)
Hadley
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[Rd] Ruuid had non-zero exit status (PR#8965)
> source("http://www.bioconductor.org/biocLite.R";)
> biocLite(c("Ruuid"))
Running getBioC version 0.1.6 with R version 2.3.1
Running biocinstall version 1.8.4 with R version 2.3.1
Your version of R requires version 1.8 of Bioconductor.
trying URL
'http://bioconductor.org/packages/1.8/bioc/src/contrib/Ruuid_1.10.0.tar.gz'
Content type 'application/x-gzip' length 72767 bytes
opened URL
==
downloaded 71Kb
* Installing *source* package 'Ruuid' ...
checking for pkg-config... /usr/local/bin/pkg-config
checking for glib-config... /usr/local/bin/glib-config
checking for glib-2.0... yes
checking PKG_CFLAGS... -I/usr/local/include/glib-2.0
-I/usr/local/lib/glib-2.0/include
checking PKG_LIBS... -L/usr/local/lib -lglib-2.0 -liconv
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... no
checking for unistd.h... yes
checking /usr/include/unistd.h usability... yes
checking /usr/include/unistd.h presence... yes
checking for /usr/include/unistd.h... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/package/R/2.3.1/lib/R/include -I/package/R/2.3.1/lib/R/include
-I/usr/local/include -I/ usr/local/include/glib-2.0
-I/usr/local/lib/glib-2.0/include -DHAVE_UNISTD_H=1 -fPIC -O2 -D_F
ILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1 -c Rinit.c -o Rinit.o
In file included from /usr/local/include/glib-2.0/glib/galloca.h:30,
from /usr/local/include/glib-2.0/glib.h:30,
from uuidP.h:33,
from Ruuid.h:5,
from Rinit.c:1:
/usr/local/include/glib-2.0/glib/gtypes.h:41: error: syntax error before
"typedef"
In file included from /usr/local/include/glib-2.0/glib.h:31,
from uuidP.h:33,
from Ruuid.h:5,
from Rinit.c:1:
/usr/local/include/glib-2.0/glib/garray.h:32: error: parse error before
"G_BEGIN_DECLS"
/usr/local/include/glib-2.0/glib/garray.h:34: error: syntax error before
"typedef"
In file included from /usr/local/include/glib-2.0/glib/gerror.h:24,
from /usr/local/include/glib-2.0/glib/gthread.h:30,
from /usr/local/include/glib-2.0/glib/gasyncqueue.h:30,
from /usr/local/include/glib-2.0/glib.h:32,
from uuidP.h:33,
from Ruuid.h:5,
from Rinit.c:1:
/usr/local/include/glib-2.0/glib/gquark.h:32: error: parse error before
"G_BEGIN_DECLS"
/usr/local/include/glib-2.0/glib/gquark.h:34: error: syntax error before
"typedef"
/usr/local/include/glib-2.0/glib/gquark.h:41: error: syntax error before
"gchar"
/usr/local/include/glib-2.0/glib/gquark.h:41: error: parse error before
"G_GNUC_CONST"
/usr/local/include/glib-2.0/glib/gquark.h:41: warning: data definition has
no type or storage cl ass
In file included from /usr/local/include/glib-2.0/glib/gthread.h:30,
from /usr/local/include/glib-2.0/glib/gasyncqueue.h:30,
from /usr/local/include/glib-2.0/glib.h:32,
from uuidP.h:33,
from Ruuid.h:5,
from Rinit.c:1:
/usr/local/include/glib-2.0/glib/gerror.h:26: error: parse error before
"G_BEGIN_DECLS"
/usr/local/include/glib-2.0/glib/gerror.h:28: error: syntax error before
"typedef"
/usr/local/include/glib-2.0/glib/gerror.h:40: error: parse error before
"G_GNUC_PRINTF"
/usr/local/include/glib-2.0/glib/gerror.h:40: warning: data definition has
no type or storage cl ass
/usr/local/include/glib-2.0/glib/gerror.h:60: error: parse error before
"G_GNUC_PRINTF"
/usr/local/include/glib-2.0/glib/gerror.h:60: warning: data definition has
no type or storage cl ass
In file included from /usr/local/include/glib-2.0/glib/gthread.h:32,
from /usr/local/include/glib-2.0/glib/gasyncqueue.h:30,
from /usr/local/include/glib-2.0/glib.h:32,
from uuidP.h:33,
from Ruuid.h:5,
from Rinit.c:1:
/usr/local/include/glib-2.0/glib/gatomic.h:35: error: parse error before
"G_BEGIN_DECLS"
/usr/local/include/glib-2.0/glib/gatomic.h:37: error: syntax error before
"gint"
In file included from /usr/local/include/glib-2.0/glib/gasyncqueue.h:30,
from /usr/local/include/glib-2.0/glib.h:
[Rd] Ruuid had non-zero exit status (PR#8966)
<> --please do not edit the information below-- Version: platform = sparc-sun-solaris2.9 arch = sparc os = solaris2.9 system = sparc, solaris2.9 status = major = 2 minor = 3.1 year = 2006 month = 06 day = 01 svn rev = 38247 language = R version.string = Version 2.3.1 (2006-06-01) Locale: C Search Path: .GlobalEnv, package:methods, package:stats, package:graphics, package:grDevices, package:utils, package:datasets, Autoloads, package:base __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Link error with glibc-2.4 on linux/PPC (PR#8967)
Full_Name: Luca Barbato Version: 2.3.1 OS: Gentoo Linux/PPC Submission from: (NULL) (151.44.163.144) system informations Portage 2.1 (default-linux/ppc/ppc32/2006.0/G4, gcc-4.1.1, glibc-2.4-r3, 2.6.17-rc5 ppc) = System uname: 2.6.17-rc5 ppc 7447A, altivec supported Gentoo Base System version 1.12.1 distcc 2.18.3 powerpc-unknown-linux-gnu (protocols 1 and 2) (default port 3632) [disabled] dev-lang/python: 2.4.3-r1 dev-python/pycrypto: 2.0.1-r5 dev-util/ccache: [Not Present] dev-util/confcache: 0.4.2-r1 sys-apps/sandbox:1.2.18.1 sys-devel/autoconf: 2.13, 2.59-r7 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2 sys-devel/binutils: 2.16.1-r2 sys-devel/gcc-config: 1.3.13-r2 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.11-r4 ACCEPT_KEYWORDS="ppc ~ppc" AUTOCLEAN="yes" CBUILD="powerpc-unknown-linux-gnu" CFLAGS="-O2 -mcpu=G4 -mtune=G4 -fno-strict-aliasing -pipe -maltivec -mabi=altivec" CHOST="powerpc-unknown-linux-gnu" Fault log gfortran -fpic -g -O2 -c xxxpr.f -o xxxpr.o powerpc-unknown-linux-gnu-gcc -shared -o libR.so Rembedded.o CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o apply.o arithmetic.o apse.o array.o attrib.o base.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o eval.o format.o fourier.o gevents.o gram.o gram-ex.o graphics.o identical.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o model.o names.o objects.o optim.o optimize.o options.o par.o paste.o pcre.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o random.o regex.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o size.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o unique.o util.o version.o vfonts.o xxxpr.o `ls ../appl/*.o ../nmath/*.o ../unix/*.o 2>/dev/null` -lgfortran -lm -lgcc_s ../extra/zlib/libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a -lreadline -ldl -lm /usr/lib/gcc/powerpc-unknown-linux-gnu/4.1.1/../../../crti.o: In function `call_gmon_start': /var/tmp/portage/glibc-2.4-r3/work/build-default-powerpc-unknown-linux-gnu-nptl/csu/crti.S:18: relocation truncated to fit: R_PPC_GOT16 against undefined symbol `__gmon_start__' CConverters.o: In function `do_setToCConverterActiveStatus': CConverters.c:(.text+0x522): relocation truncated to fit: R_PPC_GOT16 against symbol `R_NaInt' defined in .sbss section in main.o CConverters.c:(.text+0x556): relocation truncated to fit: R_PPC_GOT16 against symbol `R_FunTab' defined in .data.rel section in names.o CConverters.o: In function `R_converterMatchClass': CConverters.c:(.text+0x71a): relocation truncated to fit: R_PPC_GOT16 against symbol `R_ClassSymbol' defined in .sbss section in main.o CConverters.c:(.text+0x7f2): relocation truncated to fit: R_PPC_GOT16 against symbol `R_NilValue' defined in .sbss section in main.o CommandLineArgs.o: In function `R_common_command_line': CommandLineArgs.c:(.text+0x5e): relocation truncated to fit: R_PPC_GOT16 against symbol `R_RestoreHistory' defined in .sbss section in main.o CommandLineArgs.c:(.text+0x722): relocation truncated to fit: R_PPC_GOT16 against symbol `R_StdinEnc' defined in .data section in main.o Rdynload.o: In function `GetFullDLLPath': Rdynload.c:(.text+0x6a): relocation truncated to fit: R_PPC_GOT16 against symbol `R_osDynSymbol' defined in .sdata section in Rdynload.o Rdynload.o: In function `Rf_MakeDLLInfo': Rdynload.c:(.text+0x1c2): relocation truncated to fit: R_PPC_GOT16 against symbol `R_ClassSymbol' defined in .sbss section in main.o Rdynload.c:(.text+0x1e6): relocation truncated to fit: R_PPC_GOT16 against symbol `R_NilValue' defined in .sbss section in main.o Rdynload.c:(.text+0x3a2): additional relocation overflows omitted from the output collect2: ld returned 1 exit status __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] about integration of a library into package creation
hello,
i try to create a package , and i call a library in the namespace file
such as : useDynLib(quadprog)
after checking my directory with the command "rcmd check" (i am on
WindowsXP)
i get an error: package / namespace load failed
the path of the library is: D:\R\library\quadprog
the path of the building files is: D:\RBuild\svcR
and the comand i use to compile is: rcmd check D://RBuild//svcR
i dont understand, it is a path problem about the dll related to the
library ?
thank for help
Nicolas
* checking package subdirectories ... WARNING
Subdirectory 'src' contains no source files.
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... WARNING
Erreur : le chargement du package / espace de noms a echoue' pour 'svcR'
Sequence d'appel :
2: stop(gettextf("package/namespace load failed for '%s'",
libraryPkgName(packag
e)),
call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
FALSE)
Execution arrete'e
See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* checking replacement functions ... WARNING
Erreur : le chargement du package / espace de noms a echoue' pour 'svcR'
Sequence d'appel :
2: stop(gettextf("package/namespace load failed for '%s'",
libraryPkgName(packag
e)),
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Re: [Rd] about integration of a library into package creation
On 6/12/2006 11:02 AM, Nicolas Turenne wrote:
> hello,
>
> i try to create a package , and i call a library in the namespace file
> such as : useDynLib(quadprog)
>
> after checking my directory with the command "rcmd check" (i am on
> WindowsXP)
> i get an error: package / namespace load failed
> the path of the library is: D:\R\library\quadprog
> the path of the building files is: D:\RBuild\svcR
> and the comand i use to compile is: rcmd check D://RBuild//svcR
>
> i dont understand, it is a path problem about the dll related to the
> library ?
You didn't show the results of installing your package. Did that work?
Generally we advise to do a successful install before you try to run checks.
Duncan Murdoch
>
> thank for help
> Nicolas
>
>
> * checking package subdirectories ... WARNING
> Subdirectory 'src' contains no source files.
> * checking R files for syntax errors ... OK
> * checking R files for library.dynam ... OK
> * checking S3 generic/method consistency ... WARNING
> Erreur : le chargement du package / espace de noms a echoue' pour 'svcR'
> Sequence d'appel :
> 2: stop(gettextf("package/namespace load failed for '%s'",
> libraryPkgName(packag
> e)),
>call. = FALSE, domain = NA)
> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> FALSE)
> Execution arrete'e
> See section 'Generic functions and methods' of the 'Writing R Extensions'
> manual.
> * checking replacement functions ... WARNING
> Erreur : le chargement du package / espace de noms a echoue' pour 'svcR'
> Sequence d'appel :
> 2: stop(gettextf("package/namespace load failed for '%s'",
> libraryPkgName(packag
> e)),
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-devel
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Re: [Rd] Making a windows packages with zip
hadley wickham wrote:
>>
>> Either the latter or ask the Windows users to install the source package.
>>
>
> Installing a source package doesn't seem to help:
>
>> install.packages("classifly", repos="http://ggobi.org/r/";, type="source")
> Warning message:
> installation of package 'classifly' had non-zero exit status in:
> install.packages("classifly", repos = "http://ggobi.org/r/";,
>
> (Unfortunately I don't have access to a windows machine at present -
> this is what a user reported)
Oh well, certainly the user forgot to install the required tools as
mentioned in the "R Installation and Administration" manual.
Uwe Ligges
> Hadley
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Re: [Rd] Ruuid had non-zero exit status (PR#8965)
Ruuid is a Bioconductor package; please report bugs to Bioconductor as
they ask.
-thomas
On Mon, 12 Jun 2006, [EMAIL PROTECTED] wrote:
>> source("http://www.bioconductor.org/biocLite.R";)
>> biocLite(c("Ruuid"))
> Running getBioC version 0.1.6 with R version 2.3.1
> Running biocinstall version 1.8.4 with R version 2.3.1
> Your version of R requires version 1.8 of Bioconductor.
> trying URL
> 'http://bioconductor.org/packages/1.8/bioc/src/contrib/Ruuid_1.10.0.tar.gz'
> Content type 'application/x-gzip' length 72767 bytes
> opened URL
> ==
> downloaded 71Kb
>
> * Installing *source* package 'Ruuid' ...
> checking for pkg-config... /usr/local/bin/pkg-config
> checking for glib-config... /usr/local/bin/glib-config
> checking for glib-2.0... yes
> checking PKG_CFLAGS... -I/usr/local/include/glib-2.0
> -I/usr/local/lib/glib-2.0/include
> checking PKG_LIBS... -L/usr/local/lib -lglib-2.0 -liconv
> checking for gcc... gcc
> 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 accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking how to run the C preprocessor... gcc -E
> checking for egrep... grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... no
> checking for unistd.h... yes
> checking /usr/include/unistd.h usability... yes
> checking /usr/include/unistd.h presence... yes
> checking for /usr/include/unistd.h... yes
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> gcc -I/package/R/2.3.1/lib/R/include -I/package/R/2.3.1/lib/R/include
> -I/usr/local/include -I/ usr/local/include/glib-2.0
> -I/usr/local/lib/glib-2.0/include -DHAVE_UNISTD_H=1 -fPIC -O2 -D_F
> ILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1 -c Rinit.c -o Rinit.o
> In file included from /usr/local/include/glib-2.0/glib/galloca.h:30,
> from /usr/local/include/glib-2.0/glib.h:30,
> from uuidP.h:33,
> from Ruuid.h:5,
> from Rinit.c:1:
> /usr/local/include/glib-2.0/glib/gtypes.h:41: error: syntax error before
> "typedef"
> In file included from /usr/local/include/glib-2.0/glib.h:31,
> from uuidP.h:33,
> from Ruuid.h:5,
> from Rinit.c:1:
> /usr/local/include/glib-2.0/glib/garray.h:32: error: parse error before
> "G_BEGIN_DECLS"
> /usr/local/include/glib-2.0/glib/garray.h:34: error: syntax error before
> "typedef"
> In file included from /usr/local/include/glib-2.0/glib/gerror.h:24,
> from /usr/local/include/glib-2.0/glib/gthread.h:30,
> from /usr/local/include/glib-2.0/glib/gasyncqueue.h:30,
> from /usr/local/include/glib-2.0/glib.h:32,
> from uuidP.h:33,
> from Ruuid.h:5,
> from Rinit.c:1:
> /usr/local/include/glib-2.0/glib/gquark.h:32: error: parse error before
> "G_BEGIN_DECLS"
> /usr/local/include/glib-2.0/glib/gquark.h:34: error: syntax error before
> "typedef"
> /usr/local/include/glib-2.0/glib/gquark.h:41: error: syntax error before
> "gchar"
> /usr/local/include/glib-2.0/glib/gquark.h:41: error: parse error before
> "G_GNUC_CONST"
> /usr/local/include/glib-2.0/glib/gquark.h:41: warning: data definition has
> no type or storage cl ass
> In file included from /usr/local/include/glib-2.0/glib/gthread.h:30,
> from /usr/local/include/glib-2.0/glib/gasyncqueue.h:30,
> from /usr/local/include/glib-2.0/glib.h:32,
> from uuidP.h:33,
> from Ruuid.h:5,
> from Rinit.c:1:
> /usr/local/include/glib-2.0/glib/gerror.h:26: error: parse error before
> "G_BEGIN_DECLS"
> /usr/local/include/glib-2.0/glib/gerror.h:28: error: syntax error before
> "typedef"
> /usr/local/include/glib-2.0/glib/gerror.h:40: error: parse error before
> "G_GNUC_PRINTF"
> /usr/local/include/glib-2.0/glib/gerror.h:40: warning: data definition has
> no type or storage cl ass
> /usr/local/include/glib-2.0/glib/gerror.h:60: error: parse error before
> "G_GNUC_PRINTF"
> /usr/local/include/glib-2.0/glib/gerror.h:60: warning: data definition has
> no type or storage cl ass
> In file included from /usr/local/include/glib-2.0/glib/gthread.h:32,
> from /usr/local/include/glib-2.0/glib/gasyncqueue.h:30,
> from /usr/local/include/glib-2.0/glib.h:32,
> from uuidP.h:33,
> from Ruuid.h:5,
> from
Re: [Rd] about integration of a library into package creation
>
>
>You didn't show the results of installing your package. Did that work?
>
>Generally we advise to do a successful install before you try to run
checks.
>
>Duncan Murdoch
D:\RBuild\svcR> rcmd build D://RBuild//svcR --force --docs='all' --binary
hence i obtain the file svcR_1.0.zip
and following messages :
D:\RBuild\svcR>rcmd build D://RBuild//svcR --force --docs='all' --binary
* checking for file 'D://RBuild//svcR/DESCRIPTION' ... OK
* preparing 'D://RBuild//svcR':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* removing junk files
tar: svcR/svcR_1.0.tar: file is the archive; not dumped
* excluding invalid files from 'svcR'
Subdirectory 'R' contains invalid file names:
ade4.dll quadprog.dll spdep.dll
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building binary distribution
WARNING
* some HTML links may not be found
installing R.css in C:/DOCUME~1/Nicolas/LOCALS~1/Temp/Rinst249298526
Using auto-selected zip options ''
-- Making package svcR
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
installing R files
installing data files
installing man source files
installing indices
not zipping data
installing help
>>> Building/Updating help pages for package 'svcR'
Formats: text html latex example chm
iris_att texthtmllatex chm
iris_mat texthtmllatex chm
iris_var texthtmllatex chm
svcR texthtmllatex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling
c:\DOCUME~1\Nicolas\LOCALS~1\Temp\Rbuild249291931\svcR\chm\svcR.chm
Compile time: 0 minutes, 1 second
5 Topics
8 Local links
1 Internet link
1 Graphic
Created
c:\DOCUME~1\Nicolas\LOCALS~1\Temp\Rbuild249291931\svcR\chm\svcR.chm, 18,
283 bytes
Compression increased file by 6,096 bytes.
preparing package svcR for lazy loading
adding MD5 sums
packaged installation of package 'svcR' as svcR_1.0.zip
* DONE (svcR)
in R environment (Rgui front-end)
i write:
> install.packages("D:/RBuild/svcR/svcR_1.0.zip", repos=NULL)
package 'svcR' successfully unpacked and MD5 sums checked
updating HTML package descriptions
> library(svcR)
Attachement du package : 'svcR'
The following object(s) are masked _by_ .GlobalEnv :
findModelCluster
>
and finally when i typewrite my function
i obtain :
impossible de trouver la fonction "dudi.coa"
it can not find the function called in the library that i call in the R
source code
by library(ade4)
if i call my function by source(), it works well
thank you for help
-
Nicolas
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] do.call and hist
Hi everyone, here is something I noticed when playing around with do.call: do.call(hist, list(x=1:10)) uses for the main title and also the axis labels "c(1,2,3,4,5,6,7,8,9,10)" So do.call(hist, list(x=1:1)) nicely fills up your screen with numbers. Is there a way to get the deparsing from the list names to the labels right. Cheers, Florian PS: My sessionInfo: Version 2.3.1 Patched (2006-06-01 r38258) x86_64-unknown-linux-gnu attached base packages: [1] "grid" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: geneplotter annotateprada RColorBrewer Biobase "1.10.0" "1.10.0" "1.9.5" "0.2-3" "1.10.0" -- Florian Hahne Abt. Molekulare Genomanalyse (B050) Deutsches Krebsforschungszentrum (DKFZ) Im Neuenheimer Feld 580 D-69120 Heidelberg phone: 0049 6221 424764 fax: 0049 6221 423454 web: www.dkfz.de/mga __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Link error with glibc-2.4 on linux/PPC (PR#8967)
Does this system need -fPIC?
R cannot be expected to know the settings needed in config.site for all
possible systems, and as you will see from the notes in configure.ac,
ppc32 does not appear to need -fPIC according to the gcc documentation.
Indeed, the manual INSTALL asked you to read says:
Variables such as @env{CPICFLAGS} are determined where possible by
@command{configure}. Some systems allows two types of PIC flags, for
example @samp{-fpic} and @samp{-fPIC}, and if they differ the first
allows only a limited number of symbols in a shared library. Since @R{}
as a shared library has about 6200 symbols, if in doubt use the larger
version.
and an issue discussed in the installation manual is hardly a bug.
On Mon, 12 Jun 2006, [EMAIL PROTECTED] wrote:
> Full_Name: Luca Barbato
> Version: 2.3.1
> OS: Gentoo Linux/PPC
> Submission from: (NULL) (151.44.163.144)
>
>
> system informations
>
> Portage 2.1 (default-linux/ppc/ppc32/2006.0/G4, gcc-4.1.1, glibc-2.4-r3,
> 2.6.17-rc5 ppc)
> =
> System uname: 2.6.17-rc5 ppc 7447A, altivec supported
> Gentoo Base System version 1.12.1
> distcc 2.18.3 powerpc-unknown-linux-gnu (protocols 1 and 2) (default port
> 3632)
> [disabled]
> dev-lang/python: 2.4.3-r1
> dev-python/pycrypto: 2.0.1-r5
> dev-util/ccache: [Not Present]
> dev-util/confcache: 0.4.2-r1
> sys-apps/sandbox:1.2.18.1
> sys-devel/autoconf: 2.13, 2.59-r7
> sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2
> sys-devel/binutils: 2.16.1-r2
> sys-devel/gcc-config: 1.3.13-r2
> sys-devel/libtool: 1.5.22
> virtual/os-headers: 2.6.11-r4
> ACCEPT_KEYWORDS="ppc ~ppc"
> AUTOCLEAN="yes"
> CBUILD="powerpc-unknown-linux-gnu"
> CFLAGS="-O2 -mcpu=G4 -mtune=G4 -fno-strict-aliasing -pipe -maltivec
> -mabi=altivec"
> CHOST="powerpc-unknown-linux-gnu"
>
> Fault log
>
> gfortran -fpic -g -O2 -c xxxpr.f -o xxxpr.o
> powerpc-unknown-linux-gnu-gcc -shared -o libR.so Rembedded.o CConverters.o
> CommandLineArgs.o Rdynload.o Renviron.o RNG.o apply.o arithmetic.o apse.o
> array.o attrib.o base.o bind.o builtin.o character.o coerce.o colors.o
> complex.o
> connections.o context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o
> dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o eval.o
> format.o fourier.o gevents.o gram.o gram-ex.o graphics.o identical.o
> internet.o
> iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o
> memory.o model.o names.o objects.o optim.o optimize.o options.o par.o paste.o
> pcre.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o
> printvector.o
> printutils.o qsort.o random.o regex.o registration.o relop.o rlocale.o
> saveload.o scan.o seq.o serialize.o size.o sort.o source.o split.o sprintf.o
> startup.o subassign.o subscript.o subset.o summary.o sysutils.o unique.o
> util.o
> version.o vfonts.o xxxpr.o `ls ../appl/*.o ../nmath/*.o ../unix/*.o
> 2>/dev/null` -lgfortran -lm -lgcc_s ../extra/zlib/libz.a
> ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a -lreadline -ldl -lm
> /usr/lib/gcc/powerpc-unknown-linux-gnu/4.1.1/../../../crti.o: In function
> `call_gmon_start':
> /var/tmp/portage/glibc-2.4-r3/work/build-default-powerpc-unknown-linux-gnu-nptl/csu/crti.S:18:
> relocation truncated to fit: R_PPC_GOT16 against undefined symbol
> `__gmon_start__'
> CConverters.o: In function `do_setToCConverterActiveStatus':
> CConverters.c:(.text+0x522): relocation truncated to fit: R_PPC_GOT16 against
> symbol `R_NaInt' defined in .sbss section in main.o
> CConverters.c:(.text+0x556): relocation truncated to fit: R_PPC_GOT16 against
> symbol `R_FunTab' defined in .data.rel section in names.o
> CConverters.o: In function `R_converterMatchClass':
> CConverters.c:(.text+0x71a): relocation truncated to fit: R_PPC_GOT16 against
> symbol `R_ClassSymbol' defined in .sbss section in main.o
> CConverters.c:(.text+0x7f2): relocation truncated to fit: R_PPC_GOT16 against
> symbol `R_NilValue' defined in .sbss section in main.o
> CommandLineArgs.o: In function `R_common_command_line':
> CommandLineArgs.c:(.text+0x5e): relocation truncated to fit: R_PPC_GOT16
> against
> symbol `R_RestoreHistory' defined in .sbss section in main.o
> CommandLineArgs.c:(.text+0x722): relocation truncated to fit: R_PPC_GOT16
> against symbol `R_StdinEnc' defined in .data section in main.o
> Rdynload.o: In function `GetFullDLLPath':
> Rdynload.c:(.text+0x6a): relocation truncated to fit: R_PPC_GOT16 against
> symbol
> `R_osDynSymbol' defined in .sdata section in Rdynload.o
> Rdynload.o: In function `Rf_MakeDLLInfo':
> Rdynload.c:(.text+0x1c2): relocation truncated to fit: R_PPC_GOT16 against
> symbol `R_ClassSymbol' defined in .sbss section in main.o
> Rdynload.c:(.text+0x1e6): relocation truncated to fit: R_PPC_GOT16 against
> symbol `R_NilValue' defined in .sbss section in main.o
> Rdynload.c:(.text+0x3a2): additional relocation overflows omitted from the
Re: [Rd] about integration of a library into package creation
On Mon, 12 Jun 2006, Duncan Murdoch wrote:
> On 6/12/2006 11:02 AM, Nicolas Turenne wrote:
>> hello,
>>
>> i try to create a package , and i call a library in the namespace file
>> such as : useDynLib(quadprog)
>>
>> after checking my directory with the command "rcmd check" (i am on
>> WindowsXP)
>> i get an error: package / namespace load failed
>> the path of the library is: D:\R\library\quadprog
>> the path of the building files is: D:\RBuild\svcR
>> and the comand i use to compile is: rcmd check D://RBuild//svcR
>>
>> i dont understand, it is a path problem about the dll related to the
>> library ?
>
> You didn't show the results of installing your package. Did that work?
>
> Generally we advise to do a successful install before you try to run checks.
And also to load the package, maybe with
rterm R_DEFAULT_PACKAGES=NULL
> library(svcR)
as these messages often indicate missing package dependencies.
>> * checking package subdirectories ... WARNING
>> Subdirectory 'src' contains no source files.
>> * checking R files for syntax errors ... OK
>> * checking R files for library.dynam ... OK
>> * checking S3 generic/method consistency ... WARNING
>> Erreur : le chargement du package / espace de noms a echoue' pour 'svcR'
>> Sequence d'appel :
>> 2: stop(gettextf("package/namespace load failed for '%s'",
>> libraryPkgName(packag
>> e)),
>>call. = FALSE, domain = NA)
>> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
>> FALSE)
>> Execution arrete'e
>> See section 'Generic functions and methods' of the 'Writing R Extensions'
>> manual.
>> * checking replacement functions ... WARNING
>> Erreur : le chargement du package / espace de noms a echoue' pour 'svcR'
>> Sequence d'appel :
>> 2: stop(gettextf("package/namespace load failed for '%s'",
>> libraryPkgName(packag
>> e)),
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] do.call and hist
Try x <- 1:10 do.call(hist, list(quote(x))) or do.call(hist, list(x = 1:10, xlab = "x")) On 6/12/06, Florian Hahne <[EMAIL PROTECTED]> wrote: > Hi everyone, > here is something I noticed when playing around with do.call: > do.call(hist, list(x=1:10)) > uses for the main title and also the axis labels "c(1,2,3,4,5,6,7,8,9,10)" > So > do.call(hist, list(x=1:1)) > nicely fills up your screen with numbers. > Is there a way to get the deparsing from the list names to the labels > right. > Cheers, > Florian > > PS: My sessionInfo: > Version 2.3.1 Patched (2006-06-01 r38258) > x86_64-unknown-linux-gnu > > attached base packages: > [1] "grid" "tools" "methods" "stats" "graphics" "grDevices" > [7] "utils" "datasets" "base" > > other attached packages: > geneplotter annotateprada RColorBrewer Biobase >"1.10.0" "1.10.0" "1.9.5" "0.2-3" "1.10.0" > > -- > Florian Hahne > Abt. Molekulare Genomanalyse (B050) > Deutsches Krebsforschungszentrum (DKFZ) > Im Neuenheimer Feld 580 > D-69120 Heidelberg > phone: 0049 6221 424764 > fax: 0049 6221 423454 > web: www.dkfz.de/mga > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] do.call and hist
Thanks, that did the trick... Gabor Grothendieck wrote: > Try > > x <- 1:10 > do.call(hist, list(quote(x))) > > or > > do.call(hist, list(x = 1:10, xlab = "x")) > > > On 6/12/06, Florian Hahne <[EMAIL PROTECTED]> wrote: >> Hi everyone, >> here is something I noticed when playing around with do.call: >> do.call(hist, list(x=1:10)) >> uses for the main title and also the axis labels >> "c(1,2,3,4,5,6,7,8,9,10)" >> So >> do.call(hist, list(x=1:1)) >> nicely fills up your screen with numbers. >> Is there a way to get the deparsing from the list names to the labels >> right. >> Cheers, >> Florian >> >> PS: My sessionInfo: >> Version 2.3.1 Patched (2006-06-01 r38258) >> x86_64-unknown-linux-gnu >> >> attached base packages: >> [1] "grid" "tools" "methods" "stats" "graphics" >> "grDevices" >> [7] "utils" "datasets" "base" >> >> other attached packages: >> geneplotter annotateprada RColorBrewer Biobase >>"1.10.0" "1.10.0" "1.9.5" "0.2-3" "1.10.0" >> >> -- >> Florian Hahne >> Abt. Molekulare Genomanalyse (B050) >> Deutsches Krebsforschungszentrum (DKFZ) >> Im Neuenheimer Feld 580 >> D-69120 Heidelberg >> phone: 0049 6221 424764 >> fax: 0049 6221 423454 >> web: www.dkfz.de/mga >> >> __ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> -- Florian Hahne Abt. Molekulare Genomanalyse (B050) Deutsches Krebsforschungszentrum (DKFZ) Im Neuenheimer Feld 580 D-69120 Heidelberg phone: 0049 6221 424764 fax: 0049 6221 423454 web: www.dkfz.de/mga __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] about integration of a library into package creation
in that sense, it is useless to load the library from R source code
making my package
which is supposed to include it and load it
so if i understand the R philosophy it is not possible to load dll from
outside ;
the user has to load my package and manually has to load the necessary
libraries
each time he has to use my library, right ?
--
Nicolas
Prof Brian Ripley a écrit :
>
> And also to load the package, maybe with
>
> rterm R_DEFAULT_PACKAGES=NULL
>
>> library(svcR)
>
>
> as these messages often indicate missing package dependencies.
>
>>> * checking package subdirectories ... WARNING
>>> Subdirectory 'src' contains no source files.
>>> * checking R files for syntax errors ... OK
>>> * checking R files for library.dynam ... OK
>>> * checking S3 generic/method consistency ... WARNING
>>> Erreur : le chargement du package / espace de noms a echoue' pour
>>> 'svcR'
>>> Sequence d'appel :
>>> 2: stop(gettextf("package/namespace load failed for '%s'",
>>> libraryPkgName(packag
>>> e)),
>>>call. = FALSE, domain = NA)
>>> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
>>> FALSE)
>>> Execution arrete'e
>>> See section 'Generic functions and methods' of the 'Writing R
>>> Extensions'
>>> manual.
>>> * checking replacement functions ... WARNING
>>> Erreur : le chargement du package / espace de noms a echoue' pour
>>> 'svcR'
>>> Sequence d'appel :
>>> 2: stop(gettextf("package/namespace load failed for '%s'",
>>> libraryPkgName(packag
>>> e)),
>>
>
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] about integration of a library into package creation
On 6/12/2006 11:48 AM, Nicolas Turenne wrote:
> >
> >
> >You didn't show the results of installing your package. Did that work?
> >
> >Generally we advise to do a successful install before you try to run
> checks.
> >
> >Duncan Murdoch
>
> D:\RBuild\svcR> rcmd build D://RBuild//svcR --force --docs='all' --binary
> hence i obtain the file svcR_1.0.zip
> and following messages :
>
> D:\RBuild\svcR>rcmd build D://RBuild//svcR --force --docs='all' --binary
> * checking for file 'D://RBuild//svcR/DESCRIPTION' ... OK
> * preparing 'D://RBuild//svcR':
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> * removing junk files
> tar: svcR/svcR_1.0.tar: file is the archive; not dumped
> * excluding invalid files from 'svcR'
> Subdirectory 'R' contains invalid file names:
> ade4.dll quadprog.dll spdep.dll
You shouldn't have .dll files in the R directory. Normally you have
just one, built in the src directory, and then R will install it into
the libs directory. If you want multiple .dlls, I believe you can
build them in inst/libs, and they'll be copied to libs on installation.
However, the names of your dlls match the names of R packages, which
makes me think you are trying to incorporate routines from other
packages in your code. If that's what you are doing, this is not the
right way to do it. You should call other packages through their R
interfaces. There are plans to allow direct calls into the dlls, but so
far I don't think they exist.
Duncan Murdoch
> * checking for LF line-endings in source files
> * checking for empty or unneeded directories
> * building binary distribution
> WARNING
> * some HTML links may not be found
> installing R.css in C:/DOCUME~1/Nicolas/LOCALS~1/Temp/Rinst249298526
>
> Using auto-selected zip options ''
>
> -- Making package svcR
> adding build stamp to DESCRIPTION
> installing NAMESPACE file and metadata
> installing R files
> installing data files
> installing man source files
> installing indices
> not zipping data
> installing help
> >>> Building/Updating help pages for package 'svcR'
> Formats: text html latex example chm
> iris_att texthtmllatex chm
> iris_mat texthtmllatex chm
> iris_var texthtmllatex chm
> svcR texthtmllatex example chm
> Microsoft HTML Help Compiler 4.74.8702
>
> Compiling
> c:\DOCUME~1\Nicolas\LOCALS~1\Temp\Rbuild249291931\svcR\chm\svcR.chm
>
>
> Compile time: 0 minutes, 1 second
> 5 Topics
> 8 Local links
> 1 Internet link
> 1 Graphic
>
>
> Created
> c:\DOCUME~1\Nicolas\LOCALS~1\Temp\Rbuild249291931\svcR\chm\svcR.chm, 18,
> 283 bytes
> Compression increased file by 6,096 bytes.
> preparing package svcR for lazy loading
> adding MD5 sums
>
> packaged installation of package 'svcR' as svcR_1.0.zip
> * DONE (svcR)
>
>
>
> in R environment (Rgui front-end)
> i write:
> > install.packages("D:/RBuild/svcR/svcR_1.0.zip", repos=NULL)
> package 'svcR' successfully unpacked and MD5 sums checked
> updating HTML package descriptions
> > library(svcR)
>
> Attachement du package : 'svcR'
>
>
> The following object(s) are masked _by_ .GlobalEnv :
>
> findModelCluster
>
> >
>
>
> and finally when i typewrite my function
> i obtain :
> impossible de trouver la fonction "dudi.coa"
> it can not find the function called in the library that i call in the R
> source code
> by library(ade4)
>
> if i call my function by source(), it works well
>
> thank you for help
>
> -
>
> Nicolas
__
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Re: [Rd] Making a windows packages with zip
On 6/12/2006 11:25 AM, Uwe Ligges wrote:
> hadley wickham wrote:
>>>
>>> Either the latter or ask the Windows users to install the source package.
>>>
>>
>> Installing a source package doesn't seem to help:
>>
>>> install.packages("classifly", repos="http://ggobi.org/r/";, type="source")
>> Warning message:
>> installation of package 'classifly' had non-zero exit status in:
>> install.packages("classifly", repos = "http://ggobi.org/r/";,
>>
>> (Unfortunately I don't have access to a windows machine at present -
>> this is what a user reported)
>
>
> Oh well, certainly the user forgot to install the required tools as
> mentioned in the "R Installation and Administration" manual.
Or has the path incorrect while running Rgui. I normally do all source
installs from the command line where I have the path set to work
properly; if I start R from a shortcut, none of the tools are visible,
so the install.packages command requires the pre-compiled packages.
Duncan Murdoch
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Re: [Rd] about integration of a library into package creation
On 6/12/2006 12:25 PM, Nicolas Turenne wrote:
> in that sense, it is useless to load the library from R source code
> making my package
> which is supposed to include it and load it
>
> so if i understand the R philosophy it is not possible to load dll from
> outside ;
> the user has to load my package and manually has to load the necessary
> libraries
> each time he has to use my library, right ?
Not at all. When set up correctly, the user should just need to say
library(svcR) and all necessary packages and DLLs will be loaded.
The way to specify other packages is through the "Depends" line in the
DESCRIPTION file, and/or the import/importFrom lines in your NAMESPACE file.
Duncan Murdoch
>
> --
> Nicolas
>
> Prof Brian Ripley a écrit :
>
>>
>> And also to load the package, maybe with
>>
>> rterm R_DEFAULT_PACKAGES=NULL
>>
>>> library(svcR)
>>
>>
>> as these messages often indicate missing package dependencies.
>>
* checking package subdirectories ... WARNING
Subdirectory 'src' contains no source files.
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... WARNING
Erreur : le chargement du package / espace de noms a echoue' pour
'svcR'
Sequence d'appel :
2: stop(gettextf("package/namespace load failed for '%s'",
libraryPkgName(packag
e)),
call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
FALSE)
Execution arrete'e
See section 'Generic functions and methods' of the 'Writing R
Extensions'
manual.
* checking replacement functions ... WARNING
Erreur : le chargement du package / espace de noms a echoue' pour
'svcR'
Sequence d'appel :
2: stop(gettextf("package/namespace load failed for '%s'",
libraryPkgName(packag
e)),
>>>
>>
>
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Re: [Rd] about integration of a library into package creation
your answer is correct after checking some doc
but examples are rare
when i write in the description file
Depends: R (>= 2.3), quadprog, ade4, spdep
and in the namespcae file
useDynLib(quadprog)
useDynLib(spdep)
useDynLib(ade4)
importFrom("dist.dudi", "ade4")
importFrom("solve.QP", "quadprog")
importFrom("mstree", "ade4")
importFrom("neig2mat", "ade4")
importFrom("dist.dudi", "ade4")
importFrom("dudi.pca", "ade4")
importFrom("dudi.coa", "ade4")
importFrom("knearneigh", "spdep")
i obtain :
Namespace dependencies not required:
dist.dudi dudi.coa dudi.pca knearneigh mstree neig2mat solve.QP
if i delete the importFrom lines
i get an error about "loading / namespace not succesful" for svcr
i think the solution is not far but it is disturbing
thank for help
---
Nicolas
Duncan Murdoch a écrit :
> On 6/12/2006 12:25 PM, Nicolas Turenne wrote:
>
>> in that sense, it is useless to load the library from R source code
>> making my package
>> which is supposed to include it and load it
>>
>> so if i understand the R philosophy it is not possible to load dll
>> from outside ;
>> the user has to load my package and manually has to load the
>> necessary libraries
>> each time he has to use my library, right ?
>
>
> Not at all. When set up correctly, the user should just need to say
> library(svcR) and all necessary packages and DLLs will be loaded.
>
> The way to specify other packages is through the "Depends" line in the
> DESCRIPTION file, and/or the import/importFrom lines in your NAMESPACE
> file.
>
> Duncan Murdoch
>
>>
>> --
>> Nicolas
>>
>> Prof Brian Ripley a écrit :
>>
>>>
>>> And also to load the package, maybe with
>>>
>>> rterm R_DEFAULT_PACKAGES=NULL
>>>
library(svcR)
>>>
>>>
>>>
>>> as these messages often indicate missing package dependencies.
>>>
> * checking package subdirectories ... WARNING
> Subdirectory 'src' contains no source files.
> * checking R files for syntax errors ... OK
> * checking R files for library.dynam ... OK
> * checking S3 generic/method consistency ... WARNING
> Erreur : le chargement du package / espace de noms a echoue' pour
> 'svcR'
> Sequence d'appel :
> 2: stop(gettextf("package/namespace load failed for '%s'",
> libraryPkgName(packag
> e)),
>call. = FALSE, domain = NA)
> 1: library(package, lib.loc = lib.loc, character.only = TRUE,
> verbose =
> FALSE)
> Execution arrete'e
> See section 'Generic functions and methods' of the 'Writing R
> Extensions'
> manual.
> * checking replacement functions ... WARNING
> Erreur : le chargement du package / espace de noms a echoue' pour
> 'svcR'
> Sequence d'appel :
> 2: stop(gettextf("package/namespace load failed for '%s'",
> libraryPkgName(packag
> e)),
>>>
>>
>> __
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>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
>
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Re: [Rd] about integration of a library into package creation
Nicolas Turenne wrote:
> your answer is correct after checking some doc
> but examples are rare
>
> when i write in the description file
> Depends: R (>= 2.3), quadprog, ade4, spdep
>
> and in the namespcae file
>
> useDynLib(quadprog)
> useDynLib(spdep)
> useDynLib(ade4)
> importFrom("dist.dudi", "ade4")
Please do it the right way (package name first!):
importFrom("ade4", "dist.dudi")
Uwe Ligges
> importFrom("solve.QP", "quadprog")
> importFrom("mstree", "ade4")
> importFrom("neig2mat", "ade4")
> importFrom("dist.dudi", "ade4")
> importFrom("dudi.pca", "ade4")
> importFrom("dudi.coa", "ade4")
> importFrom("knearneigh", "spdep")
>
> i obtain :
> Namespace dependencies not required:
> dist.dudi dudi.coa dudi.pca knearneigh mstree neig2mat solve.QP
>
> if i delete the importFrom lines
> i get an error about "loading / namespace not succesful" for svcr
>
> i think the solution is not far but it is disturbing
>
> thank for help
>
> ---
> Nicolas
>
>
> Duncan Murdoch a écrit :
>
>> On 6/12/2006 12:25 PM, Nicolas Turenne wrote:
>>
>>> in that sense, it is useless to load the library from R source code
>>> making my package
>>> which is supposed to include it and load it
>>>
>>> so if i understand the R philosophy it is not possible to load dll
>>> from outside ;
>>> the user has to load my package and manually has to load the
>>> necessary libraries
>>> each time he has to use my library, right ?
>>
>> Not at all. When set up correctly, the user should just need to say
>> library(svcR) and all necessary packages and DLLs will be loaded.
>>
>> The way to specify other packages is through the "Depends" line in the
>> DESCRIPTION file, and/or the import/importFrom lines in your NAMESPACE
>> file.
>>
>> Duncan Murdoch
>>
>>> --
>>> Nicolas
>>>
>>> Prof Brian Ripley a écrit :
>>>
And also to load the package, maybe with
rterm R_DEFAULT_PACKAGES=NULL
> library(svcR)
as these messages often indicate missing package dependencies.
>> * checking package subdirectories ... WARNING
>> Subdirectory 'src' contains no source files.
>> * checking R files for syntax errors ... OK
>> * checking R files for library.dynam ... OK
>> * checking S3 generic/method consistency ... WARNING
>> Erreur : le chargement du package / espace de noms a echoue' pour
>> 'svcR'
>> Sequence d'appel :
>> 2: stop(gettextf("package/namespace load failed for '%s'",
>> libraryPkgName(packag
>> e)),
>>call. = FALSE, domain = NA)
>> 1: library(package, lib.loc = lib.loc, character.only = TRUE,
>> verbose =
>> FALSE)
>> Execution arrete'e
>> See section 'Generic functions and methods' of the 'Writing R
>> Extensions'
>> manual.
>> * checking replacement functions ... WARNING
>> Erreur : le chargement du package / espace de noms a echoue' pour
>> 'svcR'
>> Sequence d'appel :
>> 2: stop(gettextf("package/namespace load failed for '%s'",
>> libraryPkgName(packag
>> e)),
>
>>> __
>>> R-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>
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Re: [Rd] about integration of a library into package creation
> "UweL" == Uwe Ligges <[EMAIL PROTECTED]>
> on Mon, 12 Jun 2006 19:48:04 +0200 writes:
UweL> Nicolas Turenne wrote:
>> your answer is correct after checking some doc
>> but examples are rare
>>
>> when i write in the description file
>> Depends: R (>= 2.3), quadprog, ade4, spdep
>>
>> and in the namespcae file
>>
>> useDynLib(quadprog)
>> useDynLib(spdep)
>> useDynLib(ade4)
>> importFrom("dist.dudi", "ade4")
UweL> Please do it the right way (package name first!):
UweL> importFrom("ade4", "dist.dudi")
UweL> Uwe Ligges
and also add a Line
Imports: ade4, quadprog, spdep
to your DESCRIPTION file
[[yes, it is slightly unfortunate that things have to be *both*
in DESCRIPTION and in NAMESPACE,
but that's the way it currently is ]]
>> importFrom("solve.QP", "quadprog")
>> importFrom("mstree", "ade4")
>> importFrom("neig2mat", "ade4")
>> importFrom("dist.dudi", "ade4")
>> importFrom("dudi.pca", "ade4")
>> importFrom("dudi.coa", "ade4")
>> importFrom("knearneigh", "spdep")
>>
>> i obtain :
>> Namespace dependencies not required:
>> dist.dudi dudi.coa dudi.pca knearneigh mstree neig2mat solve.QP
>>
>> if i delete the importFrom lines
>> i get an error about "loading / namespace not succesful" for svcr
>>
>> i think the solution is not far but it is disturbing
>>
>> thank for help
>>
>> ---
>> Nicolas
>>
>>
>> Duncan Murdoch a écrit :
>>
>>> On 6/12/2006 12:25 PM, Nicolas Turenne wrote:
>>>
in that sense, it is useless to load the library from R source code
making my package
which is supposed to include it and load it
so if i understand the R philosophy it is not possible to load dll
from outside ;
the user has to load my package and manually has to load the
necessary libraries
each time he has to use my library, right ?
>>>
>>> Not at all. When set up correctly, the user should just need to say
>>> library(svcR) and all necessary packages and DLLs will be loaded.
>>>
>>> The way to specify other packages is through the "Depends" line in the
>>> DESCRIPTION file, and/or the import/importFrom lines in your NAMESPACE
>>> file.
>>>
>>> Duncan Murdoch
>>>
--
Nicolas
Prof Brian Ripley a écrit :
> And also to load the package, maybe with
>
> rterm R_DEFAULT_PACKAGES=NULL
>
> library(svcR)
>
>
> as these messages often indicate missing package dependencies.
>
>>> * checking package subdirectories ... WARNING
>>> Subdirectory 'src' contains no source files.
>>> * checking R files for syntax errors ... OK
>>> * checking R files for library.dynam ... OK
>>> * checking S3 generic/method consistency ... WARNING
>>> Erreur : le chargement du package / espace de noms a echoue' pour
>>> 'svcR'
>>> Sequence d'appel :
>>> 2: stop(gettextf("package/namespace load failed for '%s'",
>>> libraryPkgName(packag
>>> e)),
>>> call. = FALSE, domain = NA)
>>> 1: library(package, lib.loc = lib.loc, character.only = TRUE,
>>> verbose =
>>> FALSE)
>>> Execution arrete'e
>>> See section 'Generic functions and methods' of the 'Writing R
>>> Extensions'
>>> manual.
>>> * checking replacement functions ... WARNING
>>> Erreur : le chargement du package / espace de noms a echoue' pour
>>> 'svcR'
>>> Sequence d'appel :
>>> 2: stop(gettextf("package/namespace load failed for '%s'",
>>> libraryPkgName(packag
>>> e)),
>>
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[Rd] documentation for "Startup" should be clearer about system Rprofile (PR#8969)
Full_Name: Hsiu-Khuern Tang Version: 2.3.0 OS: Debian GNU/Linux Submission from: (NULL) (15.243.169.73) On reading ?Startup, I cannot find anything that says that R_HOME/library/base/R/Rprofile is always run. The "Note" section does say that R_HOME/etc/Renviron is distinct from the site-wide Renviron file, so I think this is a natural place to also mention that base/R/Rprofile is distinct from the site-wide Rprofile file. In addition, it would be helpful to indicate when base/R/Rprofile is run: after reading the Renviron files and before reading the site-wide Rprofile file. I suppose one possible reason for not including this information is that users are not supposed to alter base/R/Rprofile. Thanks, Hsiu-Khuern. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] normalizePath() warning
I've been getting the following warning after running 'install.packages()' recently: Warning message: insufficient OS support on this platform in: normalizePath(path) Does anyone know what this means? And does anyone know how I can get rid of the warning? I've just installed R on a fresh FC5 system so I feel I might have forgotten to install a package/library or something. Thanks, -roger __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] segfault with layout() after closing X11() device (PR#8970)
Full_Name: Don Maszle Version: 2.3.0 OS: Solaris 9 - 64 bit compile Submission from: (NULL) (206.86.87.3) After closing an X11() window by either clicking on the close button or by calling dev.off(), R 2.3.0 segfaults as shown below. Calling layout() before any X11() device is opened just opens a new device and applies the layout. $ R R : Copyright 2006, The R Foundation for Statistical Computing Version 2.3.0 (2006-04-24) 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. 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. > X11() > layout(matrix(1:2,1,2)) > # close window with mouse, or call dev.off() > layout(matrix(1:2,1,2)) *** caught segfault *** address 0, cause 'memory not mapped' Traceback: 1: X11() 2: layout(matrix(1:2, 1, 2)) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Building R package: make pdf & _masked_by_GlobalEnv
Hi I am assembling an R package (under Windows XP, R v.2.3) and have a very basic question. Running R CMD build does not generate a pdf. R CMD check generates a .dvi, but I cannot figure out how to automatically create the pdf. I thought from reading the "writing r extensions' manual that R CMD build was supposed to generate the pdf. I am having no success using various permutations of the Rd2dvi and texi2dvi, and I'm a bit frustrated. I have miktex 2.4, which should (I thought) have the necessary pdftex tools to do this. Maybe it does; I definitely have various directories named 'dvipdfm', 'pdftex', etc on my computer, but I have no idea whether there might be a problem. When I install the package, I receive the message that most of my functions are "masked _by_ .GlobalEnv". I have no idea what this means; I'm sure that this is amply documented, but I confess that I have a rather difficult time with much of the documentation on writing packages. Apologies for the elementary level of these questions, and thanks in advance for your help! ~Dan Rabosky Dan Rabosky Department of Ecology and Evolutionary Biology 237 Corson Hall Cornell University Ithaca, NY14853-2701 USA 607 254 4262 (office) 607 592 4636 (cell) [EMAIL PROTECTED] web: http://www.birds.cornell.edu/evb/Graduates_Dan.htm __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] normalizePath() warning
On 6/12/2006 4:53 PM, Roger D. Peng wrote: > I've been getting the following warning after running 'install.packages()' > recently: > > Warning message: > insufficient OS support on this platform in: normalizePath(path) > > Does anyone know what this means? And does anyone know how I can get rid of > the > warning? I've just installed R on a fresh FC5 system so I feel I might have > forgotten to install a package/library or something. This is printed when your R source was compiled without these defines: #if defined(HAVE_GETCWD) && defined(HAVE_REALPATH) I guess you can look in your config log to see why you don't have those. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Building R package: make pdf & _masked_by_GlobalEnv
On 6/12/2006 9:47 PM, Dan Rabosky wrote: > Hi > > I am assembling an R package (under Windows XP, R v.2.3) and have a very > basic question. Running R CMD build does not generate a pdf. R CMD check > generates a .dvi, but I cannot figure out how to automatically create the > pdf. I thought from reading the "writing r extensions' manual that R CMD > build was supposed to generate the pdf. I am having no success using > various permutations of the Rd2dvi and texi2dvi, and I'm a bit > frustrated. I have miktex 2.4, which should (I thought) have the necessary > pdftex tools to do this. Maybe it does; I definitely have various > directories named 'dvipdfm', 'pdftex', etc on my computer, but I have no > idea whether there might be a problem. You need to give a bit more detail. What is the .pdf being created from? What do things look like when you run a build? Does install work? > > When I install the package, I receive the message that most of my functions > are "masked _by_ .GlobalEnv". I have no idea what this means; I'm sure > that this is amply documented, but I confess that I have a rather difficult > time with much of the documentation on writing packages. This means that you have variables in your workspace with the same names as ones in your package. You probably want to clean out your workspace, because most uses will find those versions before the ones in the package -- and that really messes up testing, etc. Duncan Murdoch > > Apologies for the elementary level of these questions, and thanks in > advance for your help! > > ~Dan Rabosky > > > > > > > Dan Rabosky > Department of Ecology and Evolutionary Biology > 237 Corson Hall > Cornell University > Ithaca, NY14853-2701 USA > 607 254 4262 (office) > 607 592 4636 (cell) > [EMAIL PROTECTED] > web: http://www.birds.cornell.edu/evb/Graduates_Dan.htm > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Building R package: make pdf & _masked_by_GlobalEnv
>> >>I am assembling an R package (under Windows XP, R v.2.3) and have a very >>basic question. Running R CMD build does not generate a pdf. R CMD >>check generates a .dvi, but I cannot figure out how to automatically >>create the pdf. I thought from reading the "writing r extensions' manual >>that R CMD build was supposed to generate the pdf. I am having no >>success using various permutations of the Rd2dvi and texi2dvi, and I'm a >>bit frustrated. I have miktex 2.4, which should (I thought) have the >>necessary pdftex tools to do this. Maybe it does; I definitely have >>various directories named 'dvipdfm', 'pdftex', etc on my computer, but I >>have no idea whether there might be a problem. > >You need to give a bit more detail. What is the .pdf being created >from? What do things look like when you run a build? Does install work? I guess I'm not sure what the .pdf is being created from - I don't know how this works. I assumed that my set of .Rd files from the man dir would automatically be converted into .pdf, much like 'check' reads them into a dvi document. When I run a build, I get an archive with all of my .R source files, the DESCRIPTION, the .Rd files, my datafiles, and any documentation I've placed in inst/doc. When I install this from CMD, the html help & chtml files compile, examples are copied from the /man directory to their own .Rd files, and everything - to me - appears OK. 'Install' from R CMD works with no problem - it warns me that my 'examples' directory is empty, but it proceeds to create the examples from my .Rd files anyway. I only get a .dvi manual when running 'check'. >>When I install the package, I receive the message that most of my >>functions are "masked _by_ .GlobalEnv". I have no idea what this means; >>I'm sure that this is amply documented, but I confess that I have a >>rather difficult time with much of the documentation on writing packages. > >This means that you have variables in your workspace with the same names >as ones in your package. You probably want to clean out your workspace, >because most uses will find those versions before the ones in the package >-- and that really messes up testing, etc. thanks for the clarification! __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R-2.3.1 does not install on FreeBSD 4.11-RELEASE (PR#8971)
Full_Name: Kenji Rikitake
Version: 2.3.1
OS: FreeBSD 4.11-RELEASE-p18
Submission from: (NULL) (220.157.163.221)
After doing
./configure --disable-mbcs
(as default in FreeBSD 4.x)
and
make
the compilation stops at src/main/printutils.c as:
printutils.c: In function `Rvprintf':
printutils.c:582: `va_start' used in function with fixed args
printutils.c:591: syntax error before `}'
the following patch includes two fixes:
1) removing unnecessary va_start() and va_end() macro for Rvprintf() in
src/main/printutils.c
2) fixing error by adding {} around calling error() in src/main/printutils.c
--- src/main/printutils.c.FCS Mon Apr 10 07:19:28 2006
+++ src/main/printutils.c Tue Jun 13 12:07:05 2006
@@ -579,14 +579,15 @@
(con->vfprintf)(con, format, argcopy);
va_end(argcopy);
#else /* don't support sink(,split=TRUE) */
- va_start(arg, format);
+ /* va_start(arg, format); */ /* not for FREEBSD_4 */
(con->vfprintf)(con, format, arg);
- va_end(arg);
+ /* va_end(arg); */
+ /* not for FREEBSD_4 */
#endif
con->fflush(con);
con_num = getActiveSink(i++);
#ifndef HAVE_VA_COPY
- if (con_num>0) error("Internal error: this platform does not support
split output")
+ if (con_num>0) {error("Internal error: this platform does not support
split output");}
#endif
} while(con_num>0);
Also, I needed to fix the permission after doing
make install
using the following set of commands:
cd /usr/local/lib/R/exec
chmod 0755 R
cd /usr/local/lib/R/lib
chmod 0755 libRlapack.so
cd /usr/local/lib/R/base
chmod 755 Meta R R-ex demo help html latex man po
find . -type d -not -perm -001 | xargs chmod go+rx
find . -type f -and -not -perm -444 | xargs chmod go+r
cd /usr/local/lib/R/modules
chmod 755 *.so
[End of bug report]
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Re: [Rd] R-2.3.1 does not install on FreeBSD 4.11-RELEASE (PR#8971)
The first point is already changed in R-patched: please try it and
confirm. The NEWS file says:
o There were problems in src/main/printutils.c on platforms
that did not have va_copy.
What architecture and compiler is this (and is FreeBSD 4.11-RELEASE not
rather old)? va_copy is a C99 feature, and was introduced as __va_copy
well before 1999. (__va_copy was in gcc 2.95.3 for example, and 2.3.1
builds on platforms with __va_copy and not va_copy.)
Your second point seems to be covered by the instructions to set umask
appropriately: people who have are not having to change permissions after
installation.
On Tue, 13 Jun 2006, [EMAIL PROTECTED] wrote:
> Full_Name: Kenji Rikitake
> Version: 2.3.1
> OS: FreeBSD 4.11-RELEASE-p18
> Submission from: (NULL) (220.157.163.221)
>
>
> After doing
> ./configure --disable-mbcs
> (as default in FreeBSD 4.x)
Why do you claim that is `default in FreeBSD 4.x'?
> and
> make
> the compilation stops at src/main/printutils.c as:
> printutils.c: In function `Rvprintf':
> printutils.c:582: `va_start' used in function with fixed args
> printutils.c:591: syntax error before `}'
>
> the following patch includes two fixes:
>
> 1) removing unnecessary va_start() and va_end() macro for Rvprintf() in
> src/main/printutils.c
> 2) fixing error by adding {} around calling error() in src/main/printutils.c
>
> --- src/main/printutils.c.FCS Mon Apr 10 07:19:28 2006
> +++ src/main/printutils.c Tue Jun 13 12:07:05 2006
> @@ -579,14 +579,15 @@
> (con->vfprintf)(con, format, argcopy);
> va_end(argcopy);
> #else /* don't support sink(,split=TRUE) */
> - va_start(arg, format);
> + /* va_start(arg, format); */ /* not for FREEBSD_4 */
> (con->vfprintf)(con, format, arg);
> - va_end(arg);
> + /* va_end(arg); */
> + /* not for FREEBSD_4 */
> #endif
> con->fflush(con);
> con_num = getActiveSink(i++);
> #ifndef HAVE_VA_COPY
> - if (con_num>0) error("Internal error: this platform does not support
> split output")
> + if (con_num>0) {error("Internal error: this platform does not support
> split output");}
> #endif
> } while(con_num>0);
>
> Also, I needed to fix the permission after doing
> make install
> using the following set of commands:
>
> cd /usr/local/lib/R/exec
> chmod 0755 R
> cd /usr/local/lib/R/lib
> chmod 0755 libRlapack.so
> cd /usr/local/lib/R/base
> chmod 755 Meta R R-ex demo help html latex man po
> find . -type d -not -perm -001 | xargs chmod go+rx
> find . -type f -and -not -perm -444 | xargs chmod go+r
> cd /usr/local/lib/R/modules
> chmod 755 *.so
>
> [End of bug report]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Building R package: make pdf & _masked_by_GlobalEnv
On Mon, 12 Jun 2006, Dan Rabosky wrote: > >>> >>> I am assembling an R package (under Windows XP, R v.2.3) and have a very >>> basic question. Running R CMD build does not generate a pdf. R CMD >>> check generates a .dvi, but I cannot figure out how to automatically >>> create the pdf. I thought from reading the "writing r extensions' manual >>> that R CMD build was supposed to generate the pdf. I am having no >>> success using various permutations of the Rd2dvi and texi2dvi, and I'm a >>> bit frustrated. I have miktex 2.4, which should (I thought) have the >>> necessary pdftex tools to do this. Maybe it does; I definitely have >>> various directories named 'dvipdfm', 'pdftex', etc on my computer, but I >>> have no idea whether there might be a problem. >> >> You need to give a bit more detail. What is the .pdf being created >> from? What do things look like when you run a build? Does install work? > > I guess I'm not sure what the .pdf is being created from - I don't know how > this works. I assumed that my set of .Rd files from the man dir would > automatically be converted into .pdf, much like 'check' reads them into a > dvi document. When I run a build, I get an archive with all of my .R [Assuming things which are not in the documentation is not a good idea.] > source files, the DESCRIPTION, the .Rd files, my datafiles, and any > documentation I've placed in inst/doc. When I install this from CMD, the > html help & chtml files compile, examples are copied from the /man > directory to their own .Rd files, and everything - to me - appears > OK. 'Install' from R CMD works with no problem - it warns me that my > 'examples' directory is empty, but it proceeds to create the examples from > my .Rd files anyway. > > I only get a .dvi manual when running 'check'. Yes, 'check' only checks that the latex can be compiled. It is not trying to create usable output for you: for that use R CMD Rd2dvi. E.g. for a PDF manual for package grDevices, use R CMD Rd2dvi --pdf .../library/grDevices which works for me. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-2.3.1 does not install on FreeBSD 4.11-RELEASE (PR#8971)
Prof. Ripley: In the message <[EMAIL PROTECTED]> dated Tue, Jun 13, 2006 at 06:53:20AM +0100, Prof Brian Ripley <[EMAIL PROTECTED]> writes: > The first point is already changed in R-patched: please try it and > confirm. [...] I'm compiling the kit R-patched_2006-06-12.tar.gz right now. The buggy code is surely removed and it's keep on building well. > What architecture and compiler is this (and is FreeBSD 4.11-RELEASE not > rather old)? va_copy is a C99 feature, and was introduced as __va_copy > well before 1999. (__va_copy was in gcc 2.95.3 for example, and 2.3.1 > builds on platforms with __va_copy and not va_copy.) gcc 2.95.4 on FreeBSD 4.11-RELEASE-p18; note that stdarg(3) says STANDARDS The va_start(), va_arg(), and va_end() macros conform to ISO/IEC 9899:1990 (``ISO C90''). And va_copy() does not exist. I think this is a common FreeBSD-related problem, fixed in a later release, on 5.x or 6.x. > Your second point seems to be covered by the instructions to set umask > appropriately: people who have are not having to change permissions after > installation. I set umask to 0022 manually and did "make install" from tcsh, but didn't get the permission flags straighten out. I'll check this out again, though I think I need to investigate a bit. > >./configure --disable-mbcs > Why do you claim that is `default in FreeBSD 4.x'? All I know is that in FreeBSD ports math/R and on 4.x, --disable-mbcs had been required to get around with the broken MBCS library handling of FreeBSD. So I followed the convention. Many thanks for your help. // Kenji Rikitake __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] normalizePath() warning
On Mon, 12 Jun 2006, Duncan Murdoch wrote: > On 6/12/2006 4:53 PM, Roger D. Peng wrote: >> I've been getting the following warning after running 'install.packages()' >> recently: >> >> Warning message: >> insufficient OS support on this platform in: normalizePath(path) >> >> Does anyone know what this means? And does anyone know how I can get rid of >> the >> warning? I've just installed R on a fresh FC5 system so I feel I might have >> forgotten to install a package/library or something. > > This is printed when your R source was compiled without these defines: > > #if defined(HAVE_GETCWD) && defined(HAVE_REALPATH) > > I guess you can look in your config log to see why you don't have those. This worked for me on a vanilla FC5 system. I guess the issue is likely to be realpath, whose definition is enclosed by #if defined __USE_BSD || defined __USE_XOPEN_EXTENDED #endif so I would review the compiler options used: -std=gnu99 is recommended (and selected by default). I do get the warning with -std=c89 and -std=c99. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-2.3.1 does not install on FreeBSD 4.11-RELEASE (PR#8971)
On Tue, 13 Jun 2006, Kenji Rikitake wrote: > Prof. Ripley: > > In the message <[EMAIL PROTECTED]> > dated Tue, Jun 13, 2006 at 06:53:20AM +0100, > Prof Brian Ripley <[EMAIL PROTECTED]> writes: >> The first point is already changed in R-patched: please try it and >> confirm. [...] > > I'm compiling the kit R-patched_2006-06-12.tar.gz right now. The buggy > code is surely removed and it's keep on building well. > >> What architecture and compiler is this (and is FreeBSD 4.11-RELEASE not >> rather old)? va_copy is a C99 feature, and was introduced as __va_copy >> well before 1999. (__va_copy was in gcc 2.95.3 for example, and 2.3.1 >> builds on platforms with __va_copy and not va_copy.) > > gcc 2.95.4 on FreeBSD 4.11-RELEASE-p18; note that stdarg(3) says > > STANDARDS > The va_start(), va_arg(), and va_end() macros conform to ISO/IEC > 9899:1990 (``ISO C90''). > > And va_copy() does not exist. I think this is a common FreeBSD-related > problem, fixed in a later release, on 5.x or 6.x. __va_copy is supposed to exist on that compiler, and the R code maps __va_copy to va_copy when the first exists and the second does not. >> Your second point seems to be covered by the instructions to set umask >> appropriately: people who have are not having to change permissions after >> installation. > > I set umask to 0022 manually and did "make install" from tcsh, but > didn't get the permission flags straighten out. I'll check this out > again, though I think I need to investigate a bit. You need to set umask when you unpack and build, not just when you install. >>> ./configure --disable-mbcs > >> Why do you claim that is `default in FreeBSD 4.x'? > > All I know is that in FreeBSD ports math/R and on 4.x, --disable-mbcs > had been required to get around with the broken MBCS library handling of > FreeBSD. So I followed the convention. Ah, `convention' rather than default (R's configure does not set it). > > Many thanks for your help. > > // Kenji Rikitake > > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-2.3.1 does not install on FreeBSD 4.11-RELEASE (PR#8971)
In the message <[EMAIL PROTECTED]> dated Tue, Jun 13, 2006 at 07:25:01AM +0100, Prof Brian Ripley <[EMAIL PROTECTED]> writes: > __va_copy is supposed to exist on that compiler, and the R code maps > __va_copy to va_copy when the first exists and the second does not. Unfortunately configure did not find the __va_copy either. It says in the config.log: configure:31136: checking whether __va_copy exists and is declared configure:31169: gcc -o conftest -g -O2 -D__NO_MATH_INLINES -I/usr/local/include -L/usr/local/lib conftest.c -lm >&5 conftest.c: In function `main': conftest.c:115: `__va_copy' undeclared (first use in this function) conftest.c:115: (Each undeclared identifier is reported only once conftest.c:115: for each function it appears in.) configure:31175: $? = 1 configure: failed program was: [rest deleted] This seems to be well-known, regarding the Google search results of "FreeBSD va_copy". > You need to set umask when you unpack and build, not just when you > install. OK I will do that. > >All I know is that in FreeBSD ports math/R and on 4.x, --disable-mbcs > >had been required to get around with the broken MBCS library handling of > >FreeBSD. So I followed the convention. > > Ah, `convention' rather than default (R's configure does not set it). Sorry for being ambiguous on this. Many thanks again, // Kenji Rikitake __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
