Re: [R-SIG-Mac] Cannot compile Fortran on macOS
Success. I also removed everything from /usr/local then reinstalled MacTex, R and gfortran, and now I can build on both 4.0 and 4.1. Presumably something has changed in the builds between 4.0 and 4.1 and that has interacted with the accumulated nearly 6 years of mess in /usr/local. > On 20 May 2020, at 5:34 pm, Adelchi Azzalini wrote: > > > >> On 20 May 2020, at 08:44, Adelchi Azzalini wrote: >> >> Thanks to everyone that provided suggestions. >> >> I was about to follow the recommended step of renaming /usr/local and >> reinstall a bunch of programs. >> However, that renaming is blocked, presumably by Apple System Integrity >> Protection. >> Is there any alternative to disabling this Apple "feature"? >> Do you recommend to re-instate it after the re-construction of /usr/local/ ? >> As you see, I am not familiar with Apple tricks. >> >> Thanks again, >> >> Adelchi > > > Please ignore the message above. > Right after sending it, I realized that the simple workaround was to move > everything in > /usr/local/ > to > /usr/local/local-2020520/ > > After reinstalling R, TeX, etc... compilation now works fine! > > Thanks for your effective help. > > Adelchi > > >> >> >> >>> On 20 May 2020, at 05:50, Simon Urbanek wrote: >>> >>> >>> Adelchi, >>> >>> as pointed out you have conflicting libraries in /usr/local - likely from >>> some conflicting package manager. I would recommend re-naming /usr/local to >>> remove the issue and installing a clean GNU Fortran (see >>> http://mac.r-project.org/tools/ or from the official GNU Fortran pages >>> which use the same binary), that's all you really need. >>> >>> Cheers, >>> Simon >>> >>> >>> On 20/05/2020, at 1:45 AM, Adelchi Azzalini wrote: Hi. In essence, my problem is that I cannot install a package which requires Fortran-77 compilation on my Mac. More in detail, this is my own package 'mnormt' which exists on CRAN since 2006; it is currently at version 1.5-7. It has been developed in successive versions on a Linux machine, where it compiles with no problems. The macOS and MS-windows versions are created on CRAN, where it passes all pertaining checks. Now, in the new pandemic world, I need create a new version of the package, but working from home, hence using my Mac laptop instead of the Linux desktop as in the past. Unfortunately, compilation or loading does not work. If I run R CMD check mnormt_1.5-7.tar.gz first I get a bunch of warning messages such as Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) [-Wconversion] Warning: ‘lxchng’ may be used uninitialized in this function [-Wmaybe-uninitialized] Warning: Label 10 at (1) defined but not used [-Wunused-label] and finally it crashes with Error: package or namespace load failed for ‘mnormt’: .onLoad failed in loadNamespace() for 'mnormt', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so': dlopen(/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so, 6): Symbol not found: ___addtf3 Referenced from: /usr/local/lib/libquadmath.0.dylib Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib in /usr/local/lib/libquadmath.0.dylib Error: loading failed Needless to say, I have no idea what this "addtf3" is or it should be. There is no such a symbol in the Fortran code. I believe to have installed all ingredients indicated at https://mac.r-project.org/tools/ See the list below with details about my system and other installed tools. Any suggestions for sorting this out? Adelchi Azzalini --- Installation info: R> R.version _ platform x86_64-apple-darwin17.0 arch x86_64 os darwin17.0 system x86_64, darwin17.0 status major 4 minor 0.0 year 2020 month 04 day24 svn rev78286 language R version.string R version 4.0.0 (2020-04-24) nickname Arbor Day --- macOS Mojave 10.14.6 --- Xcode version 11.3.1 --- Fortran [aa@mac-2013:~] gfortran -v Using built-in specs. COLLECT_GCC=gfortran
Re: [R-SIG-Mac] Cannot compile Fortran on macOS
> On 20 May 2020, at 08:44, Adelchi Azzalini wrote: > > Thanks to everyone that provided suggestions. > > I was about to follow the recommended step of renaming /usr/local and > reinstall a bunch of programs. > However, that renaming is blocked, presumably by Apple System Integrity > Protection. > Is there any alternative to disabling this Apple "feature"? > Do you recommend to re-instate it after the re-construction of /usr/local/ ? > As you see, I am not familiar with Apple tricks. > > Thanks again, > > Adelchi Please ignore the message above. Right after sending it, I realized that the simple workaround was to move everything in /usr/local/ to /usr/local/local-2020520/ After reinstalling R, TeX, etc... compilation now works fine! Thanks for your effective help. Adelchi > > > >> On 20 May 2020, at 05:50, Simon Urbanek wrote: >> >> >> Adelchi, >> >> as pointed out you have conflicting libraries in /usr/local - likely from >> some conflicting package manager. I would recommend re-naming /usr/local to >> remove the issue and installing a clean GNU Fortran (see >> http://mac.r-project.org/tools/ or from the official GNU Fortran pages which >> use the same binary), that's all you really need. >> >> Cheers, >> Simon >> >> >> >>> On 20/05/2020, at 1:45 AM, Adelchi Azzalini wrote: >>> >>> Hi. >>> In essence, my problem is that I cannot install a package which requires >>> Fortran-77 compilation on my Mac. >>> >>> More in detail, this is my own package 'mnormt' which exists on CRAN since >>> 2006; it is currently at version 1.5-7. It has been developed in successive >>> versions on a Linux machine, where it compiles with no problems. The macOS >>> and MS-windows versions are created on CRAN, where it passes all pertaining >>> checks. >>> >>> Now, in the new pandemic world, I need create a new version of the package, >>> but working from home, hence using my Mac laptop instead of the Linux >>> desktop as in the past. Unfortunately, compilation or loading does not >>> work. If I run >>> >>> R CMD check mnormt_1.5-7.tar.gz >>> >>> first I get a bunch of warning messages such as >>> >>> Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) >>> [-Wconversion] >>> Warning: ‘lxchng’ may be used uninitialized in this function >>> [-Wmaybe-uninitialized] >>> Warning: Label 10 at (1) defined but not used [-Wunused-label] >>> >>> and finally it crashes with >>> >>> Error: package or namespace load failed for ‘mnormt’: >>> .onLoad failed in loadNamespace() for 'mnormt', details: >>> call: dyn.load(file, DLLpath = DLLpath, ...) >>> error: unable to load shared object >>> '/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so': >>> dlopen(/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so, >>> 6): Symbol not found: ___addtf3 >>> Referenced from: /usr/local/lib/libquadmath.0.dylib >>> Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib >>> in /usr/local/lib/libquadmath.0.dylib >>> Error: loading failed >>> >>> Needless to say, I have no idea what this "addtf3" is or it should be. >>> There is no such a symbol in the Fortran code. >>> >>> I believe to have installed all ingredients indicated at >>> https://mac.r-project.org/tools/ >>> See the list below with details about my system and other installed tools. >>> >>> Any suggestions for sorting this out? >>> >>> Adelchi Azzalini >>> >>> >>> --- >>> Installation info: >>> >>> R> R.version >>> _ >>> platform x86_64-apple-darwin17.0 >>> arch x86_64 >>> os darwin17.0 >>> system x86_64, darwin17.0 >>> status >>> major 4 >>> minor 0.0 >>> year 2020 >>> month 04 >>> day24 >>> svn rev78286 >>> language R >>> version.string R version 4.0.0 (2020-04-24) >>> nickname Arbor Day >>> >>> --- macOS Mojave 10.14.6 >>> >>> --- Xcode version 11.3.1 >>> >>> --- Fortran >>> >>> [aa@mac-2013:~] gfortran -v >>> Using built-in specs. >>> COLLECT_GCC=gfortran >>> COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin18/8.2.0/lto-wrapper >>> Target: x86_64-apple-darwin18 >>> Configured with: ../gcc-8.2.0/configure --prefix=/usr/local/gfortran >>> --with-gmp=/Users/fx/devel/gcc/build_package/deps >>> --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin18 >>> --disable-multilib --with-native-system-header-dir=/usr/include >>> --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk >>> Thread model: posix >>> gcc version
Re: [R-SIG-Mac] Cannot compile Fortran on macOS
Thanks to everyone that provided suggestions. I was about to follow the recommended step of renaming /usr/local and reinstall a bunch of programs. However, that renaming is blocked, presumably by Apple System Integrity Protection. Is there any alternative to disabling this Apple "feature"? Do you recommend to re-instate it after the re-construction of /usr/local/ ? As you see, I am not familiar with Apple tricks. Thanks again, Adelchi > On 20 May 2020, at 05:50, Simon Urbanek wrote: > > > Adelchi, > > as pointed out you have conflicting libraries in /usr/local - likely from > some conflicting package manager. I would recommend re-naming /usr/local to > remove the issue and installing a clean GNU Fortran (see > http://mac.r-project.org/tools/ or from the official GNU Fortran pages which > use the same binary), that's all you really need. > > Cheers, > Simon > > > >> On 20/05/2020, at 1:45 AM, Adelchi Azzalini wrote: >> >> Hi. >> In essence, my problem is that I cannot install a package which requires >> Fortran-77 compilation on my Mac. >> >> More in detail, this is my own package 'mnormt' which exists on CRAN since >> 2006; it is currently at version 1.5-7. It has been developed in successive >> versions on a Linux machine, where it compiles with no problems. The macOS >> and MS-windows versions are created on CRAN, where it passes all pertaining >> checks. >> >> Now, in the new pandemic world, I need create a new version of the package, >> but working from home, hence using my Mac laptop instead of the Linux >> desktop as in the past. Unfortunately, compilation or loading does not work. >> If I run >> >> R CMD check mnormt_1.5-7.tar.gz >> >> first I get a bunch of warning messages such as >> >> Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) >> [-Wconversion] >> Warning: ‘lxchng’ may be used uninitialized in this function >> [-Wmaybe-uninitialized] >> Warning: Label 10 at (1) defined but not used [-Wunused-label] >> >> and finally it crashes with >> >> Error: package or namespace load failed for ‘mnormt’: >> .onLoad failed in loadNamespace() for 'mnormt', details: >> call: dyn.load(file, DLLpath = DLLpath, ...) >> error: unable to load shared object >> '/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so': >> dlopen(/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so, >> 6): Symbol not found: ___addtf3 >> Referenced from: /usr/local/lib/libquadmath.0.dylib >> Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib >> in /usr/local/lib/libquadmath.0.dylib >> Error: loading failed >> >> Needless to say, I have no idea what this "addtf3" is or it should be. There >> is no such a symbol in the Fortran code. >> >> I believe to have installed all ingredients indicated at >> https://mac.r-project.org/tools/ >> See the list below with details about my system and other installed tools. >> >> Any suggestions for sorting this out? >> >> Adelchi Azzalini >> >> >> --- >> Installation info: >> >> R> R.version >> _ >> platform x86_64-apple-darwin17.0 >> arch x86_64 >> os darwin17.0 >> system x86_64, darwin17.0 >> status >> major 4 >> minor 0.0 >> year 2020 >> month 04 >> day24 >> svn rev78286 >> language R >> version.string R version 4.0.0 (2020-04-24) >> nickname Arbor Day >> >> --- macOS Mojave 10.14.6 >> >> --- Xcode version 11.3.1 >> >> --- Fortran >> >> [aa@mac-2013:~] gfortran -v >> Using built-in specs. >> COLLECT_GCC=gfortran >> COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin18/8.2.0/lto-wrapper >> Target: x86_64-apple-darwin18 >> Configured with: ../gcc-8.2.0/configure --prefix=/usr/local/gfortran >> --with-gmp=/Users/fx/devel/gcc/build_package/deps >> --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin18 >> --disable-multilib --with-native-system-header-dir=/usr/include >> --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk >> Thread model: posix >> gcc version 8.2.0 (GCC) >> >> [aa@mac-2013:~] echo $PATH >> .:/Users/aa/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin/:/usr/X11R6/bin:/opt/local/bin:/Library/TeX/texbin:/usr/local/gfortran/bin >> >> -- other tools indicated at https://mac.r-project.org/tools/ >> xz-5.2.5/ is installed >> PCRE2 10.34 built with --disable-jit >> bzip2 Version 1.0.6 is installed >> >> ___ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >>
Re: [R-SIG-Mac] Cannot compile Fortran on macOS
Simon, I’m going to investigate further, but the problem is that 4.0 works fine but 4.1 doesn’t. I will check what is going wrong. Ken > On 20 May 2020, at 1:47 pm, Simon Urbanek wrote: > > Ken, > > R can be built with just Xcode and GFortran (see also > http://mac.r-project.org/tools/ ). If you have issues, those are very often > due to conflicting package managers (Homebrew, macoports, fink ...) so a good > exercise is to simply re-name /usr/local/ and setup a clean environment as > above which is known to work. If you use CRAN R builds (either release or > from http://mac.r-project.org/ ) then most packages will compile with just > Xcode alone. > > Cheers, > Simon > > >> On 20/05/2020, at 12:58 PM, Ken Beath wrote: >> >> Plus one of the duties of package managers is to make sure that they build >> and pass CRAN checks. Doing that with a non standard environment seems a bit >> risky. >> >> At the moment I can’t get anything to build on R-Devel which is making life >> difficult and I may raise a question if it still isn’t working when I’ve >> finished with the new experience that is online teaching. >> >>> On 20 May 2020, at 10:49 am, David Winsemius wrote: >>> >>> >>> On 5/19/20 1:46 PM, Yoshihiko Baba via R-SIG-Mac wrote: Adelchi, Why don’t you try Fink version of R? Fink build mnormt on R 4.0 as well (although it is experimental). https://github.com/fink/fink-distributions/issues/623 >>> >>> >>> This should be considered contrary to recommended practice: From the >>> page for macOS tools that was cited by the OP we see: >>> >>> >>> "Although it is possible to compile R using tools from other package >>> managers such as Homebrew, MacPorts or Fink, such binaries are by >>> definition incompatible with macOS native libraries and applications. If >>> you choose one of those package managers, make sure you >>> compile/everything/using those tools including R and all packages and >>> libraries you intend to use." >>> >>> >>> I think it should have been offered as advice to only be followed by >>> persons with great experience in compiling and building packages on Macs. >>> >>> Best; >>> >>> David >>> Fink allows you to install different versions of R (3.6, 3.5, 3.4, 3.3, 3.2 and 3.1). For different versions, CRAN packages are separately installed (/sw/lib/R/3.6/site-library and so on). > 2020/05/19 22:45、Adelchi Azzalini のメール: > > Hi. > In essence, my problem is that I cannot install a package which requires > Fortran-77 compilation on my Mac. > > More in detail, this is my own package 'mnormt' which exists on CRAN > since 2006; it is currently at version 1.5-7. It has been developed in > successive versions on a Linux machine, where it compiles with no > problems. The macOS and MS-windows versions are created on CRAN, where it > passes all pertaining checks. > > Now, in the new pandemic world, I need create a new version of the > package, but working from home, hence using my Mac laptop instead of the > Linux desktop as in the past. Unfortunately, compilation or loading does > not work. If I run > > R CMD check mnormt_1.5-7.tar.gz > > first I get a bunch of warning messages such as > > Warning: Possible change of value in conversion from REAL(8) to > INTEGER(4) [-Wconversion] > Warning: ‘lxchng’ may be used uninitialized in this function > [-Wmaybe-uninitialized] > Warning: Label 10 at (1) defined but not used [-Wunused-label] > > and finally it crashes with > > Error: package or namespace load failed for ‘mnormt’: > .onLoad failed in loadNamespace() for 'mnormt', details: > call: dyn.load(file, DLLpath = DLLpath, ...) > error: unable to load shared object > '/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so': > dlopen(/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so, > 6): Symbol not found: ___addtf3 > Referenced from: /usr/local/lib/libquadmath.0.dylib > Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib > in /usr/local/lib/libquadmath.0.dylib > Error: loading failed > > Needless to say, I have no idea what this "addtf3" is or it should be. > There is no such a symbol in the Fortran code. > > I believe to have installed all ingredients indicated at > https://mac.r-project.org/tools/ > See the list below with details about my system and other installed tools. > > Any suggestions for sorting this out? > > Adelchi Azzalini > > > --- > Installation info: > > R> R.version > _ > platform x86_64-apple-darwin17.0 > arch x86_64 > os darwin17.0 > system
Re: [R-SIG-Mac] Cannot compile Fortran on macOS
Adelchi, as pointed out you have conflicting libraries in /usr/local - likely from some conflicting package manager. I would recommend re-naming /usr/local to remove the issue and installing a clean GNU Fortran (see http://mac.r-project.org/tools/ or from the official GNU Fortran pages which use the same binary), that's all you really need. Cheers, Simon > On 20/05/2020, at 1:45 AM, Adelchi Azzalini wrote: > > Hi. > In essence, my problem is that I cannot install a package which requires > Fortran-77 compilation on my Mac. > > More in detail, this is my own package 'mnormt' which exists on CRAN since > 2006; it is currently at version 1.5-7. It has been developed in successive > versions on a Linux machine, where it compiles with no problems. The macOS > and MS-windows versions are created on CRAN, where it passes all pertaining > checks. > > Now, in the new pandemic world, I need create a new version of the package, > but working from home, hence using my Mac laptop instead of the Linux desktop > as in the past. Unfortunately, compilation or loading does not work. If I run > > R CMD check mnormt_1.5-7.tar.gz > > first I get a bunch of warning messages such as > > Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) > [-Wconversion] > Warning: ‘lxchng’ may be used uninitialized in this function > [-Wmaybe-uninitialized] > Warning: Label 10 at (1) defined but not used [-Wunused-label] > > and finally it crashes with > > Error: package or namespace load failed for ‘mnormt’: > .onLoad failed in loadNamespace() for 'mnormt', details: > call: dyn.load(file, DLLpath = DLLpath, ...) > error: unable to load shared object > '/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so': > > dlopen(/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so, > 6): Symbol not found: ___addtf3 > Referenced from: /usr/local/lib/libquadmath.0.dylib > Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib > in /usr/local/lib/libquadmath.0.dylib > Error: loading failed > > Needless to say, I have no idea what this "addtf3" is or it should be. There > is no such a symbol in the Fortran code. > > I believe to have installed all ingredients indicated at > https://mac.r-project.org/tools/ > See the list below with details about my system and other installed tools. > > Any suggestions for sorting this out? > > Adelchi Azzalini > > > --- > Installation info: > > R> R.version > _ > platform x86_64-apple-darwin17.0 > arch x86_64 > os darwin17.0 > system x86_64, darwin17.0 > status > major 4 > minor 0.0 > year 2020 > month 04 > day24 > svn rev78286 > language R > version.string R version 4.0.0 (2020-04-24) > nickname Arbor Day > > --- macOS Mojave 10.14.6 > > --- Xcode version 11.3.1 > > --- Fortran > > [aa@mac-2013:~] gfortran -v > Using built-in specs. > COLLECT_GCC=gfortran > COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin18/8.2.0/lto-wrapper > Target: x86_64-apple-darwin18 > Configured with: ../gcc-8.2.0/configure --prefix=/usr/local/gfortran > --with-gmp=/Users/fx/devel/gcc/build_package/deps > --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin18 > --disable-multilib --with-native-system-header-dir=/usr/include > --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk > Thread model: posix > gcc version 8.2.0 (GCC) > > [aa@mac-2013:~] echo $PATH > .:/Users/aa/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin/:/usr/X11R6/bin:/opt/local/bin:/Library/TeX/texbin:/usr/local/gfortran/bin > > -- other tools indicated at https://mac.r-project.org/tools/ > xz-5.2.5/ is installed > PCRE2 10.34 built with --disable-jit > bzip2 Version 1.0.6 is installed > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Cannot compile Fortran on macOS
Ken, R can be built with just Xcode and GFortran (see also http://mac.r-project.org/tools/ ). If you have issues, those are very often due to conflicting package managers (Homebrew, macoports, fink ...) so a good exercise is to simply re-name /usr/local/ and setup a clean environment as above which is known to work. If you use CRAN R builds (either release or from http://mac.r-project.org/ ) then most packages will compile with just Xcode alone. Cheers, Simon > On 20/05/2020, at 12:58 PM, Ken Beath wrote: > > Plus one of the duties of package managers is to make sure that they build > and pass CRAN checks. Doing that with a non standard environment seems a bit > risky. > > At the moment I can’t get anything to build on R-Devel which is making life > difficult and I may raise a question if it still isn’t working when I’ve > finished with the new experience that is online teaching. > >> On 20 May 2020, at 10:49 am, David Winsemius wrote: >> >> >> On 5/19/20 1:46 PM, Yoshihiko Baba via R-SIG-Mac wrote: >>> Adelchi, >>> >>> Why don’t you try Fink version of R? >>> >>> Fink build mnormt on R 4.0 as well (although it is experimental). >>> https://github.com/fink/fink-distributions/issues/623 >> >> >> This should be considered contrary to recommended practice: From the >> page for macOS tools that was cited by the OP we see: >> >> >> "Although it is possible to compile R using tools from other package >> managers such as Homebrew, MacPorts or Fink, such binaries are by >> definition incompatible with macOS native libraries and applications. If >> you choose one of those package managers, make sure you >> compile/everything/using those tools including R and all packages and >> libraries you intend to use." >> >> >> I think it should have been offered as advice to only be followed by >> persons with great experience in compiling and building packages on Macs. >> >> Best; >> >> David >> >>> >>> Fink allows you to install different versions of R (3.6, 3.5, 3.4, 3.3, 3.2 >>> and 3.1). >>> >>> For different versions, CRAN packages are separately installed >>> (/sw/lib/R/3.6/site-library and so on). >>> >>> 2020/05/19 22:45、Adelchi Azzalini のメール: Hi. In essence, my problem is that I cannot install a package which requires Fortran-77 compilation on my Mac. More in detail, this is my own package 'mnormt' which exists on CRAN since 2006; it is currently at version 1.5-7. It has been developed in successive versions on a Linux machine, where it compiles with no problems. The macOS and MS-windows versions are created on CRAN, where it passes all pertaining checks. Now, in the new pandemic world, I need create a new version of the package, but working from home, hence using my Mac laptop instead of the Linux desktop as in the past. Unfortunately, compilation or loading does not work. If I run R CMD check mnormt_1.5-7.tar.gz first I get a bunch of warning messages such as Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) [-Wconversion] Warning: ‘lxchng’ may be used uninitialized in this function [-Wmaybe-uninitialized] Warning: Label 10 at (1) defined but not used [-Wunused-label] and finally it crashes with Error: package or namespace load failed for ‘mnormt’: .onLoad failed in loadNamespace() for 'mnormt', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so': dlopen(/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so, 6): Symbol not found: ___addtf3 Referenced from: /usr/local/lib/libquadmath.0.dylib Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib in /usr/local/lib/libquadmath.0.dylib Error: loading failed Needless to say, I have no idea what this "addtf3" is or it should be. There is no such a symbol in the Fortran code. I believe to have installed all ingredients indicated at https://mac.r-project.org/tools/ See the list below with details about my system and other installed tools. Any suggestions for sorting this out? Adelchi Azzalini --- Installation info: R> R.version _ platform x86_64-apple-darwin17.0 arch x86_64 os darwin17.0 system x86_64, darwin17.0 status major 4 minor 0.0 year 2020 month 04 day24 svn rev78286 language R version.string R version 4.0.0 (2020-04-24) nickname Arbor Day --- macOS Mojave 10.14.6 --- Xcode
Re: [R-SIG-Mac] Cannot compile Fortran on macOS
Plus one of the duties of package managers is to make sure that they build and pass CRAN checks. Doing that with a non standard environment seems a bit risky. At the moment I can’t get anything to build on R-Devel which is making life difficult and I may raise a question if it still isn’t working when I’ve finished with the new experience that is online teaching. > On 20 May 2020, at 10:49 am, David Winsemius wrote: > > > On 5/19/20 1:46 PM, Yoshihiko Baba via R-SIG-Mac wrote: >> Adelchi, >> >> Why don’t you try Fink version of R? >> >> Fink build mnormt on R 4.0 as well (although it is experimental). >> https://github.com/fink/fink-distributions/issues/623 > > > This should be considered contrary to recommended practice: From the > page for macOS tools that was cited by the OP we see: > > > "Although it is possible to compile R using tools from other package > managers such as Homebrew, MacPorts or Fink, such binaries are by > definition incompatible with macOS native libraries and applications. If > you choose one of those package managers, make sure you > compile/everything/using those tools including R and all packages and > libraries you intend to use." > > > I think it should have been offered as advice to only be followed by > persons with great experience in compiling and building packages on Macs. > > Best; > > David > >> >> Fink allows you to install different versions of R (3.6, 3.5, 3.4, 3.3, 3.2 >> and 3.1). >> >> For different versions, CRAN packages are separately installed >> (/sw/lib/R/3.6/site-library and so on). >> >> >>> 2020/05/19 22:45、Adelchi Azzalini のメール: >>> >>> Hi. >>> In essence, my problem is that I cannot install a package which requires >>> Fortran-77 compilation on my Mac. >>> >>> More in detail, this is my own package 'mnormt' which exists on CRAN since >>> 2006; it is currently at version 1.5-7. It has been developed in successive >>> versions on a Linux machine, where it compiles with no problems. The macOS >>> and MS-windows versions are created on CRAN, where it passes all pertaining >>> checks. >>> >>> Now, in the new pandemic world, I need create a new version of the package, >>> but working from home, hence using my Mac laptop instead of the Linux >>> desktop as in the past. Unfortunately, compilation or loading does not >>> work. If I run >>> >>> R CMD check mnormt_1.5-7.tar.gz >>> >>> first I get a bunch of warning messages such as >>> >>> Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) >>> [-Wconversion] >>> Warning: ‘lxchng’ may be used uninitialized in this function >>> [-Wmaybe-uninitialized] >>> Warning: Label 10 at (1) defined but not used [-Wunused-label] >>> >>> and finally it crashes with >>> >>> Error: package or namespace load failed for ‘mnormt’: >>> .onLoad failed in loadNamespace() for 'mnormt', details: >>> call: dyn.load(file, DLLpath = DLLpath, ...) >>> error: unable to load shared object >>> '/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so': >>> >>> dlopen(/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so, >>> 6): Symbol not found: ___addtf3 >>> Referenced from: /usr/local/lib/libquadmath.0.dylib >>> Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib >>> in /usr/local/lib/libquadmath.0.dylib >>> Error: loading failed >>> >>> Needless to say, I have no idea what this "addtf3" is or it should be. >>> There is no such a symbol in the Fortran code. >>> >>> I believe to have installed all ingredients indicated at >>> https://mac.r-project.org/tools/ >>> See the list below with details about my system and other installed tools. >>> >>> Any suggestions for sorting this out? >>> >>> Adelchi Azzalini >>> >>> >>> --- >>> Installation info: >>> >>> R> R.version >>> _ >>> platform x86_64-apple-darwin17.0 >>> arch x86_64 >>> os darwin17.0 >>> system x86_64, darwin17.0 >>> status >>> major 4 >>> minor 0.0 >>> year 2020 >>> month 04 >>> day24 >>> svn rev78286 >>> language R >>> version.string R version 4.0.0 (2020-04-24) >>> nickname Arbor Day >>> >>> --- macOS Mojave 10.14.6 >>> >>> --- Xcode version 11.3.1 >>> >>> --- Fortran >>> >>> [aa@mac-2013:~] gfortran -v >>> Using built-in specs. >>> COLLECT_GCC=gfortran >>> COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin18/8.2.0/lto-wrapper >>> Target: x86_64-apple-darwin18 >>> Configured with: ../gcc-8.2.0/configure --prefix=/usr/local/gfortran >>> --with-gmp=/Users/fx/devel/gcc/build_package/deps >>> --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin18 >>> --disable-multilib --with-native-system-header-dir=/usr/include >>> --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk >>> Thread model: posix >>> gcc version
Re: [R-SIG-Mac] Cannot compile Fortran on macOS
On 5/19/20 1:54 PM, Kevin Ushey wrote: The main thing that stands out to me in that error: Referenced from: /usr/local/lib/libquadmath.0.dylib Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib R bundles its own copies of libquadmath and libgcc: kevinushey@Kevins-MBP:/Library/Frameworks/R.framework/Resources/lib $ ls -la total 19120 drwxrwxr-x 11 root admin 352 Apr 24 03:23 . drwxrwxr-x 18 root admin 576 Apr 29 11:46 .. -rwxrwxr-x 1 root admin 4070896 Apr 24 03:23 libR.dylib drwxrwxr-x 3 root admin 96 Apr 24 03:22 libR.dylib.dSYM -rwxrwxr-x 1 root admin 201472 Apr 24 03:23 libRblas.dylib drwxrwxr-x 3 root admin 96 Apr 24 03:22 libRblas.dylib.dSYM -rwxrwxr-x 1 root admin 2181472 Apr 24 03:23 libRlapack.dylib drwxrwxr-x 3 root admin 96 Apr 24 03:22 libRlapack.dylib.dSYM -rw-rw-r-- 1 root admin 160624 Apr 24 03:23 libgcc_s.1.dylib -rwxrwxr-x 1 root admin 2851008 Apr 24 03:23 libgfortran.5.dylib -rwxrwxr-x 1 root admin 309648 Apr 24 03:23 libquadmath.0.dylib which should normally be used during the link step. However, versions in /usr/local/lib are being discovered instead, which presumably aren't compatible. Kevin; Is that the sort of situation that might be cause by mixing homebrew-compiled and R.Framework-compiled packages? David. The simplest fix is (likely) to move those files out of the way. Otherwise, you'd likely have to muck around with Makevars / Makeconf to adjust the linker flags so the correct versions of these libraries are found. Best, Kevin On Tue, May 19, 2020 at 6:46 AM Adelchi Azzalini wrote: Hi. In essence, my problem is that I cannot install a package which requires Fortran-77 compilation on my Mac. More in detail, this is my own package 'mnormt' which exists on CRAN since 2006; it is currently at version 1.5-7. It has been developed in successive versions on a Linux machine, where it compiles with no problems. The macOS and MS-windows versions are created on CRAN, where it passes all pertaining checks. Now, in the new pandemic world, I need create a new version of the package, but working from home, hence using my Mac laptop instead of the Linux desktop as in the past. Unfortunately, compilation or loading does not work. If I run R CMD check mnormt_1.5-7.tar.gz first I get a bunch of warning messages such as Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) [-Wconversion] Warning: ‘lxchng’ may be used uninitialized in this function [-Wmaybe-uninitialized] Warning: Label 10 at (1) defined but not used [-Wunused-label] and finally it crashes with Error: package or namespace load failed for ‘mnormt’: .onLoad failed in loadNamespace() for 'mnormt', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so': dlopen(/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so, 6): Symbol not found: ___addtf3 Referenced from: /usr/local/lib/libquadmath.0.dylib Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib in /usr/local/lib/libquadmath.0.dylib Error: loading failed Needless to say, I have no idea what this "addtf3" is or it should be. There is no such a symbol in the Fortran code. I believe to have installed all ingredients indicated at https://mac.r-project.org/tools/ See the list below with details about my system and other installed tools. Any suggestions for sorting this out? Adelchi Azzalini --- Installation info: R> R.version _ platform x86_64-apple-darwin17.0 arch x86_64 os darwin17.0 system x86_64, darwin17.0 status major 4 minor 0.0 year 2020 month 04 day24 svn rev78286 language R version.string R version 4.0.0 (2020-04-24) nickname Arbor Day --- macOS Mojave 10.14.6 --- Xcode version 11.3.1 --- Fortran [aa@mac-2013:~] gfortran -v Using built-in specs. COLLECT_GCC=gfortran COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin18/8.2.0/lto-wrapper Target: x86_64-apple-darwin18 Configured with: ../gcc-8.2.0/configure --prefix=/usr/local/gfortran --with-gmp=/Users/fx/devel/gcc/build_package/deps --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin18 --disable-multilib --with-native-system-header-dir=/usr/include --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk Thread model: posix gcc version 8.2.0 (GCC) [aa@mac-2013:~] echo $PATH .:/Users/aa/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin/:/usr/X11R6/bin:/opt/local/bin:/Library/TeX/texbin:/usr/local/gfortran/bin -- other tools indicated at https://mac.r-project.org/tools/ xz-5.2.5/ is installed PCRE2 10.34 built with --disable-jit bzip2 Version 1.0.6 is installed
Re: [R-SIG-Mac] Cannot compile Fortran on macOS
On 5/19/20 1:46 PM, Yoshihiko Baba via R-SIG-Mac wrote: > Adelchi, > > Why don’t you try Fink version of R? > > Fink build mnormt on R 4.0 as well (although it is experimental). > https://github.com/fink/fink-distributions/issues/623 This should be considered contrary to recommended practice: From the page for macOS tools that was cited by the OP we see: "Although it is possible to compile R using tools from other package managers such as Homebrew, MacPorts or Fink, such binaries are by definition incompatible with macOS native libraries and applications. If you choose one of those package managers, make sure you compile/everything/using those tools including R and all packages and libraries you intend to use." I think it should have been offered as advice to only be followed by persons with great experience in compiling and building packages on Macs. Best; David > > Fink allows you to install different versions of R (3.6, 3.5, 3.4, 3.3, 3.2 > and 3.1). > > For different versions, CRAN packages are separately installed > (/sw/lib/R/3.6/site-library and so on). > > >> 2020/05/19 22:45、Adelchi Azzalini のメール: >> >> Hi. >> In essence, my problem is that I cannot install a package which requires >> Fortran-77 compilation on my Mac. >> >> More in detail, this is my own package 'mnormt' which exists on CRAN since >> 2006; it is currently at version 1.5-7. It has been developed in successive >> versions on a Linux machine, where it compiles with no problems. The macOS >> and MS-windows versions are created on CRAN, where it passes all pertaining >> checks. >> >> Now, in the new pandemic world, I need create a new version of the package, >> but working from home, hence using my Mac laptop instead of the Linux >> desktop as in the past. Unfortunately, compilation or loading does not work. >> If I run >> >> R CMD check mnormt_1.5-7.tar.gz >> >> first I get a bunch of warning messages such as >> >> Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) >> [-Wconversion] >> Warning: ‘lxchng’ may be used uninitialized in this function >> [-Wmaybe-uninitialized] >> Warning: Label 10 at (1) defined but not used [-Wunused-label] >> >> and finally it crashes with >> >> Error: package or namespace load failed for ‘mnormt’: >> .onLoad failed in loadNamespace() for 'mnormt', details: >> call: dyn.load(file, DLLpath = DLLpath, ...) >> error: unable to load shared object >> '/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so': >> >> dlopen(/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so, >> 6): Symbol not found: ___addtf3 >> Referenced from: /usr/local/lib/libquadmath.0.dylib >> Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib >> in /usr/local/lib/libquadmath.0.dylib >> Error: loading failed >> >> Needless to say, I have no idea what this "addtf3" is or it should be. There >> is no such a symbol in the Fortran code. >> >> I believe to have installed all ingredients indicated at >> https://mac.r-project.org/tools/ >> See the list below with details about my system and other installed tools. >> >> Any suggestions for sorting this out? >> >> Adelchi Azzalini >> >> >> --- >> Installation info: >> >> R> R.version >>_ >> platform x86_64-apple-darwin17.0 >> arch x86_64 >> os darwin17.0 >> system x86_64, darwin17.0 >> status >> major 4 >> minor 0.0 >> year 2020 >> month 04 >> day24 >> svn rev78286 >> language R >> version.string R version 4.0.0 (2020-04-24) >> nickname Arbor Day >> >> --- macOS Mojave 10.14.6 >> >> --- Xcode version 11.3.1 >> >> --- Fortran >> >> [aa@mac-2013:~] gfortran -v >> Using built-in specs. >> COLLECT_GCC=gfortran >> COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin18/8.2.0/lto-wrapper >> Target: x86_64-apple-darwin18 >> Configured with: ../gcc-8.2.0/configure --prefix=/usr/local/gfortran >> --with-gmp=/Users/fx/devel/gcc/build_package/deps >> --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin18 >> --disable-multilib --with-native-system-header-dir=/usr/include >> --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk >> Thread model: posix >> gcc version 8.2.0 (GCC) >> >> [aa@mac-2013:~] echo $PATH >> .:/Users/aa/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin/:/usr/X11R6/bin:/opt/local/bin:/Library/TeX/texbin:/usr/local/gfortran/bin >> >> -- other tools indicated at https://mac.r-project.org/tools/ >>xz-5.2.5/ is installed >>PCRE2 10.34 built with --disable-jit >>bzip2 Version 1.0.6 is installed >> >> ___ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > ___ > R-SIG-Mac mailing list >
Re: [R-SIG-Mac] Cannot compile Fortran on macOS
The main thing that stands out to me in that error: Referenced from: /usr/local/lib/libquadmath.0.dylib Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib R bundles its own copies of libquadmath and libgcc: kevinushey@Kevins-MBP:/Library/Frameworks/R.framework/Resources/lib $ ls -la total 19120 drwxrwxr-x 11 root admin 352 Apr 24 03:23 . drwxrwxr-x 18 root admin 576 Apr 29 11:46 .. -rwxrwxr-x 1 root admin 4070896 Apr 24 03:23 libR.dylib drwxrwxr-x 3 root admin 96 Apr 24 03:22 libR.dylib.dSYM -rwxrwxr-x 1 root admin 201472 Apr 24 03:23 libRblas.dylib drwxrwxr-x 3 root admin 96 Apr 24 03:22 libRblas.dylib.dSYM -rwxrwxr-x 1 root admin 2181472 Apr 24 03:23 libRlapack.dylib drwxrwxr-x 3 root admin 96 Apr 24 03:22 libRlapack.dylib.dSYM -rw-rw-r-- 1 root admin 160624 Apr 24 03:23 libgcc_s.1.dylib -rwxrwxr-x 1 root admin 2851008 Apr 24 03:23 libgfortran.5.dylib -rwxrwxr-x 1 root admin 309648 Apr 24 03:23 libquadmath.0.dylib which should normally be used during the link step. However, versions in /usr/local/lib are being discovered instead, which presumably aren't compatible. The simplest fix is (likely) to move those files out of the way. Otherwise, you'd likely have to muck around with Makevars / Makeconf to adjust the linker flags so the correct versions of these libraries are found. Best, Kevin On Tue, May 19, 2020 at 6:46 AM Adelchi Azzalini wrote: > Hi. > In essence, my problem is that I cannot install a package which requires > Fortran-77 compilation on my Mac. > > More in detail, this is my own package 'mnormt' which exists on CRAN since > 2006; it is currently at version 1.5-7. It has been developed in successive > versions on a Linux machine, where it compiles with no problems. The macOS > and MS-windows versions are created on CRAN, where it passes all pertaining > checks. > > Now, in the new pandemic world, I need create a new version of the > package, but working from home, hence using my Mac laptop instead of the > Linux desktop as in the past. Unfortunately, compilation or loading does > not work. If I run > > R CMD check mnormt_1.5-7.tar.gz > > first I get a bunch of warning messages such as > > Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) > [-Wconversion] > Warning: ‘lxchng’ may be used uninitialized in this function > [-Wmaybe-uninitialized] > Warning: Label 10 at (1) defined but not used [-Wunused-label] > > and finally it crashes with > > Error: package or namespace load failed for ‘mnormt’: > .onLoad failed in loadNamespace() for 'mnormt', details: > call: dyn.load(file, DLLpath = DLLpath, ...) > error: unable to load shared object > '/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so': > > dlopen(/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so, > 6): Symbol not found: ___addtf3 > Referenced from: /usr/local/lib/libquadmath.0.dylib > Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib > in /usr/local/lib/libquadmath.0.dylib > Error: loading failed > > Needless to say, I have no idea what this "addtf3" is or it should be. > There is no such a symbol in the Fortran code. > > I believe to have installed all ingredients indicated at > https://mac.r-project.org/tools/ > See the list below with details about my system and other installed tools. > > Any suggestions for sorting this out? > > Adelchi Azzalini > > > --- > Installation info: > > R> R.version >_ > platform x86_64-apple-darwin17.0 > arch x86_64 > os darwin17.0 > system x86_64, darwin17.0 > status > major 4 > minor 0.0 > year 2020 > month 04 > day24 > svn rev78286 > language R > version.string R version 4.0.0 (2020-04-24) > nickname Arbor Day > > --- macOS Mojave 10.14.6 > > --- Xcode version 11.3.1 > > --- Fortran > > [aa@mac-2013:~] gfortran -v > Using built-in specs. > COLLECT_GCC=gfortran > > COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin18/8.2.0/lto-wrapper > Target: x86_64-apple-darwin18 > Configured with: ../gcc-8.2.0/configure --prefix=/usr/local/gfortran > --with-gmp=/Users/fx/devel/gcc/build_package/deps > --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin18 > --disable-multilib --with-native-system-header-dir=/usr/include > --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk > Thread model: posix > gcc version 8.2.0 (GCC) > > [aa@mac-2013:~] echo $PATH > > .:/Users/aa/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin/:/usr/X11R6/bin:/opt/local/bin:/Library/TeX/texbin:/usr/local/gfortran/bin > > -- other tools indicated at https://mac.r-project.org/tools/ >xz-5.2.5/ is installed >PCRE2 10.34 built with --disable-jit >bzip2 Version 1.0.6 is installed > > ___ >
Re: [R-SIG-Mac] Cannot compile Fortran on macOS
Adelchi, Why don’t you try Fink version of R? Fink build mnormt on R 4.0 as well (although it is experimental). https://github.com/fink/fink-distributions/issues/623 Fink allows you to install different versions of R (3.6, 3.5, 3.4, 3.3, 3.2 and 3.1). For different versions, CRAN packages are separately installed (/sw/lib/R/3.6/site-library and so on). > 2020/05/19 22:45、Adelchi Azzalini のメール: > > Hi. > In essence, my problem is that I cannot install a package which requires > Fortran-77 compilation on my Mac. > > More in detail, this is my own package 'mnormt' which exists on CRAN since > 2006; it is currently at version 1.5-7. It has been developed in successive > versions on a Linux machine, where it compiles with no problems. The macOS > and MS-windows versions are created on CRAN, where it passes all pertaining > checks. > > Now, in the new pandemic world, I need create a new version of the package, > but working from home, hence using my Mac laptop instead of the Linux desktop > as in the past. Unfortunately, compilation or loading does not work. If I run > > R CMD check mnormt_1.5-7.tar.gz > > first I get a bunch of warning messages such as > > Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) > [-Wconversion] > Warning: ‘lxchng’ may be used uninitialized in this function > [-Wmaybe-uninitialized] > Warning: Label 10 at (1) defined but not used [-Wunused-label] > > and finally it crashes with > > Error: package or namespace load failed for ‘mnormt’: > .onLoad failed in loadNamespace() for 'mnormt', details: > call: dyn.load(file, DLLpath = DLLpath, ...) > error: unable to load shared object > '/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so': > > dlopen(/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so, > 6): Symbol not found: ___addtf3 > Referenced from: /usr/local/lib/libquadmath.0.dylib > Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib > in /usr/local/lib/libquadmath.0.dylib > Error: loading failed > > Needless to say, I have no idea what this "addtf3" is or it should be. There > is no such a symbol in the Fortran code. > > I believe to have installed all ingredients indicated at > https://mac.r-project.org/tools/ > See the list below with details about my system and other installed tools. > > Any suggestions for sorting this out? > > Adelchi Azzalini > > > --- > Installation info: > > R> R.version > _ > platform x86_64-apple-darwin17.0 > arch x86_64 > os darwin17.0 > system x86_64, darwin17.0 > status > major 4 > minor 0.0 > year 2020 > month 04 > day24 > svn rev78286 > language R > version.string R version 4.0.0 (2020-04-24) > nickname Arbor Day > > --- macOS Mojave 10.14.6 > > --- Xcode version 11.3.1 > > --- Fortran > > [aa@mac-2013:~] gfortran -v > Using built-in specs. > COLLECT_GCC=gfortran > COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin18/8.2.0/lto-wrapper > Target: x86_64-apple-darwin18 > Configured with: ../gcc-8.2.0/configure --prefix=/usr/local/gfortran > --with-gmp=/Users/fx/devel/gcc/build_package/deps > --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin18 > --disable-multilib --with-native-system-header-dir=/usr/include > --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk > Thread model: posix > gcc version 8.2.0 (GCC) > > [aa@mac-2013:~] echo $PATH > .:/Users/aa/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin/:/usr/X11R6/bin:/opt/local/bin:/Library/TeX/texbin:/usr/local/gfortran/bin > > -- other tools indicated at https://mac.r-project.org/tools/ > xz-5.2.5/ is installed > PCRE2 10.34 built with --disable-jit > bzip2 Version 1.0.6 is installed > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Cannot compile Fortran on macOS
Hi. In essence, my problem is that I cannot install a package which requires Fortran-77 compilation on my Mac. More in detail, this is my own package 'mnormt' which exists on CRAN since 2006; it is currently at version 1.5-7. It has been developed in successive versions on a Linux machine, where it compiles with no problems. The macOS and MS-windows versions are created on CRAN, where it passes all pertaining checks. Now, in the new pandemic world, I need create a new version of the package, but working from home, hence using my Mac laptop instead of the Linux desktop as in the past. Unfortunately, compilation or loading does not work. If I run R CMD check mnormt_1.5-7.tar.gz first I get a bunch of warning messages such as Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) [-Wconversion] Warning: ‘lxchng’ may be used uninitialized in this function [-Wmaybe-uninitialized] Warning: Label 10 at (1) defined but not used [-Wunused-label] and finally it crashes with Error: package or namespace load failed for ‘mnormt’: .onLoad failed in loadNamespace() for 'mnormt', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so': dlopen(/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so, 6): Symbol not found: ___addtf3 Referenced from: /usr/local/lib/libquadmath.0.dylib Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib in /usr/local/lib/libquadmath.0.dylib Error: loading failed Needless to say, I have no idea what this "addtf3" is or it should be. There is no such a symbol in the Fortran code. I believe to have installed all ingredients indicated at https://mac.r-project.org/tools/ See the list below with details about my system and other installed tools. Any suggestions for sorting this out? Adelchi Azzalini --- Installation info: R> R.version _ platform x86_64-apple-darwin17.0 arch x86_64 os darwin17.0 system x86_64, darwin17.0 status major 4 minor 0.0 year 2020 month 04 day24 svn rev78286 language R version.string R version 4.0.0 (2020-04-24) nickname Arbor Day --- macOS Mojave 10.14.6 --- Xcode version 11.3.1 --- Fortran [aa@mac-2013:~] gfortran -v Using built-in specs. COLLECT_GCC=gfortran COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin18/8.2.0/lto-wrapper Target: x86_64-apple-darwin18 Configured with: ../gcc-8.2.0/configure --prefix=/usr/local/gfortran --with-gmp=/Users/fx/devel/gcc/build_package/deps --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin18 --disable-multilib --with-native-system-header-dir=/usr/include --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk Thread model: posix gcc version 8.2.0 (GCC) [aa@mac-2013:~] echo $PATH .:/Users/aa/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin/:/usr/X11R6/bin:/opt/local/bin:/Library/TeX/texbin:/usr/local/gfortran/bin -- other tools indicated at https://mac.r-project.org/tools/ xz-5.2.5/ is installed PCRE2 10.34 built with --disable-jit bzip2 Version 1.0.6 is installed ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
