> On 21 Apr 2016, at 19:15, David Winsemius <dwinsem...@comcast.net> wrote: > > 18 months ago I volunteered to fix a very tiny error in the documentation in > the abandoned package, muhaz, so I am now the maintainer. I'm trying to be a > responsible maintainer and test my package with R 3.3.0 in advance of its > release. (I hope the fact that I have not gotten any email notices from CRAN > about failed installation attempts means that all is well with my package > under the R 3.3.0 and CRAN's current build machine.) > > Since then I have migrated to El Capitan (which I believe is not yet the > current build OS for OSX branches of R). I was trying to be a responsible > maintainer and test my package with R 3.3.0 in advance of its release. I was > getting an error when building from source that my googling efforts suggested > is due to incompatibility between El Cap and earlier versions of Fortran. I > do not usually get errors with source packages because I have attempted in my > halting manner to keep an up-to-date toolchain: XCode, > Command_Line_Tools_OS_X_10.11_for_Xcode_7.3 and up until now > gfortran-4.8.2-darwin13 from the r.att.research.com site. > > * installing to library > ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’ > * installing *source* package ‘muhaz’ ... > ** package ‘muhaz’ successfully unpacked and MD5 sums checked > ** libs > gfortran-4.8 -fPIC -g -O2 -c muhaz.f -o muhaz.o > gfortran-4.8: warning: couldn’t understand kern.osversion ‘15.4.0 > f951: internal compiler error: Illegal instruction: 4 >
Are you compiling on a computer with an Intel Core 2 Duo? I had that problem too. See here https://stat.ethz.ch/pipermail/r-sig-mac/2014-May/010894.html and Simon's reply. I now have a computer with an i5 processor; the gfortran 4.8.2 from r.att.research.com works without that message. > The GNU Fortran Project mailing list has several contributions from > François-Xavier Coudert who suggests that El Cap users install Fortran from a > disk image installer that he makes available: > > http://coudert.name/software.html > > gfortran 5.2 for Yosemite: > http://coudert.name/software/gfortran-5.2-Yosemite.dmg , which I downloaded. > .... noting that the author says "works well with El Capitan" > > I've also found several other versions of gfortran at: > > http://hpc.sourceforge.net/index.php > > ... where versions 5.1, 5.3,and 6.0 are listed as appropriate for El Capitan. > > It wasn't clear to me whether I needed to have matching sets of gcc and > gfortran if I used these, but it appeared to me from the material I read in > the R Install/Admin Guide that I would not need to add that additional > complexity. > > I wondered: > 1) If I install this version of Fortran, what are my odds of failing to fix > my problem and also crippling my capacity for compiling packages from source > that were compiled and tested on Fortran 4.8.2. (I've decided to take the > risk.) > > 2) If I succeed with this for compiling muhaz, then will I later need to > revert and what will I need to do to revert if needed. > In this thread https://stat.ethz.ch/pipermail/r-sig-mac/2015-October/011641.html Brian Ripley in reply to my query said that Coudert's gfortran could be used. Berend > Arguably I could have posted this on the package-devel mailing list, but > since my best-guess is that specific interfaces with the Mac OS are at the > heart of this issue, I'm sticking with R-sig-mac until advised to move on. > > I've attempted to read through the Install/Admin document and have derived > some knowledge: > > a) from section 6.3 and $ R CMD INSTALL --help: may use: > > --configure-args=ARGS > to set arguments for the configure scripts (if any) > > b) sect 6.3.2: "Entries [to either > `/Library/Frameworks/R.framework/Resources/etc/Makeconf` or `~/.R/Makevars`] > which may need to be changed include ‘CC’, ‘CXX’, ‘FC’, ‘F77’, ‘FLIBS’ and > the corresponding flags, and perhaps ‘CXXCPP’, ‘DYLIB_LD’, ‘MAIN_LD’, > ‘SHLIB_CXXLD’, ‘SHLIB_FCLD’ and ‘SHLIB_LD’." > > c) modifications to these might be placed in `~/.R/Makevars` but the next > subsection says they could be placed in `HOME/.R/Makevars-R_PLATFORM` which > I'm quite sure is a different location. > > And then there is a three line example for setting up Fortran on a Mac which > appeared extremely relevant to my growing list of questions. I noticed that > it has reference to /usr/local/gfortran/bin/gfortran and then uses FLIBS = > -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin14/5.2.0 which appeared to > be a good match to the gfortran referenced above. > > Emboldened by the resemblance of this worked example to the disk image > mentioned above I ran the installation dialog and do now have exactly the > folder structure implied by that three line config example. Now believe I can > either repeat the INSTALL command with trailing configure-args, or modify > Makeconf , or I can construct a config file of some sort in > HOME/.R/Makevars-R_PLATFORM. I chose to do the second options since I was > unable to divine what the proper incantation might be for the "R-PLATFORM" > section of that string. I decided to replace the "gfortran section" with > this, attempting to alter only those lines that matched the three altered > lines in the Admin/Install example: > > FC = /usr/local/gfortran/bin/gfortran > FCFLAGS = -Wall -g -O2 $(LTO) > ## additional libs needed when linking with $(FC), e.g. on Solaris > FCLIBS = > F77 = /usr/local/gfortran/bin/gfortran > F77_VISIBILITY = > FFLAGS = -g -O2 $(LTO) > FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin14/5.2.0 > -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm > FCPICFLAGS = -fPIC > FPICFLAGS = -fPIC > > Then: > > $ R CMD INSTALL /Users/davidwinsemius/muhaz_1.2.6.tar.gz > > Followed by compiler messages and R message and finally ... > * DONE (muhaz) > > OK. I guess reading the manual and googling really does "work". > > -- > > David Winsemius > Alameda, CA, USA > > _______________________________________________ > 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
