Re: [Rd] package compile error on RHEL x86_64
This is a problem with your compiler: it should be linking against a shared version of libstdc++. Please take this up with your OS support. On Wed, 14 Jun 2006, Dan Lipsitt wrote: > I am unable to install the gmp package on an x86_64 (Xeon) machine. I > have had the same problem with other packages (eg. MCMCpack) as well. > I am running Red Hat Enterprise Linux 4.1. > I get the following error: > > g++ -shared -L/usr/local/lib64 -o gmp.so biginteger.o > biginteger_operator.o bigintegerR.o bigrational.o > bigrational_operator.o bigrationalR.o factor.o -L/usr/local/lib/ -lgmp > /usr/bin/ld: > /usr/lib/gcc/x86_64-redhat-linux/3.4.3/libstdc++.a(functexcept.o): > relocation R_X86_64_32 against `std::bad_exception::~bad_exception()' > can not be used when making a shared object; recompile with -fPIC > /usr/lib/gcc/x86_64-redhat-linux/3.4.3/libstdc++.a: could not read > symbols: Bad value > > However, I have found that if I run "R CMD SHLIB" twice in the src/ > directory, once to build the .o files, and once to link, I can build > the shared library. If I run it on the .o files instead of the .cc > files it uses gcc instead of g++. This appears to be the change that > allows the lib to build. "-fPIC" seems to have nothing to do with it. > > So my question is: How do I get "R CMD INSTALL" to link with gcc > instead of g++? I have tried adding "LINK.cc = $(LINK.c)" to the top > of src/Makevars.in and then running "R CMD check" in the top dir of > the package, but it uses g++ anyway. Any other fix or workaround > suggestions would be appreciated as well. > > A commandline transcript follows below. > > Thanks, > Dan > > $ sudo R CMD INSTALL gmp_0.3-4.tar.gz > * Installing *source* package 'gmp' ... > creating cache ./config.cache > checking for __gmpz_ui_sub in -lgmp... yes > updating cache ./config.cache > creating ./config.status > creating src/Makevars > ** libs > g++ -I/usr/lib/R/include -I/usr/local/include/ -Wno-conversion > -I/usr/local/include -fPIC -O2 -g -c biginteger.cc -o biginteger.o > g++ -I/usr/lib/R/include -I/usr/local/include/ -Wno-conversion > -I/usr/local/include -fPIC -O2 -g -c biginteger_operator.cc -o > biginteger_operator.o > g++ -I/usr/lib/R/include -I/usr/local/include/ -Wno-conversion > -I/usr/local/include -fPIC -O2 -g -c bigintegerR.cc -o > bigintegerR.o > g++ -I/usr/lib/R/include -I/usr/local/include/ -Wno-conversion > -I/usr/local/include -fPIC -O2 -g -c bigrational.cc -o > bigrational.o > g++ -I/usr/lib/R/include -I/usr/local/include/ -Wno-conversion > -I/usr/local/include -fPIC -O2 -g -c bigrational_operator.cc -o > bigrational_operator.o > g++ -I/usr/lib/R/include -I/usr/local/include/ -Wno-conversion > -I/usr/local/include -fPIC -O2 -g -c bigrationalR.cc -o > bigrationalR.o > g++ -I/usr/lib/R/include -I/usr/local/include/ -Wno-conversion > -I/usr/local/include -fPIC -O2 -g -c factor.cc -o factor.o > g++ -shared -L/usr/local/lib64 -o gmp.so biginteger.o > biginteger_operator.o bigintegerR.o bigrational.o > bigrational_operator.o bigrationalR.o factor.o -L/usr/local/lib/ -lgmp > /usr/bin/ld: > /usr/lib/gcc/x86_64-redhat-linux/3.4.3/libstdc++.a(functexcept.o): > relocation R_X86_64_32 against `std::bad_exception::~bad_exception()' > can not be used when making a shared object; recompile with -fPIC > /usr/lib/gcc/x86_64-redhat-linux/3.4.3/libstdc++.a: could not read > symbols: Bad value > collect2: ld returned 1 exit status > make: *** [gmp.so] Error 1 > ERROR: compilation failed for package 'gmp' > > $ tar xzf gmp_0.3-4.tar.gz > $ cd gmp/src > $ R CMD SHLIB *.cc > g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -c > biginteger.cc -o biginteger.o > g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -c > biginteger_operator.cc -o biginteger_operator.o > g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -c > bigintegerR.cc -o bigintegerR.o > g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -c > bigrational.cc -o bigrational.o > g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -c > bigrational_operator.cc -o bigrational_operator.o > g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -c > bigrationalR.cc -o bigrationalR.o > g++ -I/usr/lib/R/include -I/usr/local/include -fPIC -O2 -g -c > factor.cc -o factor.o > g++ -shared -L/usr/local/lib64 -o biginteger.so biginteger.o > biginteger_operator.o bigintegerR.o bigrational.o > bigrational_operator.o bigrationalR.o factor.o > /usr/bin/ld: > /usr/lib/gcc/x86_64-redhat-linux/3.4.3/libstdc++.a(functexcept.o): > relocation R_X86_64_32 against `std::bad_exception::~bad_exception()' > can not be used when making a shared object; recompile with -fPIC > /usr/lib/gcc/x86_64-redhat-linux/3.4.3/libstdc++.a: could not read > symbols: Bad value > collect2: ld returned 1 exit status > make: *** [biginteger.so] Error 1 > $ R CMD SHLIB *.o > gcc -shared -L/usr/local/lib64 -o biginteger.so biginteger.o > biginteger_operator.o bigintegerR.o bigra
[Rd] statically linked embedded R
Hello, I am trying to compile a stripped down libR.a that I can statically link into an application running in a limited system environment (i.e. no shared libraries, no dynamic loading, no graphics, no threads, single process, etc). I have tried configuring --with-x=NO and --enable-Rshlib and --enable- static=yes without success. But I suspect I need to get my hands a bit dirtier. Can anyone give me some pointers to the best way to approach building this? Thank you very much Sean __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] separators in data()
Ben, you confused read.csv and read.csv2. Separator in read.csv is ",", while it is ";" in read.csv2. This is due to use of different decimal symbols in some european languages - mine is one of them and I really hate this. So the situation is: decimal separator english . , some european lang. , ; There is then of course also a need to handle decimal separator and this is done in read.csv2. > just out of curiosity: > > why is the default behavior in data() for reading in .csv files > to use sep=";" (semicolon rather than comma)? is this a historical > artifact of some sort, or is there other logic to it? It caught > me by surprise since I was expecting it to be sep="," as in > read.csv() ... > > cheers > Ben Bolker -- Lep pozdrav / With regards, Gregor Gorjanc -- University of Ljubljana PhD student Biotechnical Faculty Zootechnical Department URI: http://www.bfro.uni-lj.si/MR/ggorjan Groblje 3 mail: gregor.gorjanc bfro.uni-lj.si SI-1230 Domzale tel: +386 (0)1 72 17 861 Slovenia, Europefax: +386 (0)1 72 17 888 -- "One must learn by doing the thing; for though you think you know it, you have no certainty until you try." Sophocles ~ 450 B.C. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] separators in data()
I don't think the poster is confused. He is referring to the data() command and that one uses semicolon, not comma, and the poster is wondering what the motivation is for that choice. From ?data Currently, four formats of data files are supported: 1. files ending '.R' or '.r' are 'source()'d in, with the R working directory changed temporarily to the directory containing the respective file. 2. files ending '.RData' or '.rda' are 'load()'ed. 3. files ending '.tab', '.txt' or '.TXT' are read using 'read.table(..., header = TRUE)', and hence result in a data frame. 4. files ending '.csv' or '.CSV' are read using 'read.table(..., header = TRUE, sep = ";")', and also result in a data frame. On 6/15/06, Gregor Gorjanc <[EMAIL PROTECTED]> wrote: > Ben, > > you confused read.csv and read.csv2. Separator in read.csv is ",", while > it is ";" in read.csv2. This is due to use of different decimal symbols > in some european languages - mine is one of them and I really hate > this. So the situation is: > > decimal separator > english . , > some european lang. , ; > > There is then of course also a need to handle decimal separator and this > is done in read.csv2. > > > just out of curiosity: > > > > why is the default behavior in data() for reading in .csv files > > to use sep=";" (semicolon rather than comma)? is this a historical > > artifact of some sort, or is there other logic to it? It caught > > me by surprise since I was expecting it to be sep="," as in > > read.csv() ... > > > > cheers > > Ben Bolker > > > -- > Lep pozdrav / With regards, >Gregor Gorjanc > > -- > University of Ljubljana PhD student > Biotechnical Faculty > Zootechnical Department URI: http://www.bfro.uni-lj.si/MR/ggorjan > Groblje 3 mail: gregor.gorjanc bfro.uni-lj.si > > SI-1230 Domzale tel: +386 (0)1 72 17 861 > Slovenia, Europefax: +386 (0)1 72 17 888 > > -- > "One must learn by doing the thing; for though you think you know it, > you have no certainty until you try." Sophocles ~ 450 B.C. > > __ > 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
[Rd] download.file() yields incomplete files with method="internal"
Dear all,
as the bug # 7991 is flagged not-reproducible, let me give you some pieces
of code, as I have the same or similar problem. The problem always shows up
with the first example (a small text file) and only sometimes (but without
obvious pattern) with the second example, which is a binary file.
> download.file("ftp://ftp.nhc.noaa.gov/pub/atcf/btk/bal012006.dat";,
"C:/temp/bal012006.dat", method = 'internal', mode = 'w', cacheOK = FALSE)
trying URL 'ftp://ftp.nhc.noaa.gov/pub/atcf/btk/bal012006.dat'
ftp data connection made, file length 5110 bytes
opened URL
downloaded 0 bytes
Warning message:
downloaded length 0 != reported length 5110
>
download.file("ftp://ftp.nhc.noaa.gov/pub/atcf/aid_public/aal012006.dat.gz";,
"C:/temp/aal012006.dat.gz", method = 'internal', mode = 'wb', cacheOK =
FALSE)
trying URL 'ftp://ftp.nhc.noaa.gov/pub/atcf/aid_public/aal012006.dat.gz'
ftp data connection made, file length 173760 bytes
opened URL
downloaded 155Kb
Warning message:
downloaded length 159140 != reported length 173760
Finally, is the spec of the system I'm working on:
> version
_
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)
> win.version()
[1] "Windows XP Professional (build 2600) Service Pack 2.0"
Many thanks in advance and best regards,
Jan
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[Rd] Ganador del premio (Winner of a prize) (PR#8985)
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Re: [Rd] download.file() yields incomplete files with method="internal"
Hi Jan!
* [EMAIL PROTECTED] <[EMAIL PROTECTED]> [060615 15:10]:
>
> Dear all,
>
> as the bug # 7991 is flagged not-reproducible, let me give you some pieces
> of code, as I have the same or similar problem. The problem always shows up
> with the first example (a small text file) and only sometimes (but without
> obvious pattern) with the second example, which is a binary file.
>
> > download.file("ftp://ftp.nhc.noaa.gov/pub/atcf/btk/bal012006.dat";,
> "C:/temp/bal012006.dat", method = 'internal', mode = 'w', cacheOK = FALSE)
> trying URL 'ftp://ftp.nhc.noaa.gov/pub/atcf/btk/bal012006.dat'
> ftp data connection made, file length 5110 bytes
> opened URL
> downloaded 0 bytes
>
> Warning message:
> downloaded length 0 != reported length 5110
when I tried the first example (Windows NT, R 2.3.1), it worked
correctly two times, and then gave exactly the error message you cited
in the third run.
The second example worked once, and then gave the behaviour cited by
you, only the downloaded length differed. Specs:
> version
_
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)
> win.version()
[1] "Windows NT 4.0 (build 1381) Service Pack 6"
No problems on Linux, R 2.3.1 (after replacing "C:/temp" by /tmp/).
Regards,
Johannes
>
> >
> download.file("ftp://ftp.nhc.noaa.gov/pub/atcf/aid_public/aal012006.dat.gz";,
> "C:/temp/aal012006.dat.gz", method = 'internal', mode = 'wb', cacheOK =
> FALSE)
> trying URL 'ftp://ftp.nhc.noaa.gov/pub/atcf/aid_public/aal012006.dat.gz'
> ftp data connection made, file length 173760 bytes
> opened URL
> downloaded 155Kb
>
> Warning message:
> downloaded length 159140 != reported length 173760
>
>
> Finally, is the spec of the system I'm working on:
> > version
>_
> 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)
> > win.version()
> [1] "Windows XP Professional (build 2600) Service Pack 2.0"
>
>
> Many thanks in advance and best regards,
> Jan
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
--
Dr. Johannes Ranke [EMAIL PROTECTED]
UFT Bremen, Leobenerstr. 1 +49 421 218 8971
D-28359 Bremen http://www.uft.uni-bremen.de/chemie/ranke
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[Rd] problem to read data into a package
Hello i have this following error making a package -- 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 Error in read.table(zfile, header = TRUE) : more column than column names this kind of error is produced when spaces are met in data . in my case there are only tabulations and three columns of real numbers (with 3 digits) i have no idea what it happens thank for help -- Nicolas __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] S4 class slot name 'names' is not allowed (PR#8768 S4Methods)
Hello,
Besides the problem with using "names," one has a similar problem using
".Data" together with "VIRTUAL."
Consider the top of p. 295 of the green book. This should work (I had to
change "structure" to "junk" because "structure" is a sealed class
definition):
setClass("junk",
representation(.Data="vector",VIRTUAL))
but this is what one gets
setClass("junk",
+ representation(.Data="vector",VIRTUAL))
Error in representation(.Data = "vector", VIRTUAL) :
object "VIRTUAL" not found
Now consider p. 5 of "S4 Classes in 15 pages, more or less." This should
work:
setClass("myVclass", representation(a = "character", "VIRTUAL"))
and indeed it does:
setClass("myVclass", representation(a = "character", "VIRTUAL"))
[1] "myVclass"
The need to quote "VIRTUAL" is the first bug, but read on.
Now take the above example, and change the first slot's name to ".Data."
Now, one gets:
setClass("myVclass", representation(.Data = "character", "VIRTUAL"))
Error in makePrototypeFromClassDef(properties, ClassDef, immediate,
where) : in constructing the prototype for class "myVclass": prototype has
class "list", but the data part specifies class "character"
So "names" is not the only problematic slot name.
Marshall Feldman
Dr. Marshall Feldman
Acting Director of Research and Academic Affairs
Center for Urban Studies and Research
The University of Rhode Island
80 Washington Street
Providence, RI 02903-1819
email: marsh @ uri.edu (remove spaces)
telephone: (401) 277-5218
fax: (401) 277-5099
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Re: [Rd] package compile error on RHEL x86_64
On 6/15/06, Prof Brian Ripley <[EMAIL PROTECTED]> wrote: > This is a problem with your compiler: it should be linking against a > shared version of libstdc++. Please take this up with your OS support. Okay, will do. In the meantime, do you know of a way I can convince R CMD INSTALL to use gcc instead of g++ for the link step? Thanks, Dan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] separators in data()
On Thu, 15 Jun 2006, Gabor Grothendieck wrote: > Currently, four formats of data files are supported: > >1. files ending '.R' or '.r' are 'source()'d in, with the R >working directory changed temporarily to the directory >containing the respective file. > >2. files ending '.RData' or '.rda' are 'load()'ed. > >3. files ending '.tab', '.txt' or '.TXT' are read using > 'read.table(..., header = TRUE)', and hence result in a data > frame. > >4. files ending '.csv' or '.CSV' are read using > 'read.table(..., header = TRUE, sep = ";")', and also result > in a data frame. As an aside, I have wondered why there is no intrinsic support for dot-tsv extension (*.tsv) that would trigger use of read.delim method. -- SIGSIG -- signature too long (core dumped) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] cat, print and documentation disagree (PR#8988)
Full_Name: Paul Bailey Version: 2.3.1 OS: OS X (10.4.6) Submission from: (NULL) (128.135.133.123) according to cat's help file, "'cat' converts numeric/complex vectors in the same way as 'print' (and not in the same way as 'as.character' which is used by the S equivalent), so 'options' '"digits"' and '"scipen"' are relevant." But, run this (what I got after # marks) -- a <- c(0.1,.0111) > print(a) [1] 0.1000 0.0111 > cat(a) 0.1 0.0111> -- I would expect the two to make the same conversion and send the same number of digits (zeros or not) to standard out, OR for the documentation to point out that there are differences in that the same output can lead to different things being sent to standard out. I observed this same problem in Win XP with R 2.3.0 Cheers, Paul __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] download.file() yields incomplete files with method="internal"
On Thu, 15 Jun 2006 [EMAIL PROTECTED] wrote:
> as the bug # 7991 is flagged not-reproducible, let me give you some pieces
> of code, as I have the same or similar problem. The problem always shows up
> with the first example (a small text file) and only sometimes (but without
> obvious pattern) with the second example, which is a binary file.
>
> > download.file("ftp://ftp.nhc.noaa.gov/pub/atcf/btk/bal012006.dat";,
> "C:/temp/bal012006.dat", method = 'internal', mode = 'w', cacheOK = FALSE)
> trying URL 'ftp://ftp.nhc.noaa.gov/pub/atcf/btk/bal012006.dat'
> ftp data connection made, file length 5110 bytes
> opened URL
> downloaded 0 bytes
>
> Warning message:
> downloaded length 0 != reported length 5110
Two versions of curl (7.10.6 and 7.15.1) on my Linux
box fail on this ftp server also. They timeout when
starting "Extended Passive Mode". Does this sort of
failure indicate a firewall is getting in the way?
% curl --version
curl 7.10.6 (i386-redhat-linux-gnu) libcurl/7.10.6 OpenSSL/0.9.7a ipv6
zlib/1.1.4
Protocols: ftp gopher telnet dict ldap http file https ftps
Features: IPv6 SSL libz NTLM
% /usr/bin/curl --verbose --output /tmp/junk
ftp://ftp.nhc.noaa.gov/pub/atcf/btk/bal012006.dat
* About to connect() to ftp.nhc.noaa.gov:21
* Connected to dogfish.nhc.noaa.gov (140.90.48.37) port 21
... login warning messages and PWD's ...
< 229 Entering Extended Passive Mode (|||36993|)
* About to connect() to ftp.nhc.noaa.gov:36993
... long wait ...
* socket error: 110
* Connected the data stream with PASV!
curl: (7) socket error: 110
* Closing connection #0
This doesn't look like a good site for testing. It login
message starts with
< 220-**WARNING**WARNING**WARNING**
< 220-
< 220-This is a United States (DOC/NOAA/NCEP) computer system, which may be
< 220-accessed and used only for official Government business by authorized
< 220-personnel. Unauthorized access or use of this computer system may
< 220-subject violators to criminal, civil, and/or administrative action.
>
> >
> download.file("ftp://ftp.nhc.noaa.gov/pub/atcf/aid_public/aal012006.dat.gz";,
> "C:/temp/aal012006.dat.gz", method = 'internal', mode = 'wb', cacheOK =
> FALSE)
> trying URL 'ftp://ftp.nhc.noaa.gov/pub/atcf/aid_public/aal012006.dat.gz'
> ftp data connection made, file length 173760 bytes
> opened URL
> downloaded 155Kb
>
> Warning message:
> downloaded length 159140 != reported length 173760
>
>
> Finally, is the spec of the system I'm working on:
> > version
>_
> 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)
> > win.version()
> [1] "Windows XP Professional (build 2600) Service Pack 2.0"
>
>
> Many thanks in advance and best regards,
> Jan
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
Bill Dunlap
Insightful Corporation
bill at insightful dot com
360-428-8146
"All statements in this message represent the opinions of the author and do
not necessarily reflect Insightful Corporation policy or position."
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