[Rcpp-devel] Rcpp 0.12.3 does not compile properly under Solaris 11.2/sparc Error: Could not find a match for std::wstring::basic_string(const char*, const char*) needed in
Dirk Eddelbuettel
edd at debian.org
Wed Feb 10 14:15:51 CET 2016
(This message got to me directly, but bounced at the mailserver. You are
subscribed as d.v at gmail.com, right?)
On 10 February 2016 at 14:02, Dimitar Vassilev wrote:
| Hi All,
| Nothing in my environment that calls it explicitly
Sorry -- You need to chase that at your end.
Rcpp calls R to call R CMD COMPILE ... on the files in the package. This can
all be traced back as it tedious as it may seem. Maybe you have CXXFLAGS
somewhere. We do not know -- we can only point you to the CRAN page with
successful builds and tests on Solaris sparc + x86 when gcc is used.
| -bash-4.1# pwd
| /usr/local/R
| -bash-4.1# more etc/Renviron
| ### etc/Renviron. Generated from Renviron.in by configure.
| ###
| ### ${R_HOME}/etc/Renviron
| ###
| ### Record R system environment variables.
|
| R_PLATFORM=${R_PLATFORM-'sparc-sun-solaris2.10'}
| ## Default printer paper size: first record if user set R_PAPERSIZE
| R_PAPERSIZE_USER=${R_PAPERSIZE}
| R_PAPERSIZE=${R_PAPERSIZE-'a4'}
| ## Default print command
| R_PRINTCMD=${R_PRINTCMD-'lpr'}
| # for Rd2pdf, reference manual
| R_RD4PDF=${R_RD4PDF-'times,inconsolata,hyper'}
| ## used for options("texi2dvi")
| R_TEXI2DVICMD=${R_TEXI2DVICMD-${TEXI2DVI-'/ade/aime_systemr_228172/systemr/port
| /Solaris-SPARC64/bin/texinfo/bin/texi2dvi'}}
| ## used by INSTALL, untar() and installing grDevices
| R_GZIPCMD=${R_GZIPCMD-'/usr/local/bin/gzip'}
| ## Default zip/unzip commands
| R_UNZIPCMD=${R_UNZIPCMD-'/ade/aime_systemr_228172/buildtools/bin/unzip'}
| R_ZIPCMD=${R_ZIPCMD-'/ade/aime_systemr_228172/buildtools/bin/zip'}
| R_BZIPCMD=${R_BZIPCMD-'/usr/local/bin/bzip2'}
| ## Default browser
| R_BROWSER=${R_BROWSER-'/usr/local/bin/firefox'}
| ## Default editor
| EDITOR=${EDITOR-${VISUAL-vi}}
| ## Default pager
| PAGER=${PAGER-'/usr/local/bin/less'}
| ## Default PDF viewer
| R_PDFVIEWER=${R_PDFVIEWER-'/usr/local/bin/acroread'}
| ## Used by libtool
| LN_S='ln -s'
| MAKE=${MAKE-'gmake'}
| ## Prefer a POSIX-compliant sed on e.g. Solaris
| SED=${SED-'/usr/xpg4/bin/sed'}
| ## Prefer a tar that can automagically read compressed archives
| ## Used in R CMD INSTALL for binary packages
| TAR=${TAR-'/usr/local/bin/gtar'}
|
| ## System and compiler types.
| R_SYSTEM_ABI='solaris,solcc,solCC,solf95,solf95'
|
| R_LIBS_USER=${R_LIBS_USER-'~/R/sparc-sun-solaris2.10-library/3.2'}
| #R_LIBS_USER=${R_LIBS_USER-'~/Library/R/3.2/library'}
|
| ### Local Variables: ***
| ### mode: sh ***
| ### sh-indentation: 2 ***
| ### End: ***
| -bash-4.1#
|
| Looking further I found something interesting things
| http://blog.zorinaq.com/?e=30
| https://www.prelude-siem.org/issues/288
|
| The solution is either:
|
| 1. Build both Perl and this module with the same C compiler, either
| by using the Sun C compiler for both or gcc for both.
| 2. Try generating the Makefile for this module like this perl
| perl Makefile.PL CC=gcc CCCDLFLAGS=-fPIC OPTIMIZE=" " LD=gcc
| make test
3. Use another OS ;-)
| Tried the magic things, but still no joy, Any idea how to make it work on
| command line?
Indeed, if you build your entire stack (Perl should not be needed) with gcc
it should 'just work'. See the appendices of the 'R Installation and
Administration' manual.
Rcpp is 'just another' R package, albeit one that uses C++ as well.
Dirk
| Thanks!
|
| 2016-02-10 12:16 GMT+01:00 Dirk Eddelbuettel <edd at debian.org>:
|
|
| On 10 February 2016 at 11:52, Dimitar Vassilev wrote:
| | Thanks Dirk,
| | Tried today with gcc-4.8.2 and g++ - 4.8.2
| |
| | > install.packages("ggplot2");
| | also installing the dependencies 'Rcpp', 'plyr', 'reshape2', 'scales'
| |
| | trying URL 'http://cran.uni-muenster.de/src/contrib/Rcpp_0.12.3.tar.gz'
| | Content type 'application/x-gzip' length 2374320 bytes (2.3 MB)
| | ==================================================
| | downloaded 2.3 MB
| |
| | trying URL 'http://cran.uni-muenster.de/src/contrib/plyr_1.8.3.tar.gz'
| | Content type 'application/x-gzip' length 392337 bytes (383 KB)
| | ==================================================
| | downloaded 383 KB
| |
| | trying URL 'http://cran.uni-muenster.de/src/contrib/reshape2_1.4.1.tar.gz
| '
| | Content type 'application/x-gzip' length 34693 bytes (33 KB)
| | ==================================================
| | downloaded 33 KB
| |
| | trying URL 'http://cran.uni-muenster.de/src/contrib/scales_0.3.0.tar.gz'
| | Content type 'application/x-gzip' length 57030 bytes (55 KB)
| | ==================================================
| | downloaded 55 KB
| |
| | trying URL 'http://cran.uni-muenster.de/src/contrib/ggplot2_2.0.0.tar.gz'
| | Content type 'application/x-gzip' length 1546130 bytes (1.5 MB)
| | ==================================================
| | downloaded 1.5 MB
| |
| | * installing *source* package 'Rcpp' ...
| | ** package 'Rcpp' successfully unpacked and MD5 sums checked
| | ** libs
| | g++ -I/usr/local/R/include -DNDEBUG -I../inst/include/ -KPIC -g -c
| | Date.cpp -o Date.o
| | g++: error: unrecognized command line option '-KPIC'
| | gmake: *** [Date.o] Error 1
|
| Rcpp does not add -KPIC to the compilation flags.
|
| They may be on your system (check the file Makeconf in the etc/ directory
| of
| your R installation) and you will need to override them -- either via
| corresponding environment variables or by editing the file.
|
| As the CRAN results page show, Rcpp can be very happy with gcc/g++ on
| Solaris.
|
| Dirk
|
| | ERROR: compilation failed for package 'Rcpp'
| | * removing '/usr/local/R/library/Rcpp'
| | ERROR: dependency 'Rcpp' is not available for package 'plyr'
| | * removing '/usr/local/R/library/plyr'
| | ERROR: dependencies 'plyr', 'Rcpp' are not available for package
| 'reshape2'
| | * removing '/usr/local/R/library/reshape2'
| | ERROR: dependencies 'plyr', 'Rcpp' are not available for package 'scales'
| | * removing '/usr/local/R/library/scales'
| | ERROR: dependencies 'plyr', 'reshape2', 'scales' are not available for
| package
| | 'ggplot2'
| | * removing '/usr/local/R/library/ggplot2'
| |
| | The downloaded source packages are in
| | '/tmp/RtmpZmVEUH/downloaded_packages'
| | Updating HTML index of packages in '.Library'
| | Making 'packages.html' ... done
| | Warning messages:
| | 1: In install.packages("ggplot2") :
| | installation of package 'Rcpp' had non-zero exit status
| | 2: In install.packages("ggplot2") :
| | installation of package 'plyr' had non-zero exit status
| | 3: In install.packages("ggplot2") :
| | installation of package 'reshape2' had non-zero exit status
| | 4: In install.packages("ggplot2") :
| | installation of package 'scales' had non-zero exit status
| | 5: In install.packages("ggplot2") :
| | installation of package 'ggplot2' had non-zero exit status
| |
| | -bash-4.1# /usr/bin/g
| | Display all 349 possibilities? (y or n)
| | -bash-4.1# /usr/bin/g++
| | g++: fatal error: no input files
| | compilation terminated.
| | -bash-4.1# /usr/bin/g++ -v
| | Using built-in specs.
| | COLLECT_GCC=/usr/bin/g++
| | COLLECT_LTO_WRAPPER=/usr/gcc/4.8/lib/gcc/sparc-sun-solaris2.11/4.8.2/
| | lto-wrapper
| | Target: sparc-sun-solaris2.11
| | Configured with: /export/home/hudson/workspace/nightly-update/build/sparc
| /
| | components/gcc48/gcc-4.8.2/configure CC=/usr/gcc/4.7/bin/gcc CXX=/usr/gcc
| /4.7/
| | bin/g++ --prefix=/usr/gcc/4.8 --mandir=/usr/gcc/4.8/share/man --bindir=/
| usr/gcc
| | /4.8/bin --libdir=/usr/gcc/4.8/lib --sbindir=/usr/gcc/4.8/sbin --infodir=
| /usr/
| | gcc/4.8/share/info --libexecdir=/usr/gcc/4.8/lib --enable-languages=
| | c,c++,fortran,objc --enable-shared --with-gmp-include=/usr/include/gmp
| | --with-mpfr-include=/usr/include/mpfr --without-gnu-ld --with-ld=/usr/bin
| /ld
| | --without-gnu-as --with-as=/usr/bin/as CFLAGS='-g -O2 -mtune=ultrasparc
| -mcpu=
| | ultrasparc -mno-unaligned-doubles' CXXFLAGS='-g -O2 -mtune=ultrasparc
| -mcpu=
| | ultrasparc -mno-unaligned-doubles'
| | Thread model: posix
| | gcc version 4.8.2 (GCC)
| |
| | Barfing at KPIC. Any idea how to go further?
| | Regards,
| | Dimitar
| |
| | 2016-02-09 13:54 GMT+01:00 Dirk Eddelbuettel <edd at debian.org>:
| |
| |
| | On 9 February 2016 at 13:41, Dimitar Vassilev wrote:
| | | Thanks gents,
| | | I will use gcc for the future. Got version 4.8 in the official
| | repository. What
| | | I'm afraid of that I may hit a nice dependency hell/soup when you
| have
| | things
| | | compiled in Sun Studio ( Oracle R community edition) and on top
| you're
| | | compiling things with gcc.
| |
| | I am wondering about that too ... but it could just work (as
| everything is
| | behind 'export "C"' layers making it a more portable C interface).
| Very
| | worst case just drop the 'community R' from your "friendly
| neighbourhood
| | database seller" and install R from source. It will still talk to the
| db
| | backends.
| |
| | Cheers, Dirk
| |
| | | Best,
| | | Dimitar
| | |
| | | 2016-02-09 13:31 GMT+01:00 JJ Allaire <jj.allaire at gmail.com>:
| | |
| | | Yes, all the checks pass on CRAN because they use the gcc
| toolchain
| | for
| | | Rcpp and all packages that depend on it:
| | |
| | | https://cran.r-project.org/web/checks/check_results_Rcpp.html
| | |
| | |
| | | On Tue, Feb 9, 2016 at 7:28 AM, Dirk Eddelbuettel <
| edd at debian.org>
| | wrote:
| | |
| | |
| | | Hi Dimitar,
| | |
| | | On 9 February 2016 at 12:08, Dimitar Vassilev wrote:
| | | | Hello,
| | | | I’m building on top of Oracle R Community edition 3.2,
| Sun
| | Studio
| | | 12.4 and
| | | | Solaris 11.2 some packages for internal use.
| | |
| | | The problem is likely the Sun Studio compiler. 'Nobody
| here' uses
| | that
| | | anymore, and even CRAN / Oxford which tests on Solaris
| | (x86,sparc) uses
| | | gcc
| | | per the tests page:
| | |
| | | https://cloud.r-project.org/web/checks/
| check_results_Rcpp.html
| | |
| | | | The error I get when trying to install Rcpp is:
| | | | > install.packages("dplyr");
| | | | also installing the dependency 'Rcpp'
| | | |
| | | | trying URL 'http://cran.uni-muenster.de/src/contrib/
| | | Rcpp_0.12.3.tar.gz'
| | | | Content type 'application/x-gzip' length 2374320 bytes
| (2.3 MB)
| | | | ==================================================
| | | | downloaded 2.3 MB
| | | |
| | | | trying URL 'http://cran.uni-muenster.de/src/contrib/
| | | dplyr_0.4.3.tar.gz'
| | | | Content type 'application/x-gzip' length 655997 bytes
| (640 KB)
| | | | ==================================================
| | | | downloaded 640 KB
| | | |
| | | | * installing *source* package 'Rcpp' ...
| | | | ** package 'Rcpp' successfully unpacked and MD5 sums
| checked
| | | | ** libs
| | | | /opt/SunProd/studio12u3/solarisstudio12.3/bin/CC -m64 -I/
| usr/
| | local/R/
| | | include
| | | | -DNDEBUG -I../inst/include/ -KPIC -g -c Date.cpp -o
| | Date.o
| | | | "../inst/include/Rcpp/Interrupt.h", line 60: Warning
| | (Anachronism):
| | | Using void
| | | | (*)(void*) to initialize extern "C" void(*)(void*).
| | | | "../inst/include/Rcpp/vector/MatrixRow.h", line 43:
| Error:
| | | iterator_traits is
| | | | not a member of std.
| | |
| | | We are doing things in C++ which are standard now, but for
| which
| | Sun
| | | Studio
| | | does not seem to have caught up.
| | |
| | | Maybe you need to look into installing the gcc toolchain.
| | |
| | | Maybe another list reader has a better idea but I fear that
| is
| | all we
| | | can say
| | | here.
| | |
| | | Greetings, Dirk
| | |
| | | | "../inst/include/Rcpp/vector/MatrixRow.h", line 43:
| Error: A
| | | declaration does
| | | | not specify a tag or an identifier.
| | | | "../inst/include/Rcpp/vector/MatrixRow.h", line 43:
| Error: Use
| | ";" to
| | | terminate
| | | | declarations.
| | | | "../inst/include/Rcpp/vector/MatrixRow.h", line 43:
| Error: "}"
| | | expected instead
| | | | of "<".
| | | | "../inst/include/Rcpp/vector/MatrixRow.h", line 188:
| Error:
| | | iterator_traits is
| | | | not a member of std.
| | | | "../inst/include/Rcpp/vector/MatrixRow.h", line 188:
| Error: A
| | | declaration does
| | | | not specify a tag or an identifier.
| | | | "../inst/include/Rcpp/vector/MatrixRow.h", line 188:
| Error: Use
| | ";"
| | | to
| | | | terminate declarations.
| | | | "../inst/include/Rcpp/vector/MatrixRow.h", line 188:
| Error: "}"
| | | expected
| | | | instead of "<".
| | | | "../inst/include/Rcpp/String.h", line 67: Warning: enc
| hides
| | | Rcpp::String::enc.
| | | | "../inst/include/Rcpp/String.h", line 81: Warning: enc
| hides
| | | Rcpp::String::enc.
| | | | "../inst/include/Rcpp/String.h", line 95: Warning: enc
| hides
| | | Rcpp::String::enc.
| | | | "../inst/include/Rcpp/String.h", line 107: Warning: enc
| hides
| | | | Rcpp::String::enc.
| | | | "../inst/include/Rcpp/String.h", line 378: Error: Could
| not
| | find a
| | | match for
| | | | std::wstring::basic_string(const char*, const char*)
| needed in
| | | | Rcpp::String::operator std::wstring () const.
| | | | 9 Error(s) and 5 Warning(s) detected.
| | | | *** Error code 2
| | | | make: Fatal error: Command failed for target `Date.o'
| | | | ERROR: compilation failed for package 'Rcpp'
| | | | * removing '/usr/local/R/library/Rcpp'
| | | | ERROR: dependency 'Rcpp' is not available for package
| 'dplyr'
| | | | * removing '/usr/local/R/library/dplyr'
| | | |
| | | | The downloaded source packages are in
| | | | '/tmp/RtmpPbHqdD/downloaded_packages'
| | | | Updating HTML index of packages in '.Library'
| | | | Making 'packages.html' ... done
| | | | Warning messages:
| | | | 1: In install.packages("dplyr") :
| | | | installation of package 'Rcpp' had non-zero exit status
| | | | 2: In install.packages("dplyr") :
| | | | installation of package 'dplyr' had non-zero exit
| status
| | | | > q();
| | | |
| | | | Can you point me what should I do further?
| | | | My .Renviron is as follows
| | | | TZ=CET
| | | | TERM=vt220
| | | | TAR=/usr/bin/tar
| | | | R_UNZIPCMD=/usr/bin/unzip
| | | | R_ZIPCMD=/usr/bin/zip
| | | | MAKE=/usr/bin/make
| | | | LD_LIBRARY_PATH=/usr/lib:/usr/local/R/lib:/lib:/usr/local
| /lib
| | | | PAGER=/usr/bin/less
| | | | R_BZIPCMD=/usr/bin/bzip2
| | | | R_GZIPCMD=/usr/bin/gzip
| | | | I made a symlink so that the compilation works.
| Unfortunately
| | the R
| | | modules
| | | | have hard-coded the path to the compiler.
| | | | -bash-4.1# ls -la /opt/SunProd/studio12u3/
| solarisstudio12.3/
| | bin
| | | | lrwxrwxrwx 1 root root 26 Feb 4 15:22 /
| opt/
| | SunProd/
| | | studio12u3/
| | | | solarisstudio12.3/bin -> /opt/solarisstudio12.4/bin
| | | |
| | | | Can someone point me which compiler options/configure
| arguments
| | are
| | | needed so
| | | | that the conversion and compilation is successful?
| | | | Thanks!
| | | |
| | | | _______________________________________________
| | | | Rcpp-devel mailing list
| | | | Rcpp-devel at lists.r-forge.r-project.org
| | | | https://lists.r-forge.r-project.org/cgi-bin/mailman/
| listinfo/
| | | rcpp-devel
| | |
| | | --
| | | http://dirk.eddelbuettel.com | @eddelbuettel |
| edd at debian.org
| | | _______________________________________________
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| listinfo/
| | rcpp-devel
| | |
| | |
| | |
| | |
| |
| | --
| | http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
| |
| |
|
| --
| http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
|
|
--
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
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