From bhh at xs4all.nl Sat Aug 1 07:34:52 2015 From: bhh at xs4all.nl (Berend Hasselman) Date: Sat, 1 Aug 2015 07:34:52 +0200 Subject: [R-SIG-Mac] Problems to install a package In-Reply-To: <65B461DE-3B1F-4EBD-9949-0B01BA1E5D57@gmail.com> References: <342FA42B-46CF-4FB8-B71B-4DE94B98F826@r-project.org> <5BA35FA4-78BB-4212-B494-926A5DBA1590@stat.ubc.ca> <8B91C180-586F-46CD-96A3-BF7D24027006@ed.ac.uk> <8F0C666C-07E0-4D0A-93D0-FF1B085E938D@gmail.com> <2CF1B54C-5D68-47ED-83C0-7465CBB84AC0@xs4all.nl> <65B461DE-3B1F-4EBD-9949-0B01BA1E5D57@gmail.com> Message-ID: <40E1469C-C041-46D7-9456-9D600D6A3FC6@xs4all.nl> > On 31-07-2015, at 22:14, peter dalgaard wrote: > >> >> On 31 Jul 2015, at 21:36 , Berend Hasselman wrote: >> >>> >>> On 31-07-2015, at 20:46, peter dalgaard wrote: >>> >>>> >>>> On 31 Jul 2015, at 12:33 , Timothy Bates wrote: >>>> >>>> This happened for me too: that Intel Core 2 is just too old for the compiler. >>>> >>>> I used it as a stimulus to buy a new laptop? As a bonus, everything is ~10x faster >>>> Best, tim >>> >>> Hum, well, I wasn't actually planning to switch out my MB Air just now. >>> >>> I'm actually baffled that I haven't bumped into this before. Both my laptop and my office desktop are Core 2 Duo machines (and the latter is the one that builds the R source releases!). >>> >> >> If you use gfortran: which version? >> If you are not using any floating point then gfortran-4.8 will probably work without problems. >> I think. >> > > It's 4.2.1 and 4.2.3, it seems. That's for the local builds; for the CRAN binaries, it seems that I just never tried building a package with Fortran in it. Not sure whether I have used any Fortran binaries (is there an easy way to check whether a package contains Fortran?) But then you are still using the Snow Leopard binaries for R? I don?t know if stuff created with the older gfortran will run with an R built for mavericks. Two of my packages: nleqslv and geigen. They could not compile on my previous C2D computer with gfortran-4.8. And another one: QZ. And there are some more. You would also need the Mavericks binaries of R. Berend From pdalgd at gmail.com Sat Aug 1 11:40:54 2015 From: pdalgd at gmail.com (peter dalgaard) Date: Sat, 1 Aug 2015 11:40:54 +0200 Subject: [R-SIG-Mac] Problems to install a package In-Reply-To: <40E1469C-C041-46D7-9456-9D600D6A3FC6@xs4all.nl> References: <342FA42B-46CF-4FB8-B71B-4DE94B98F826@r-project.org> <5BA35FA4-78BB-4212-B494-926A5DBA1590@stat.ubc.ca> <8B91C180-586F-46CD-96A3-BF7D24027006@ed.ac.uk> <8F0C666C-07E0-4D0A-93D0-FF1B085E938D@gmail.com> <2CF1B54C-5D68-47ED-83C0-7465CBB84AC0@xs4all.nl> <65B461DE-3B1F-4EBD-9949-0B01BA1E5D57@gmail.com> <40E1469C-C041-46D7-9456-9D600D6A3FC6@xs4all.nl> Message-ID: <23FF1871-5F24-48DD-8B2C-2314E4053E01@gmail.com> > On 01 Aug 2015, at 07:34 , Berend Hasselman wrote: > >> >> On 31-07-2015, at 22:14, peter dalgaard wrote: >> >>> >>> On 31 Jul 2015, at 21:36 , Berend Hasselman wrote: >>> >>>> >>>> On 31-07-2015, at 20:46, peter dalgaard wrote: >>>> >>>>> >>>>> On 31 Jul 2015, at 12:33 , Timothy Bates wrote: >>>>> >>>>> This happened for me too: that Intel Core 2 is just too old for the compiler. >>>>> >>>>> I used it as a stimulus to buy a new laptop? As a bonus, everything is ~10x faster >>>>> Best, tim >>>> >>>> Hum, well, I wasn't actually planning to switch out my MB Air just now. >>>> >>>> I'm actually baffled that I haven't bumped into this before. Both my laptop and my office desktop are Core 2 Duo machines (and the latter is the one that builds the R source releases!). >>>> >>> >>> If you use gfortran: which version? >>> If you are not using any floating point then gfortran-4.8 will probably work without problems. >>> I think. >>> >> >> It's 4.2.1 and 4.2.3, it seems. That's for the local builds; for the CRAN binaries, it seems that I just never tried building a package with Fortran in it. Not sure whether I have used any Fortran binaries (is there an easy way to check whether a package contains Fortran?) > > But then you are still using the Snow Leopard binaries for R? > I don?t know if stuff created with the older gfortran will run with an R built for mavericks. Those were for local builds, which I suppose will by definition be Yosemite/Mavericks builds (laptop/desktop respectively). The corresponding C compiler is gcc, alias $ gcc --version Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 Apple LLVM version 6.1.0 (clang-602.0.53) (based on LLVM 3.6.0svn) Target: x86_64-apple-darwin14.4.0 Thread model: posix > > Two of my packages: nleqslv and geigen. They could not compile on my previous C2D computer with gfortran-4.8. > And another one: QZ. > And there are some more. > You would also need the Mavericks binaries of R. > The CRAN binaries of nleqslv seem to install, load, and run OK with the Mavericks CRAN binaries. Source build of nleqslv builds, loads, runs with a local build on Yosemite. In both cases, "runs" means that example(nleqslv) and example(testnslv) does something seemingly sensible and do not crash. (Source build with Mavericks/CRAN would obviously fail due to the absence of gfortran-4.8 and I wouldn't even try mixing the two Fortran versions.) -pd > Berend -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From pdalgd at gmail.com Mon Aug 3 11:26:15 2015 From: pdalgd at gmail.com (peter dalgaard) Date: Mon, 3 Aug 2015 11:26:15 +0200 Subject: [R-SIG-Mac] Problems to install a package In-Reply-To: <23FF1871-5F24-48DD-8B2C-2314E4053E01@gmail.com> References: <342FA42B-46CF-4FB8-B71B-4DE94B98F826@r-project.org> <5BA35FA4-78BB-4212-B494-926A5DBA1590@stat.ubc.ca> <8B91C180-586F-46CD-96A3-BF7D24027006@ed.ac.uk> <8F0C666C-07E0-4D0A-93D0-FF1B085E938D@gmail.com> <2CF1B54C-5D68-47ED-83C0-7465CBB84AC0@xs4all.nl> <65B461DE-3B1F-4EBD-9949-0B01BA1E5D57@gmail.com> <40E1469C-C041-46D7-9456-9D600D6A3FC6@xs4all.nl> <23FF1871-5F24-48DD-8B2C-2314E4053E01@gmail.com> Message-ID: On 01 Aug 2015, at 11:40 , peter dalgaard wrote: > >> On 01 Aug 2015, at 07:34 , Berend Hasselman wrote: >> >>> >>> On 31-07-2015, at 22:14, peter dalgaard wrote: >>> >>>> >>>> On 31 Jul 2015, at 21:36 , Berend Hasselman wrote: >>>> >>>>> >>>>> On 31-07-2015, at 20:46, peter dalgaard wrote: >>>>> >>>>>> >>>>>> On 31 Jul 2015, at 12:33 , Timothy Bates wrote: >>>>>> >>>>>> This happened for me too: that Intel Core 2 is just too old for the compiler. >>>>>> >>>>>> I used it as a stimulus to buy a new laptop? As a bonus, everything is ~10x faster >>>>>> Best, tim >>>>> >>>>> Hum, well, I wasn't actually planning to switch out my MB Air just now. >>>>> >>>>> I'm actually baffled that I haven't bumped into this before. Both my laptop and my office desktop are Core 2 Duo machines (and the latter is the one that builds the R source releases!). >>>>> >>>> >>>> If you use gfortran: which version? >>>> If you are not using any floating point then gfortran-4.8 will probably work without problems. >>>> I think. >>>> >>> >>> It's 4.2.1 and 4.2.3, it seems. That's for the local builds; for the CRAN binaries, it seems that I just never tried building a package with Fortran in it. Not sure whether I have used any Fortran binaries (is there an easy way to check whether a package contains Fortran?) >> >> But then you are still using the Snow Leopard binaries for R? >> I don?t know if stuff created with the older gfortran will run with an R built for mavericks. > > Those were for local builds, which I suppose will by definition be Yosemite/Mavericks builds (laptop/desktop respectively). The corresponding C compiler is gcc, alias > > $ gcc --version > Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 > Apple LLVM version 6.1.0 (clang-602.0.53) (based on LLVM 3.6.0svn) > Target: x86_64-apple-darwin14.4.0 > Thread model: posix > > > >> >> Two of my packages: nleqslv and geigen. They could not compile on my previous C2D computer with gfortran-4.8. >> And another one: QZ. >> And there are some more. >> You would also need the Mavericks binaries of R. >> > > The CRAN binaries of nleqslv seem to install, load, and run OK with the Mavericks CRAN binaries. > > Source build of nleqslv builds, loads, runs with a local build on Yosemite. > > In both cases, "runs" means that example(nleqslv) and example(testnslv) does something seemingly sensible and do not crash. > > (Source build with Mavericks/CRAN would obviously fail due to the absence of gfortran-4.8 and I wouldn't even try mixing the two Fortran versions.) -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From pdalgd at gmail.com Mon Aug 3 11:27:47 2015 From: pdalgd at gmail.com (peter dalgaard) Date: Mon, 3 Aug 2015 11:27:47 +0200 Subject: [R-SIG-Mac] Problems to install a package In-Reply-To: References: <342FA42B-46CF-4FB8-B71B-4DE94B98F826@r-project.org> <5BA35FA4-78BB-4212-B494-926A5DBA1590@stat.ubc.ca> <8B91C180-586F-46CD-96A3-BF7D24027006@ed.ac.uk> <8F0C666C-07E0-4D0A-93D0-FF1B085E938D@gmail.com> <2CF1B54C-5D68-47ED-83C0-7465CBB84AC0@xs4all.nl> <65B461DE-3B1F-4EBD-9949-0B01BA1E5D57@gmail.com> <40E1469C-C041-46D7-9456-9D600D6A3FC6@xs4all.nl> <23FF1871-5F24-48DD-8B2C-2314E4053E01@gmail.com> Message-ID: <2661FDB5-FC40-4A81-AD81-F54CBD906F63@gmail.com> [Argh. Hit send by mistake. Please ignore previous mail] On 03 Aug 2015, at 11:26 , peter dalgaard wrote: > > On 01 Aug 2015, at 11:40 , peter dalgaard wrote: > >> >>> On 01 Aug 2015, at 07:34 , Berend Hasselman wrote: -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From pdalgd at gmail.com Mon Aug 3 13:59:48 2015 From: pdalgd at gmail.com (peter dalgaard) Date: Mon, 3 Aug 2015 13:59:48 +0200 Subject: [R-SIG-Mac] Problems to install a package In-Reply-To: References: <342FA42B-46CF-4FB8-B71B-4DE94B98F826@r-project.org> <5BA35FA4-78BB-4212-B494-926A5DBA1590@stat.ubc.ca> <8B91C180-586F-46CD-96A3-BF7D24027006@ed.ac.uk> <8F0C666C-07E0-4D0A-93D0-FF1B085E938D@gmail.com> <2CF1B54C-5D68-47ED-83C0-7465CBB84AC0@xs4all.nl> <65B461DE-3B1F-4EBD-9949-0B01BA1E5D57@gmail.com> <40E1469C-C041-46D7-9456-9D600D6A3FC6@xs4all.nl> <23FF1871-5F24-48DD-8B2C-2314E4053E01@gmail.com> Message-ID: <26186A38-3725-49E6-A0DD-625A76DCB1B6@gmail.com> I have now tried doctoring $RHOME/etc/Makeconf to use a MacPorts build of gfortran-4.8 that I had lying around, and lo and behold: It does source installs of nleqslv, geigen, QZ, rms with no trouble at all. So I think the finger is pointing at the binaries on r.research.att.com/libs. -pd On 03 Aug 2015, at 11:26 , peter dalgaard wrote: > > On 01 Aug 2015, at 11:40 , peter dalgaard wrote: > >> >>> On 01 Aug 2015, at 07:34 , Berend Hasselman wrote: >>> >>>> >>>> On 31-07-2015, at 22:14, peter dalgaard wrote: >>>> >>>>> >>>>> On 31 Jul 2015, at 21:36 , Berend Hasselman wrote: >>>>> >>>>>> >>>>>> On 31-07-2015, at 20:46, peter dalgaard wrote: >>>>>> >>>>>>> >>>>>>> On 31 Jul 2015, at 12:33 , Timothy Bates wrote: >>>>>>> >>>>>>> This happened for me too: that Intel Core 2 is just too old for the compiler. >>>>>>> >>>>>>> I used it as a stimulus to buy a new laptop? As a bonus, everything is ~10x faster >>>>>>> Best, tim >>>>>> >>>>>> Hum, well, I wasn't actually planning to switch out my MB Air just now. >>>>>> >>>>>> I'm actually baffled that I haven't bumped into this before. Both my laptop and my office desktop are Core 2 Duo machines (and the latter is the one that builds the R source releases!). >>>>>> >>>>> >>>>> If you use gfortran: which version? >>>>> If you are not using any floating point then gfortran-4.8 will probably work without problems. >>>>> I think. >>>>> >>>> >>>> It's 4.2.1 and 4.2.3, it seems. That's for the local builds; for the CRAN binaries, it seems that I just never tried building a package with Fortran in it. Not sure whether I have used any Fortran binaries (is there an easy way to check whether a package contains Fortran?) >>> >>> But then you are still using the Snow Leopard binaries for R? >>> I don?t know if stuff created with the older gfortran will run with an R built for mavericks. >> >> Those were for local builds, which I suppose will by definition be Yosemite/Mavericks builds (laptop/desktop respectively). The corresponding C compiler is gcc, alias >> >> $ gcc --version >> Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 >> Apple LLVM version 6.1.0 (clang-602.0.53) (based on LLVM 3.6.0svn) >> Target: x86_64-apple-darwin14.4.0 >> Thread model: posix >> >> >> >>> >>> Two of my packages: nleqslv and geigen. They could not compile on my previous C2D computer with gfortran-4.8. >>> And another one: QZ. >>> And there are some more. >>> You would also need the Mavericks binaries of R. >>> >> >> The CRAN binaries of nleqslv seem to install, load, and run OK with the Mavericks CRAN binaries. >> >> Source build of nleqslv builds, loads, runs with a local build on Yosemite. >> >> In both cases, "runs" means that example(nleqslv) and example(testnslv) does something seemingly sensible and do not crash. >> >> (Source build with Mavericks/CRAN would obviously fail due to the absence of gfortran-4.8 and I wouldn't even try mixing the two Fortran versions.) > > -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From bhh at xs4all.nl Mon Aug 3 15:10:00 2015 From: bhh at xs4all.nl (Berend Hasselman) Date: Mon, 3 Aug 2015 15:10:00 +0200 Subject: [R-SIG-Mac] Problems to install a package In-Reply-To: <26186A38-3725-49E6-A0DD-625A76DCB1B6@gmail.com> References: <342FA42B-46CF-4FB8-B71B-4DE94B98F826@r-project.org> <5BA35FA4-78BB-4212-B494-926A5DBA1590@stat.ubc.ca> <8B91C180-586F-46CD-96A3-BF7D24027006@ed.ac.uk> <8F0C666C-07E0-4D0A-93D0-FF1B085E938D@gmail.com> <2CF1B54C-5D68-47ED-83C0-7465CBB84AC0@xs4all.nl> <65B461DE-3B1F-4EBD-9949-0B01BA1E5D57@gmail.com> <40E1469C-C041-46D7-9456-9D600D6A3FC6@xs4all.nl> <23FF1871-5F24-48DD-8B2C-2314E4053E01@gmail.com> <26186A38-3725-49E6-A0DD-625A76DCB1B6@gmail.com> Message-ID: <75744470-F49D-4686-8E3C-7A22E07B541E@xs4all.nl> > On 03-08-2015, at 13:59, peter dalgaard wrote: > > I have now tried doctoring $RHOME/etc/Makeconf to use a MacPorts build of gfortran-4.8 that I had lying around, and lo and behold: It does source installs of nleqslv, geigen, QZ, rms with no trouble at all. > Good to know that. > So I think the finger is pointing at the binaries on r.research.att.com/libs. Indeed as was confirmed by Simon last year here https://stat.ethz.ch/pipermail/r-sig-mac/2014-May/010895.html I can use the binary of r.research.att.com/libs since I now have a more modern Mac with an i5 cpu. I did some searching and found the following: http://coudert.name/software.html and https://gcc.gnu.org/wiki/GFortranBinaries#MacOS Might be a good idea to try these versions of gfortran too on a C2D. Maybe the CRAN R could be built with one of these gfortran binaries avoiding the need to compile an R provided gfortran and distributed on r.research.att.com/libs. But that is beyond me and I have no idea about possible issues doing it. Berend From pdalgd at gmail.com Mon Aug 3 15:57:19 2015 From: pdalgd at gmail.com (peter dalgaard) Date: Mon, 3 Aug 2015 15:57:19 +0200 Subject: [R-SIG-Mac] Problems to install a package In-Reply-To: <75744470-F49D-4686-8E3C-7A22E07B541E@xs4all.nl> References: <342FA42B-46CF-4FB8-B71B-4DE94B98F826@r-project.org> <5BA35FA4-78BB-4212-B494-926A5DBA1590@stat.ubc.ca> <8B91C180-586F-46CD-96A3-BF7D24027006@ed.ac.uk> <8F0C666C-07E0-4D0A-93D0-FF1B085E938D@gmail.com> <2CF1B54C-5D68-47ED-83C0-7465CBB84AC0@xs4all.nl> <65B461DE-3B1F-4EBD-9949-0B01BA1E5D57@gmail.com> <40E1469C-C041-46D7-9456-9D600D6A3FC6@xs4all.nl> <23FF1871-5F24-48DD-8B2C-2314E4053E01@gmail.com> <26186A38-3725-49E6-A0DD-625A76DCB1B6@gmail.com> <75744470-F49D-4686-8E3C-7A22E07B541E@xs4all.nl> Message-ID: <3BA15922-DD63-41AE-9DE6-E2B4E0113479@gmail.com> On 03 Aug 2015, at 15:10 , Berend Hasselman wrote: > >> On 03-08-2015, at 13:59, peter dalgaard wrote: >> >> I have now tried doctoring $RHOME/etc/Makeconf to use a MacPorts build of gfortran-4.8 that I had lying around, and lo and behold: It does source installs of nleqslv, geigen, QZ, rms with no trouble at all. >> > > Good to know that. > >> So I think the finger is pointing at the binaries on r.research.att.com/libs. > > Indeed as was confirmed by Simon last year here https://stat.ethz.ch/pipermail/r-sig-mac/2014-May/010895.html > I can use the binary of r.research.att.com/libs since I now have a more modern Mac with an i5 cpu. > > I did some searching and found the following: > > http://coudert.name/software.html > > and https://gcc.gnu.org/wiki/GFortranBinaries#MacOS > > Might be a good idea to try these versions of gfortran too on a C2D. Yes. However, I'll have to worry about overwriting and possibly breaking my build environment with 3.2.2 coming out next Friday (Simon's binary package rather carefully installs gfortran-4.8, but not gfortran, I believe. Won't know about the others until I try them.). So, not on this machine. > Maybe the CRAN R could be built with one of these gfortran binaries avoiding the need to compile an R provided gfortran and distributed on r.research.att.com/libs. I haven't seen evidence that there is a problem with the CRAN binaries of anything and we still need to provide gfortran somehow for people who need to build from source. What we could try is to compile 4.8 on a C2D or cross-compile it for that architecture. I think that the latter is doable, but I don't recall the details (gcc --target ?). -pd > But that is beyond me and I have no idea about possible issues doing it. > > Berend > -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From pdalgd at gmail.com Mon Aug 3 19:30:58 2015 From: pdalgd at gmail.com (peter dalgaard) Date: Mon, 3 Aug 2015 19:30:58 +0200 Subject: [R-SIG-Mac] Problems to install a package In-Reply-To: <3BA15922-DD63-41AE-9DE6-E2B4E0113479@gmail.com> References: <342FA42B-46CF-4FB8-B71B-4DE94B98F826@r-project.org> <5BA35FA4-78BB-4212-B494-926A5DBA1590@stat.ubc.ca> <8B91C180-586F-46CD-96A3-BF7D24027006@ed.ac.uk> <8F0C666C-07E0-4D0A-93D0-FF1B085E938D@gmail.com> <2CF1B54C-5D68-47ED-83C0-7465CBB84AC0@xs4all.nl> <65B461DE-3B1F-4EBD-9949-0B01BA1E5D57@gmail.com> <40E1469C-C041-46D7-9456-9D600D6A3FC6@xs4all.nl> <23FF1871-5F24-48DD-8B2C-2314E4053E01@gmail.com> <26186A38-3725-49E6-A0DD-625A76DCB1B6@gmail.com> <75744470-F49D-4686-8E3C-7A22E07B541E@xs4all.nl> <3BA15922-DD63-41AE-9DE6-E2B4E0113479@gmail.com> Message-ID: Some further digging in the MacPorts fora suggests that gmp is the real culprit, but I'm not through digging yet. Compiling gcc 4.8.5 from source using the binaries of gmp-5.1.3 et al. from r.research.att.com dies with a "gfortran not working" message caused by the familiar f951 illegal instruction error. Replacing with 6.0.0 and retrying "make" didn't help nor did using gmp-6.0.0a compiled locally. However, starting all over after "make distclean" actually produced a functioning gfortran with gmp-6.0.0a. (Thus, it is possible that it would have worked with the binary of 6.0.0 too, if I had tried a clean build.) (Building gcc/gfortran from scratch literally takes hours on the aging iMac, so experimenting is, um, inconvenient... In comparison, building gmp was a piece of cake, so if that suffices, it would be great.) I'll see if I can dig deeper tomorrow. -pd > On 03 Aug 2015, at 15:57 , peter dalgaard wrote: > > > On 03 Aug 2015, at 15:10 , Berend Hasselman wrote: > >> >>> On 03-08-2015, at 13:59, peter dalgaard wrote: >>> >>> I have now tried doctoring $RHOME/etc/Makeconf to use a MacPorts build of gfortran-4.8 that I had lying around, and lo and behold: It does source installs of nleqslv, geigen, QZ, rms with no trouble at all. >>> >> >> Good to know that. >> >>> So I think the finger is pointing at the binaries on r.research.att.com/libs. >> >> Indeed as was confirmed by Simon last year here https://stat.ethz.ch/pipermail/r-sig-mac/2014-May/010895.html >> I can use the binary of r.research.att.com/libs since I now have a more modern Mac with an i5 cpu. >> >> I did some searching and found the following: >> >> http://coudert.name/software.html >> >> and https://gcc.gnu.org/wiki/GFortranBinaries#MacOS >> >> Might be a good idea to try these versions of gfortran too on a C2D. > > Yes. However, I'll have to worry about overwriting and possibly breaking my build environment with 3.2.2 coming out next Friday (Simon's binary package rather carefully installs gfortran-4.8, but not gfortran, I believe. Won't know about the others until I try them.). So, not on this machine. > >> Maybe the CRAN R could be built with one of these gfortran binaries avoiding the need to compile an R provided gfortran and distributed on r.research.att.com/libs. > > I haven't seen evidence that there is a problem with the CRAN binaries of anything and we still need to provide gfortran somehow for people who need to build from source. What we could try is to compile 4.8 on a C2D or cross-compile it for that architecture. I think that the latter is doable, but I don't recall the details (gcc --target ?). > > -pd > >> But that is beyond me and I have no idea about possible issues doing it. >> >> Berend >> > > -- > Peter Dalgaard, Professor, > Center for Statistics, Copenhagen Business School > Solbjerg Plads 3, 2000 Frederiksberg, Denmark > Phone: (+45)38153501 > Office: A 4.23 > Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From simon.urbanek at r-project.org Mon Aug 3 23:48:49 2015 From: simon.urbanek at r-project.org (Simon Urbanek) Date: Mon, 3 Aug 2015 17:48:49 -0400 Subject: [R-SIG-Mac] Problems to install a package In-Reply-To: <26186A38-3725-49E6-A0DD-625A76DCB1B6@gmail.com> References: <342FA42B-46CF-4FB8-B71B-4DE94B98F826@r-project.org> <5BA35FA4-78BB-4212-B494-926A5DBA1590@stat.ubc.ca> <8B91C180-586F-46CD-96A3-BF7D24027006@ed.ac.uk> <8F0C666C-07E0-4D0A-93D0-FF1B085E938D@gmail.com> <2CF1B54C-5D68-47ED-83C0-7465CBB84AC0@xs4all.nl> <65B461DE-3B1F-4EBD-9949-0B01BA1E5D57@gmail.com> <40E1469C-C041-46D7-9456-9D600D6A3FC6@xs4all.nl> <23FF1871-5F24-48DD-8B2C-2314E4053E01@gmail.com> <26186A38-3725-49E6-A0DD-625A76DCB1B6@gmail.com> Message-ID: <6DE7ECE9-62C5-4D3C-880C-D3F54D93A4A4@r-project.org> Sorry, I thought it was obvious so I didn't elaborate in more detail - our Mavericks compiler binary (gfortran-4.8) itself is using more advanced instruction set so it doesn't work on older CPUs (C2D as it appears). It's likely something to do with gmp/mpfr since those are the only ones that use hand-coded assembler instructions and they picked the one for the host CRAN machine with is a Mac Pro (Xenon). It doesn't have an effect on the compiled result since the flags govern that - so the compiled packages will work just fine on old hardware. Given that anyone with older hardware should simply be able to use the Fortran from CRAN I didn't think it could spawn such a long thread ;). After all, the underlying GNU Fortran is the same anyway. Cheers, Simon > On Aug 3, 2015, at 7:59 AM, peter dalgaard wrote: > > I have now tried doctoring $RHOME/etc/Makeconf to use a MacPorts build of gfortran-4.8 that I had lying around, and lo and behold: It does source installs of nleqslv, geigen, QZ, rms with no trouble at all. > > So I think the finger is pointing at the binaries on r.research.att.com/libs. > > -pd > > On 03 Aug 2015, at 11:26 , peter dalgaard wrote: > >> >> On 01 Aug 2015, at 11:40 , peter dalgaard wrote: >> >>> >>>> On 01 Aug 2015, at 07:34 , Berend Hasselman wrote: >>>> >>>>> >>>>> On 31-07-2015, at 22:14, peter dalgaard wrote: >>>>> >>>>>> >>>>>> On 31 Jul 2015, at 21:36 , Berend Hasselman wrote: >>>>>> >>>>>>> >>>>>>> On 31-07-2015, at 20:46, peter dalgaard wrote: >>>>>>> >>>>>>>> >>>>>>>> On 31 Jul 2015, at 12:33 , Timothy Bates wrote: >>>>>>>> >>>>>>>> This happened for me too: that Intel Core 2 is just too old for the compiler. >>>>>>>> >>>>>>>> I used it as a stimulus to buy a new laptop? As a bonus, everything is ~10x faster >>>>>>>> Best, tim >>>>>>> >>>>>>> Hum, well, I wasn't actually planning to switch out my MB Air just now. >>>>>>> >>>>>>> I'm actually baffled that I haven't bumped into this before. Both my laptop and my office desktop are Core 2 Duo machines (and the latter is the one that builds the R source releases!). >>>>>>> >>>>>> >>>>>> If you use gfortran: which version? >>>>>> If you are not using any floating point then gfortran-4.8 will probably work without problems. >>>>>> I think. >>>>>> >>>>> >>>>> It's 4.2.1 and 4.2.3, it seems. That's for the local builds; for the CRAN binaries, it seems that I just never tried building a package with Fortran in it. Not sure whether I have used any Fortran binaries (is there an easy way to check whether a package contains Fortran?) >>>> >>>> But then you are still using the Snow Leopard binaries for R? >>>> I don?t know if stuff created with the older gfortran will run with an R built for mavericks. >>> >>> Those were for local builds, which I suppose will by definition be Yosemite/Mavericks builds (laptop/desktop respectively). The corresponding C compiler is gcc, alias >>> >>> $ gcc --version >>> Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 >>> Apple LLVM version 6.1.0 (clang-602.0.53) (based on LLVM 3.6.0svn) >>> Target: x86_64-apple-darwin14.4.0 >>> Thread model: posix >>> >>> >>> >>>> >>>> Two of my packages: nleqslv and geigen. They could not compile on my previous C2D computer with gfortran-4.8. >>>> And another one: QZ. >>>> And there are some more. >>>> You would also need the Mavericks binaries of R. >>>> >>> >>> The CRAN binaries of nleqslv seem to install, load, and run OK with the Mavericks CRAN binaries. >>> >>> Source build of nleqslv builds, loads, runs with a local build on Yosemite. >>> >>> In both cases, "runs" means that example(nleqslv) and example(testnslv) does something seemingly sensible and do not crash. >>> >>> (Source build with Mavericks/CRAN would obviously fail due to the absence of gfortran-4.8 and I wouldn't even try mixing the two Fortran versions.) >> >> > > -- > Peter Dalgaard, Professor, > Center for Statistics, Copenhagen Business School > Solbjerg Plads 3, 2000 Frederiksberg, Denmark > Phone: (+45)38153501 > Office: A 4.23 > Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > From jtbates1 at asu.edu Tue Aug 4 03:21:16 2015 From: jtbates1 at asu.edu (Jordan Bates) Date: Mon, 3 Aug 2015 18:21:16 -0700 Subject: [R-SIG-Mac] X11 support on OSX 10.10.4 Message-ID: Hello, I'm having trouble getting X11 support to work. I have XQuartz 2.7.7 installed. I've tried installing the R for Mac binaries, with homebrew from binaries, and with homebrew from source. In all cases when I run R, capabilities("X11") returns false. X11() gives the following error: > error: > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/otool: > can't open file: > /usr/local/Cellar/r/3.2.1_1/R.framework/Resources/modules/R_X11.so (No such > file or directory) > Best regards, Jordan [[alternative HTML version deleted]] From bob at rudis.net Tue Aug 4 03:27:25 2015 From: bob at rudis.net (boB Rudis) Date: Mon, 3 Aug 2015 21:27:25 -0400 Subject: [R-SIG-Mac] X11 support on OSX 10.10.4 In-Reply-To: References: Message-ID: How did you install XQuartz? It looks like it was via homebrew. The only official supported one (AFAIK) is via the actual XQuartz package. I'm on 10.10.4 with XQuartz 2.7.7 (from pkg installer) and R 3.2.1 (from CRAN d/l) and it works fine. I use homebrew for many sub-libraries (like GDAL) but not for core stuff like X11 & R itself. On Mon, Aug 3, 2015 at 9:21 PM, Jordan Bates wrote: > Hello, > > I'm having trouble getting X11 support to work. I have XQuartz 2.7.7 > installed. I've tried installing the R for Mac binaries, with homebrew > from binaries, and with homebrew from source. In all cases when I run R, > capabilities("X11") returns false. > > X11() gives the following error: > >> error: >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/otool: >> can't open file: >> /usr/local/Cellar/r/3.2.1_1/R.framework/Resources/modules/R_X11.so (No such >> file or directory) >> > > Best regards, > Jordan > > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac From jtbates1 at asu.edu Tue Aug 4 05:05:17 2015 From: jtbates1 at asu.edu (Jordan Bates) Date: Mon, 3 Aug 2015 20:05:17 -0700 Subject: [R-SIG-Mac] X11 support on OSX 10.10.4 In-Reply-To: References: Message-ID: I have XQuartz installed via the official package. I have X11 support working now with CRAN's R. I found that the error was actually different with R installed from CRAN's pkg that with homebrew's R. I just didn't have the DISPLAY variable set, which was fixed with: > $ launchctl load -w > /Library/LaunchAgents/org.macosforge.xquartz.startx.plist With homebrew's R, X11 support is not compiled in and the R_X11.so module is not there. I still haven't been able to figure that out. 2015-08-03 18:27 GMT-07:00 boB Rudis : > How did you install XQuartz? It looks like it was via homebrew. The > only official supported one (AFAIK) is via the actual XQuartz package. > I'm on 10.10.4 with XQuartz 2.7.7 (from pkg installer) and R 3.2.1 > (from CRAN d/l) and it works fine. I use homebrew for many > sub-libraries (like GDAL) but not for core stuff like X11 & R itself. > > On Mon, Aug 3, 2015 at 9:21 PM, Jordan Bates wrote: > > Hello, > > > > I'm having trouble getting X11 support to work. I have XQuartz 2.7.7 > > installed. I've tried installing the R for Mac binaries, with homebrew > > from binaries, and with homebrew from source. In all cases when I run R, > > capabilities("X11") returns false. > > > > X11() gives the following error: > > > >> error: > >> > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/otool: > >> can't open file: > >> /usr/local/Cellar/r/3.2.1_1/R.framework/Resources/modules/R_X11.so (No > such > >> file or directory) > >> > > > > Best regards, > > Jordan > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > R-SIG-Mac mailing list > > R-SIG-Mac at r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > [[alternative HTML version deleted]] From pdalgd at gmail.com Tue Aug 4 09:57:22 2015 From: pdalgd at gmail.com (peter dalgaard) Date: Tue, 4 Aug 2015 09:57:22 +0200 Subject: [R-SIG-Mac] Problems to install a package In-Reply-To: <6DE7ECE9-62C5-4D3C-880C-D3F54D93A4A4@r-project.org> References: <342FA42B-46CF-4FB8-B71B-4DE94B98F826@r-project.org> <5BA35FA4-78BB-4212-B494-926A5DBA1590@stat.ubc.ca> <8B91C180-586F-46CD-96A3-BF7D24027006@ed.ac.uk> <8F0C666C-07E0-4D0A-93D0-FF1B085E938D@gmail.com> <2CF1B54C-5D68-47ED-83C0-7465CBB84AC0@xs4all.nl> <65B461DE-3B1F-4EBD-9949-0B01BA1E5D57@gmail.com> <40E1469C-C041-46D7-9456-9D600D6A3FC6@xs4all.nl> <23FF1871-5F24-48DD-8B2C-2314E4053E01@gmail.com> <26186A38-3725-49E6-A0DD-625A76DCB1B6@gmail.com> <6DE7ECE9-62C5-4D3C-880C-D3F54D93A4A4@r-project.org> Message-ID: > On 03 Aug 2015, at 23:48 , Simon Urbanek wrote: > > Sorry, I thought it was obvious so I didn't elaborate in more detail - our Mavericks compiler binary (gfortran-4.8) itself is using more advanced instruction set so it doesn't work on older CPUs (C2D as it appears). It's likely something to do with gmp/mpfr since those are the only ones that use hand-coded assembler instructions and they picked the one for the host CRAN machine with is a Mac Pro (Xenon). It doesn't have an effect on the compiled result since the flags govern that - so the compiled packages will work just fine on old hardware. > > Given that anyone with older hardware should simply be able to use the Fortran from CRAN I didn't think it could spawn such a long thread ;). After all, the underlying GNU Fortran is the same anyway. Umm, the situation as I see it is this: The R Mavericks binaries "hardcode" gfortran-4.8 in etc/Makeconf Gfortran from CRAN is 4.2.3 It is not clear that you can mix & match the two gfortran versions Users who want to compile Fortran from source therefore get binaries for gfortran-4.8, gmp, mpfr from r.research.att.com This combination is broken on C2D machines Result: confusion (+ for some, a welcome incentive to upgrade...) If the fix can be as simple as editing Makeconf for a different Fortran (F77 and FLIBS entries), we should say so somewhere. Otherwise, I think it might be possible to "unbreak" gfortran-4.8 since the cause of the breakage is known. (I gather that it happens in something as silly as parsing floating constants in Fortran source, which at the very least can hardly be said to be a performance issue.) Na zdrav?, Peter > > Cheers, > Simon > > > >> On Aug 3, 2015, at 7:59 AM, peter dalgaard wrote: >> >> I have now tried doctoring $RHOME/etc/Makeconf to use a MacPorts build of gfortran-4.8 that I had lying around, and lo and behold: It does source installs of nleqslv, geigen, QZ, rms with no trouble at all. >> >> So I think the finger is pointing at the binaries on r.research.att.com/libs. >> >> -pd >> >> On 03 Aug 2015, at 11:26 , peter dalgaard wrote: >> >>> >>> On 01 Aug 2015, at 11:40 , peter dalgaard wrote: >>> >>>> >>>>> On 01 Aug 2015, at 07:34 , Berend Hasselman wrote: >>>>> >>>>>> >>>>>> On 31-07-2015, at 22:14, peter dalgaard wrote: >>>>>> >>>>>>> >>>>>>> On 31 Jul 2015, at 21:36 , Berend Hasselman wrote: >>>>>>> >>>>>>>> >>>>>>>> On 31-07-2015, at 20:46, peter dalgaard wrote: >>>>>>>> >>>>>>>>> >>>>>>>>> On 31 Jul 2015, at 12:33 , Timothy Bates wrote: >>>>>>>>> >>>>>>>>> This happened for me too: that Intel Core 2 is just too old for the compiler. >>>>>>>>> >>>>>>>>> I used it as a stimulus to buy a new laptop? As a bonus, everything is ~10x faster >>>>>>>>> Best, tim >>>>>>>> >>>>>>>> Hum, well, I wasn't actually planning to switch out my MB Air just now. >>>>>>>> >>>>>>>> I'm actually baffled that I haven't bumped into this before. Both my laptop and my office desktop are Core 2 Duo machines (and the latter is the one that builds the R source releases!). >>>>>>>> >>>>>>> >>>>>>> If you use gfortran: which version? >>>>>>> If you are not using any floating point then gfortran-4.8 will probably work without problems. >>>>>>> I think. >>>>>>> >>>>>> >>>>>> It's 4.2.1 and 4.2.3, it seems. That's for the local builds; for the CRAN binaries, it seems that I just never tried building a package with Fortran in it. Not sure whether I have used any Fortran binaries (is there an easy way to check whether a package contains Fortran?) >>>>> >>>>> But then you are still using the Snow Leopard binaries for R? >>>>> I don?t know if stuff created with the older gfortran will run with an R built for mavericks. >>>> >>>> Those were for local builds, which I suppose will by definition be Yosemite/Mavericks builds (laptop/desktop respectively). The corresponding C compiler is gcc, alias >>>> >>>> $ gcc --version >>>> Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 >>>> Apple LLVM version 6.1.0 (clang-602.0.53) (based on LLVM 3.6.0svn) >>>> Target: x86_64-apple-darwin14.4.0 >>>> Thread model: posix >>>> >>>> >>>> >>>>> >>>>> Two of my packages: nleqslv and geigen. They could not compile on my previous C2D computer with gfortran-4.8. >>>>> And another one: QZ. >>>>> And there are some more. >>>>> You would also need the Mavericks binaries of R. >>>>> >>>> >>>> The CRAN binaries of nleqslv seem to install, load, and run OK with the Mavericks CRAN binaries. >>>> >>>> Source build of nleqslv builds, loads, runs with a local build on Yosemite. >>>> >>>> In both cases, "runs" means that example(nleqslv) and example(testnslv) does something seemingly sensible and do not crash. >>>> >>>> (Source build with Mavericks/CRAN would obviously fail due to the absence of gfortran-4.8 and I wouldn't even try mixing the two Fortran versions.) >>> >>> >> >> -- >> Peter Dalgaard, Professor, >> Center for Statistics, Copenhagen Business School >> Solbjerg Plads 3, 2000 Frederiksberg, Denmark >> Phone: (+45)38153501 >> Office: A 4.23 >> Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com >> >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac at r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> > -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From ripley at stats.ox.ac.uk Tue Aug 4 10:34:11 2015 From: ripley at stats.ox.ac.uk (Prof Brian Ripley) Date: Tue, 4 Aug 2015 09:34:11 +0100 Subject: [R-SIG-Mac] Problems to install a package In-Reply-To: References: <342FA42B-46CF-4FB8-B71B-4DE94B98F826@r-project.org> <5BA35FA4-78BB-4212-B494-926A5DBA1590@stat.ubc.ca> <8B91C180-586F-46CD-96A3-BF7D24027006@ed.ac.uk> <8F0C666C-07E0-4D0A-93D0-FF1B085E938D@gmail.com> <2CF1B54C-5D68-47ED-83C0-7465CBB84AC0@xs4all.nl> <65B461DE-3B1F-4EBD-9949-0B01BA1E5D57@gmail.com> <40E1469C-C041-46D7-9456-9D600D6A3FC6@xs4all.nl> <23FF1871-5F24-48DD-8B2C-2314E4053E01@gmail.com> <26186A38-3725-49E6-A0DD-625A76DCB1B6@gmail.com> <6DE7ECE9-62C5-4D3C-880C-D3F54D93A4A4@r-project.org> Message-ID: <55C07903.40304@stats.ox.ac.uk> On 04/08/2015 08:57, peter dalgaard wrote: > >> On 03 Aug 2015, at 23:48 , Simon Urbanek wrote: >> >> Sorry, I thought it was obvious so I didn't elaborate in more detail - our Mavericks compiler binary (gfortran-4.8) itself is using more advanced instruction set so it doesn't work on older CPUs (C2D as it appears). It's likely something to do with gmp/mpfr since those are the only ones that use hand-coded assembler instructions and they picked the one for the host CRAN machine with is a Mac Pro (Xenon). It doesn't have an effect on the compiled result since the flags govern that - so the compiled packages will work just fine on old hardware. >> >> Given that anyone with older hardware should simply be able to use the Fortran from CRAN I didn't think it could spawn such a long thread ;). After all, the underlying GNU Fortran is the same anyway. > > Umm, the situation as I see it is this: > > The R Mavericks binaries "hardcode" gfortran-4.8 in etc/Makeconf > Gfortran from CRAN is 4.2.3 The recommended gfortran for the CRAN 'Mavericks' build has always been gfortran 4.8.0: see the R-admin manual. > It is not clear that you can mix & match the two gfortran versions It does not always work, although as FLIBS is static problems are rare (but usually segfault). And there are packages which gfortran 4.2.3 will not compile. > Users who want to compile Fortran from source therefore get binaries for > gfortran-4.8, gmp, mpfr from r.research.att.com > This combination is broken on C2D machines AFAICS you only need the binary of gfortran 4.8.0, as the gmp/mpfr libs are statically linked. > Result: confusion (+ for some, a welcome incentive to upgrade...) > > If the fix can be as simple as editing Makeconf for a different Fortran (F77 and FLIBS entries), we should say so somewhere. We do, at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#OS-X (although that was not current on CRAN when I just looked). > Otherwise, I think it might be possible to "unbreak" gfortran-4.8 since the cause of the breakage is known. (I gather that it happens in something as silly as parsing floating constants in Fortran source, which at the very least can hardly be said to be a performance issue.) As we no longer support multiple sub-architectures on OS X, the Apple drivers are not needed. I would be tempted to move to the binaries provided by Fran?ois-Xavier Coudert via the GCC wiki (also mentioned in the current manual). > Na zdrav?, > Peter > >> >> Cheers, >> Simon >> >> >> >>> On Aug 3, 2015, at 7:59 AM, peter dalgaard wrote: >>> >>> I have now tried doctoring $RHOME/etc/Makeconf to use a MacPorts build of gfortran-4.8 that I had lying around, and lo and behold: It does source installs of nleqslv, geigen, QZ, rms with no trouble at all. >>> >>> So I think the finger is pointing at the binaries on r.research.att.com/libs. >>> >>> -pd >>> >>> On 03 Aug 2015, at 11:26 , peter dalgaard wrote: >>> >>>> >>>> On 01 Aug 2015, at 11:40 , peter dalgaard wrote: >>>> >>>>> >>>>>> On 01 Aug 2015, at 07:34 , Berend Hasselman wrote: >>>>>> >>>>>>> >>>>>>> On 31-07-2015, at 22:14, peter dalgaard wrote: >>>>>>> >>>>>>>> >>>>>>>> On 31 Jul 2015, at 21:36 , Berend Hasselman wrote: >>>>>>>> >>>>>>>>> >>>>>>>>> On 31-07-2015, at 20:46, peter dalgaard wrote: >>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 31 Jul 2015, at 12:33 , Timothy Bates wrote: >>>>>>>>>> >>>>>>>>>> This happened for me too: that Intel Core 2 is just too old for the compiler. >>>>>>>>>> >>>>>>>>>> I used it as a stimulus to buy a new laptop? As a bonus, everything is ~10x faster >>>>>>>>>> Best, tim >>>>>>>>> >>>>>>>>> Hum, well, I wasn't actually planning to switch out my MB Air just now. >>>>>>>>> >>>>>>>>> I'm actually baffled that I haven't bumped into this before. Both my laptop and my office desktop are Core 2 Duo machines (and the latter is the one that builds the R source releases!). >>>>>>>>> >>>>>>>> >>>>>>>> If you use gfortran: which version? >>>>>>>> If you are not using any floating point then gfortran-4.8 will probably work without problems. >>>>>>>> I think. >>>>>>>> >>>>>>> >>>>>>> It's 4.2.1 and 4.2.3, it seems. That's for the local builds; for the CRAN binaries, it seems that I just never tried building a package with Fortran in it. Not sure whether I have used any Fortran binaries (is there an easy way to check whether a package contains Fortran?) >>>>>> >>>>>> But then you are still using the Snow Leopard binaries for R? >>>>>> I don?t know if stuff created with the older gfortran will run with an R built for mavericks. >>>>> >>>>> Those were for local builds, which I suppose will by definition be Yosemite/Mavericks builds (laptop/desktop respectively). The corresponding C compiler is gcc, alias >>>>> >>>>> $ gcc --version >>>>> Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 >>>>> Apple LLVM version 6.1.0 (clang-602.0.53) (based on LLVM 3.6.0svn) >>>>> Target: x86_64-apple-darwin14.4.0 >>>>> Thread model: posix >>>>> >>>>> >>>>> >>>>>> >>>>>> Two of my packages: nleqslv and geigen. They could not compile on my previous C2D computer with gfortran-4.8. >>>>>> And another one: QZ. >>>>>> And there are some more. >>>>>> You would also need the Mavericks binaries of R. >>>>>> >>>>> >>>>> The CRAN binaries of nleqslv seem to install, load, and run OK with the Mavericks CRAN binaries. >>>>> >>>>> Source build of nleqslv builds, loads, runs with a local build on Yosemite. >>>>> >>>>> In both cases, "runs" means that example(nleqslv) and example(testnslv) does something seemingly sensible and do not crash. >>>>> >>>>> (Source build with Mavericks/CRAN would obviously fail due to the absence of gfortran-4.8 and I wouldn't even try mixing the two Fortran versions.) >>>> >>>> >>> >>> -- >>> Peter Dalgaard, Professor, >>> Center for Statistics, Copenhagen Business School >>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark >>> Phone: (+45)38153501 >>> Office: A 4.23 >>> Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com >>> >>> _______________________________________________ >>> R-SIG-Mac mailing list >>> R-SIG-Mac at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >> > -- Brian D. Ripley, ripley at stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford 1 South Parks Road, Oxford OX1 3TG, UK From pdalgd at gmail.com Tue Aug 4 10:58:17 2015 From: pdalgd at gmail.com (peter dalgaard) Date: Tue, 4 Aug 2015 10:58:17 +0200 Subject: [R-SIG-Mac] Problems to install a package In-Reply-To: <55C07903.40304@stats.ox.ac.uk> References: <342FA42B-46CF-4FB8-B71B-4DE94B98F826@r-project.org> <5BA35FA4-78BB-4212-B494-926A5DBA1590@stat.ubc.ca> <8B91C180-586F-46CD-96A3-BF7D24027006@ed.ac.uk> <8F0C666C-07E0-4D0A-93D0-FF1B085E938D@gmail.com> <2CF1B54C-5D68-47ED-83C0-7465CBB84AC0@xs4all.nl> <65B461DE-3B1F-4EBD-9949-0B01BA1E5D57@gmail.com> <40E1469C-C041-46D7-9456-9D600D6A3FC6@xs4all.nl> <23FF1871-5F24-48DD-8B2C-2314E4053E01@gmail.com> <26186A38-3725-49E6-A0DD-625A76DCB1B6@gmail.com> <6DE7ECE9-62C5-4D3C-880C-D3F54D93A4A4@r-project.org> <55C07903.40304@stats.ox.ac.uk> Message-ID: <446C34EB-53A0-4C05-9479-ED25755A25A6@gmail.com> [Heavy trimming applied.] On 04 Aug 2015, at 10:34 , Prof Brian Ripley wrote: > On 04/08/2015 08:57, peter dalgaard wrote: >> > >> Users who want to compile Fortran from source therefore get binaries for >> gfortran-4.8, gmp, mpfr from r.research.att.com >> This combination is broken on C2D machines > > AFAICS you only need the binary of gfortran 4.8.0, as the gmp/mpfr libs are statically linked. Argh, I missed that point because I went directly for a full gcc/gfortran recompile. This also means that you cannot fix Simon's gfortran-4.8 by replacing the libs, of course. > >> Result: confusion (+ for some, a welcome incentive to upgrade...) >> >> If the fix can be as simple as editing Makeconf for a different Fortran (F77 and FLIBS entries), we should say so somewhere. > > We do, at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#OS-X (although that was not current on CRAN when I just looked). OK, but it is not really an attractive solution if it only works some of the time. > >> Otherwise, I think it might be possible to "unbreak" gfortran-4.8 since the cause of the breakage is known. (I gather that it happens in something as silly as parsing floating constants in Fortran source, which at the very least can hardly be said to be a performance issue.) > > As we no longer support multiple sub-architectures on OS X, the Apple drivers are not needed. I would be tempted to move to the binaries provided by Fran?ois-Xavier Coudert via the GCC wiki (also mentioned in the current manual). > OK, I can try those on the laptop without too much hassle. > -- > Brian D. Ripley, ripley at stats.ox.ac.uk > Emeritus Professor of Applied Statistics, University of Oxford > 1 South Parks Road, Oxford OX1 3TG, UK -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From jcchien at me.com Tue Aug 4 16:51:41 2015 From: jcchien at me.com (Josh C. Chien) Date: Tue, 04 Aug 2015 22:51:41 +0800 Subject: [R-SIG-Mac] Rmertrics-fPortfolio can't be installed on OS 10.10.4 Message-ID: Hi Mac-R, Anyone know how to figure out this issue ? > install.packages("fPortfolio") also installing the dependency ?Rsymphony? Package which is only available in source form, and may need compilation of C/C++/Fortran: ?Rsymphony? Do you want to attempt to install these from sources? y/n: y installing the source packages ?Rsymphony?, ?fPortfolio? trying URL 'https://mran.revolutionanalytics.com/snapshot/2015-07-01/src/contrib/Rsymphony_0.1-21.tar.gz' Content type 'application/octet-stream' length 7429 bytes ================================================== downloaded 7429 bytes trying URL 'https://mran.revolutionanalytics.com/snapshot/2015-07-01/src/contrib/fPortfolio_3011.81.tar.gz' Content type 'application/octet-stream' length 740344 bytes (722 KB) ================================================== downloaded 722 KB Multithreaded BLAS/LAPACK libraries detected. Using 4 cores for math algorithms. * installing *source* package ?Rsymphony? ... ** package ?Rsymphony? successfully unpacked and MD5 sums checked Cannot find SYMPHONY libraries and headers. See . ERROR: configuration failed for package ?Rsymphony? * removing ?/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsymphony? Warning in install.packages : installation of package ?Rsymphony? had non-zero exit status Multithreaded BLAS/LAPACK libraries detected. Using 4 cores for math algorithms. ERROR: dependency ?Rsymphony? is not available for package ?fPortfolio? * removing ?/Library/Frameworks/R.framework/Versions/3.2/Resources/library/fPortfolio? Warning in install.packages : installation of package ?fPortfolio? had non-zero exit status The downloaded source packages are in ?/private/var/folders/vs/tv8qhwdn4r58jtlc9yhmz35m0000gp/T/Rtmpynb7eH/downloaded_packages? ____________________________ Josh Chien Sent from my MacBook Pro [[alternative HTML version deleted]] From brandon.hurr at gmail.com Tue Aug 4 16:57:14 2015 From: brandon.hurr at gmail.com (Brandon Hurr) Date: Tue, 04 Aug 2015 14:57:14 +0000 Subject: [R-SIG-Mac] Rmertrics-fPortfolio can't be installed on OS 10.10.4 In-Reply-To: References: Message-ID: Did you install Symphony first? Cannot find SYMPHONY libraries and headers. See . On Tue, Aug 4, 2015 at 07:55 Josh C. Chien wrote: > Hi Mac-R, > Anyone know how to figure out this issue ? > > > > > install.packages("fPortfolio") > also installing the dependency ?Rsymphony? > > Package which is only available in source form, and may need compilation > of C/C++/Fortran: ?Rsymphony? > Do you want to attempt to install these from sources? > y/n: y > installing the source packages ?Rsymphony?, ?fPortfolio? > > trying URL ' > https://mran.revolutionanalytics.com/snapshot/2015-07-01/src/contrib/Rsymphony_0.1-21.tar.gz > ' > Content type 'application/octet-stream' length 7429 bytes > ================================================== > downloaded 7429 bytes > > trying URL ' > https://mran.revolutionanalytics.com/snapshot/2015-07-01/src/contrib/fPortfolio_3011.81.tar.gz > ' > Content type 'application/octet-stream' length 740344 bytes (722 KB) > ================================================== > downloaded 722 KB > > Multithreaded BLAS/LAPACK libraries detected. Using 4 cores for math > algorithms. > * installing *source* package ?Rsymphony? ... > ** package ?Rsymphony? successfully unpacked and MD5 sums checked > Cannot find SYMPHONY libraries and headers. > See . > ERROR: configuration failed for package ?Rsymphony? > * removing > ?/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsymphony? > Warning in install.packages : > installation of package ?Rsymphony? had non-zero exit status > Multithreaded BLAS/LAPACK libraries detected. Using 4 cores for math > algorithms. > ERROR: dependency ?Rsymphony? is not available for package ?fPortfolio? > * removing > ?/Library/Frameworks/R.framework/Versions/3.2/Resources/library/fPortfolio? > Warning in install.packages : > installation of package ?fPortfolio? had non-zero exit status > > The downloaded source packages are in > > ?/private/var/folders/vs/tv8qhwdn4r58jtlc9yhmz35m0000gp/T/Rtmpynb7eH/downloaded_packages? > > ____________________________ > Josh Chien > Sent from my MacBook Pro > > > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > [[alternative HTML version deleted]] From brandon.hurr at gmail.com Tue Aug 4 17:24:52 2015 From: brandon.hurr at gmail.com (Brandon Hurr) Date: Tue, 4 Aug 2015 08:24:52 -0700 Subject: [R-SIG-Mac] Rmertrics-fPortfolio can't be installed on OS 10.10.4 In-Reply-To: References: Message-ID: - *OS X*: The easiest way to get SYMPHONY on OSX is through Homebrew. It can be installed with brew install symphony. Do you have homebrew? http://brew.sh/ ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" Once the Symphony libraries are in place you should be able to install the R version of it. Usually it's not always so simple though. I had issues with the sound libraries in R. Lots of dependencies. Caveat: I've never installed Symphony myself. On Tue, Aug 4, 2015 at 8:17 AM, Josh C. Chien wrote: > HI Brandon, > thanks for your link. But, I saw this link and still can?t get understand > how to install it ? > Besides, all R library which depend on C/C++/Fortran have the same problem > that they can?t be installed successfully on OS 10.10.4 > > ____________________________ > > *Josh ChienSent from my MacBook Pro* > > > > > > > > On Aug 4, 2015, at 10:57 PM, Brandon Hurr wrote: > > Did you install Symphony first? > Cannot find SYMPHONY libraries and headers. > See . > On Tue, Aug 4, 2015 at 07:55 Josh C. Chien wrote: > >> Hi Mac-R, >> Anyone know how to figure out this issue ? >> >> >> >> > install.packages("fPortfolio") >> also installing the dependency ?Rsymphony? >> >> Package which is only available in source form, and may need compilation >> of C/C++/Fortran: ?Rsymphony? >> Do you want to attempt to install these from sources? >> y/n: y >> installing the source packages ?Rsymphony?, ?fPortfolio? >> >> trying URL ' >> https://mran.revolutionanalytics.com/snapshot/2015-07-01/src/contrib/Rsymphony_0.1-21.tar.gz >> ' >> Content type 'application/octet-stream' length 7429 bytes >> ================================================== >> downloaded 7429 bytes >> >> trying URL ' >> https://mran.revolutionanalytics.com/snapshot/2015-07-01/src/contrib/fPortfolio_3011.81.tar.gz >> ' >> Content type 'application/octet-stream' length 740344 bytes (722 KB) >> ================================================== >> downloaded 722 KB >> >> Multithreaded BLAS/LAPACK libraries detected. Using 4 cores for math >> algorithms. >> * installing *source* package ?Rsymphony? ... >> ** package ?Rsymphony? successfully unpacked and MD5 sums checked >> Cannot find SYMPHONY libraries and headers. >> See . >> ERROR: configuration failed for package ?Rsymphony? >> * removing >> ?/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsymphony? >> Warning in install.packages : >> installation of package ?Rsymphony? had non-zero exit status >> Multithreaded BLAS/LAPACK libraries detected. Using 4 cores for math >> algorithms. >> ERROR: dependency ?Rsymphony? is not available for package ?fPortfolio? >> * removing >> ?/Library/Frameworks/R.framework/Versions/3.2/Resources/library/fPortfolio? >> Warning in install.packages : >> installation of package ?fPortfolio? had non-zero exit status >> >> The downloaded source packages are in >> >> ?/private/var/folders/vs/tv8qhwdn4r58jtlc9yhmz35m0000gp/T/Rtmpynb7eH/downloaded_packages? >> >> ____________________________ >> Josh Chien >> Sent from my MacBook Pro >> >> >> >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac at r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> > > [[alternative HTML version deleted]] From pdalgd at gmail.com Tue Aug 4 21:52:14 2015 From: pdalgd at gmail.com (peter dalgaard) Date: Tue, 4 Aug 2015 21:52:14 +0200 Subject: [R-SIG-Mac] Problems to install a package In-Reply-To: <446C34EB-53A0-4C05-9479-ED25755A25A6@gmail.com> References: <342FA42B-46CF-4FB8-B71B-4DE94B98F826@r-project.org> <5BA35FA4-78BB-4212-B494-926A5DBA1590@stat.ubc.ca> <8B91C180-586F-46CD-96A3-BF7D24027006@ed.ac.uk> <8F0C666C-07E0-4D0A-93D0-FF1B085E938D@gmail.com> <2CF1B54C-5D68-47ED-83C0-7465CBB84AC0@xs4all.nl> <65B461DE-3B1F-4EBD-9949-0B01BA1E5D57@gmail.com> <40E1469C-C041-46D7-9456-9D600D6A3FC6@xs4all.nl> <23FF1871-5F24-48DD-8B2C-2314E4053E01@gmail.com> <26186A38-3725-49E6-A0DD-625A76DCB1B6@gmail.com> <6DE7ECE9-62C5-4D3C-880C-D3F54D93A4A4@r-project.org> <55C07903.40304@stats.ox.ac.uk> <446C34EB-53A0-4C05-9479-ED25755A25A6@gmail.com> Message-ID: > On 04 Aug 2015, at 10:58 , peter dalgaard wrote: > >> As we no longer support multiple sub-architectures on OS X, the Apple drivers are not needed. I would be tempted to move to the binaries provided by Fran?ois-Xavier Coudert via the GCC wiki (also mentioned in the current manual). >> > > OK, I can try those on the laptop without too much hassle. Now tried (4.9.3, and doctoring `R RHOME`/etc/Makeconf) and it seems to work. Only slight issue was that the package install required overriding security setting. Also, it clobbered /usr/local/bin/gfortran from my previous install. -pd -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From dtenenba at fredhutch.org Thu Aug 6 21:44:32 2015 From: dtenenba at fredhutch.org (Dan Tenenbaum) Date: Thu, 6 Aug 2015 12:44:32 -0700 (PDT) Subject: [R-SIG-Mac] source() command and HTTPS urls in R-3.2.2 beta In-Reply-To: <1701809646.494864.1438889550194.JavaMail.root@fredhutch.org> Message-ID: <310440674.495078.1438890272051.JavaMail.root@fredhutch.org> Hi, using the sessionInfo() below I got the following error: > source("https://bioconductor.org/biocLite.R") Error in file(filename, "r", encoding = encoding) : https:// URLs are not supported This is the CRAN binary build of R-3.2.2 beta for Snow Leopard. I thought https urls were supposed to be supported in this version? The same command works in the same version of R on linux, windows, and Mavericks (albeit with a message on Mavericks and Linux saying 'https:// URLs are not supported by the default method: trying "libcurl"'). Maybe a misconfiguration in the way that the binary was built for Snow Leopard? Thanks, Dan > sessionInfo() R version 3.2.2 beta (2015-08-05 r68859) Platform: x86_64-apple-darwin10.8.0 (64-bit) Running under: OS X 10.6.8 (Snow Leopard) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base > From pdalgd at gmail.com Thu Aug 6 21:57:41 2015 From: pdalgd at gmail.com (peter dalgaard) Date: Thu, 6 Aug 2015 21:57:41 +0200 Subject: [R-SIG-Mac] source() command and HTTPS urls in R-3.2.2 beta In-Reply-To: <310440674.495078.1438890272051.JavaMail.root@fredhutch.org> References: <310440674.495078.1438890272051.JavaMail.root@fredhutch.org> Message-ID: <1403BF98-EB09-44D9-B0AD-17779C3657FE@gmail.com> > On 06 Aug 2015, at 21:44 , Dan Tenenbaum wrote: > > Hi, using the sessionInfo() below I got the following error: > >> source("https://bioconductor.org/biocLite.R") > Error in file(filename, "r", encoding = encoding) : > https:// URLs are not supported > > This is the CRAN binary build of R-3.2.2 beta for Snow Leopard. > > I thought https urls were supposed to be supported in this version? The same command works in the same version of R on linux, windows, and Mavericks (albeit with a message on Mavericks and Linux saying 'https:// URLs are not supported by the default method: trying "libcurl"'). > > Maybe a misconfiguration in the way that the binary was built for Snow Leopard? What does capabilities() say about libcurl? -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From dtenenba at fredhutch.org Thu Aug 6 22:03:47 2015 From: dtenenba at fredhutch.org (Dan Tenenbaum) Date: Thu, 6 Aug 2015 13:03:47 -0700 (PDT) Subject: [R-SIG-Mac] source() command and HTTPS urls in R-3.2.2 beta In-Reply-To: <1403BF98-EB09-44D9-B0AD-17779C3657FE@gmail.com> Message-ID: <1729805837.495610.1438891427104.JavaMail.root@fredhutch.org> ----- Original Message ----- > From: "peter dalgaard" > To: "Dan Tenenbaum" > Cc: "r-sig-mac" > Sent: Thursday, August 6, 2015 12:57:41 PM > Subject: Re: [R-SIG-Mac] source() command and HTTPS urls in R-3.2.2 beta > > > > On 06 Aug 2015, at 21:44 , Dan Tenenbaum > > wrote: > > > > Hi, using the sessionInfo() below I got the following error: > > > >> source("https://bioconductor.org/biocLite.R") > > Error in file(filename, "r", encoding = encoding) : > > https:// URLs are not supported > > > > This is the CRAN binary build of R-3.2.2 beta for Snow Leopard. > > > > I thought https urls were supposed to be supported in this version? > > The same command works in the same version of R on linux, windows, > > and Mavericks (albeit with a message on Mavericks and Linux saying > > 'https:// URLs are not supported by the default method: trying > > "libcurl"'). > > > > Maybe a misconfiguration in the way that the binary was built for > > Snow Leopard? > > What does capabilities() say about libcurl? > FALSE. Dan > > -- > Peter Dalgaard, Professor, > Center for Statistics, Copenhagen Business School > Solbjerg Plads 3, 2000 Frederiksberg, Denmark > Phone: (+45)38153501 > Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com > > > > > > > > > From pdalgd at gmail.com Thu Aug 6 22:56:14 2015 From: pdalgd at gmail.com (peter dalgaard) Date: Thu, 6 Aug 2015 22:56:14 +0200 Subject: [R-SIG-Mac] source() command and HTTPS urls in R-3.2.2 beta In-Reply-To: <1729805837.495610.1438891427104.JavaMail.root@fredhutch.org> References: <1729805837.495610.1438891427104.JavaMail.root@fredhutch.org> Message-ID: > On 06 Aug 2015, at 22:03 , Dan Tenenbaum wrote: > >>> This is the CRAN binary build of R-3.2.2 beta for Snow Leopard. >>> >>> I thought https urls were supposed to be supported in this version? >>> The same command works in the same version of R on linux, windows, >>> and Mavericks (albeit with a message on Mavericks and Linux saying >>> 'https:// URLs are not supported by the default method: trying >>> "libcurl"'). >>> >>> Maybe a misconfiguration in the way that the binary was built for >>> Snow Leopard? >> >> What does capabilities() say about libcurl? >> > > FALSE. > Dan That'll explain it. It can't try libcurl if it isn't there. However, the Snow Leopard builds are being phased out (check out the note on https://cran.r-project.org/bin/macosx/). It is not obvious (to say the least) that there will be a 3.2.2 version - the "3.2.2 beta" may just exist due to inertia. I don't quite know the specifics, but I think the underlying issue is that it is becoming increasingly difficult to keep a build system running and updated on an OS that isn't even supported by Apple any more. There have been some silliness with linking libcurl on OS X, which makes it even less attractive to mess with the build setup. Of course, nothing is keeping you from making your own local build, perhaps using homebrew... -pd -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From dtenenba at fredhutch.org Thu Aug 6 23:01:21 2015 From: dtenenba at fredhutch.org (Dan Tenenbaum) Date: Thu, 6 Aug 2015 14:01:21 -0700 (PDT) Subject: [R-SIG-Mac] source() command and HTTPS urls in R-3.2.2 beta In-Reply-To: Message-ID: <997959424.496946.1438894881522.JavaMail.root@fredhutch.org> ----- Original Message ----- > From: "peter dalgaard" > To: "Dan Tenenbaum" > Cc: "r-sig-mac" > Sent: Thursday, August 6, 2015 1:56:14 PM > Subject: Re: [R-SIG-Mac] source() command and HTTPS urls in R-3.2.2 beta > > > > On 06 Aug 2015, at 22:03 , Dan Tenenbaum > > wrote: > > > >>> This is the CRAN binary build of R-3.2.2 beta for Snow Leopard. > >>> > >>> I thought https urls were supposed to be supported in this > >>> version? > >>> The same command works in the same version of R on linux, > >>> windows, > >>> and Mavericks (albeit with a message on Mavericks and Linux > >>> saying > >>> 'https:// URLs are not supported by the default method: trying > >>> "libcurl"'). > >>> > >>> Maybe a misconfiguration in the way that the binary was built for > >>> Snow Leopard? > >> > >> What does capabilities() say about libcurl? > >> > > > > FALSE. > > Dan > > That'll explain it. It can't try libcurl if it isn't there. > > However, the Snow Leopard builds are being phased out (check out the > note on https://cran.r-project.org/bin/macosx/). It is not obvious > (to say the least) that there will be a 3.2.2 version - the "3.2.2 > beta" may just exist due to inertia. > > I don't quite know the specifics, but I think the underlying issue is > that it is becoming increasingly difficult to keep a build system > running and updated on an OS that isn't even supported by Apple any > more. There have been some silliness with linking libcurl on OS X, > which makes it even less attractive to mess with the build setup. > > Of course, nothing is keeping you from making your own local build, > perhaps using homebrew... > I maintain the bioconductor build system and we need to use the CRAN binaries, otherwise the binary packages we produce would not be usable by most people. I understand that Snow Leopard is being phased out. However, this does mean that any package that relies on libcurl will fail on Snow Leopard (using the CRAN R binary) and so will all its reverse dependencies. Simon, do you have any thoughts on this? I know Snow Leopard is limping off into the sunset but I hope it can do so more gracefully. ;-) Dan > -pd > > -- > Peter Dalgaard, Professor, > Center for Statistics, Copenhagen Business School > Solbjerg Plads 3, 2000 Frederiksberg, Denmark > Phone: (+45)38153501 > Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com > > > > > > > > > From pdalgd at gmail.com Fri Aug 7 11:28:52 2015 From: pdalgd at gmail.com (peter dalgaard) Date: Fri, 7 Aug 2015 11:28:52 +0200 Subject: [R-SIG-Mac] source() command and HTTPS urls in R-3.2.2 beta In-Reply-To: <310440674.495078.1438890272051.JavaMail.root@fredhutch.org> References: <310440674.495078.1438890272051.JavaMail.root@fredhutch.org> Message-ID: On 06 Aug 2015, at 21:44 , Dan Tenenbaum wrote: > I thought https urls were supposed to be supported in this version? The same command works in the same version of R on linux, windows, and Mavericks (albeit with a message on Mavericks and Linux saying 'https:// URLs are not supported by the default method: trying "libcurl"'). A clarification, prompted by conversation with those who actually know about this: We can't "support" https: in the sense of making it work everywhere -- there are too many external entities involved, and libcurl support doesn't necessarily imply that https: works. What we have done in 3.2.2 is mainly to remove some stumbling blocks so that repositories can be accessed via https: *when that works* and ensure that there actually are HTTPS-speaking mirrors available. -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From grubio at mat.upv.es Tue Aug 11 20:51:41 2015 From: grubio at mat.upv.es (Gregorio Rubio Navarro) Date: Tue, 11 Aug 2015 20:51:41 +0200 Subject: [R-SIG-Mac] problems to open files and changing directory Message-ID: <016F7D26-987B-46A5-B18C-DBC8E6747924@mat.upv.es> Hi, Very often R.app crashes when I try to open a file or to change directory. The problem started with Maverick and remains with Yosemite. What can I do? thanks Gregorio From jeroen.ooms at stat.ucla.edu Thu Aug 13 16:43:24 2015 From: jeroen.ooms at stat.ucla.edu (Jeroen Ooms) Date: Thu, 13 Aug 2015 16:43:24 +0200 Subject: [R-SIG-Mac] Cairo png device not working in R 3.2.1 on OSX Message-ID: The cairo png device on R 3.2.1 gives a warning "Application built with libpng-1.5.18 but running with 1.6.17" and then produces a completely blank png image. if(isTRUE(capabilities()[["cairo"]])){ options(bitmapType = "cairo"); } png(tmp <- tempfile()) plot(cars) dev.off() system2("open", tmp) [[alternative HTML version deleted]] From timothy.c.bates at gmail.com Thu Aug 13 13:25:05 2015 From: timothy.c.bates at gmail.com (Tim Bates) Date: Thu, 13 Aug 2015 12:25:05 +0100 Subject: [R-SIG-Mac] Adobe viewer needed? Message-ID: <13A0759F-013E-4079-A89C-87DABCBAAA9C@gmail.com> Hi, In R.app 3.2.0, doing ?function -> index -> vignettes -> pdf R.app requests a version of Adobe Reader. I don?t have this installed, but all OS X users have preview.app Could the help service be coded to either: 1. just open pdfs (that way they?ll be in a stand alone app configured by the user. 2. set preview.app as the default in-app viewer? my version is _ platform x86_64-apple-darwin13.4.0 arch x86_64 os darwin13.4.0 system x86_64, darwin13.4.0 status major 3 minor 2.0 year 2015 month 04 day 16 svn rev 68180 language R version.string R version 3.2.0 (2015-04-16) nickname Full of Ingredients > From pdalgd at gmail.com Thu Aug 13 17:11:55 2015 From: pdalgd at gmail.com (peter dalgaard) Date: Thu, 13 Aug 2015 17:11:55 +0200 Subject: [R-SIG-Mac] Cairo png device not working in R 3.2.1 on OSX In-Reply-To: References: Message-ID: That particular horse has been flogged to death repeatedly over the last weeks. Please try 3.2.2 RC. -pd > On 13 Aug 2015, at 16:43 , Jeroen Ooms wrote: > > The cairo png device on R 3.2.1 gives a warning "Application built with > libpng-1.5.18 but running with 1.6.17" and then produces a completely blank > png image. > > if(isTRUE(capabilities()[["cairo"]])){ > options(bitmapType = "cairo"); > } > > png(tmp <- tempfile()) > plot(cars) > dev.off() > system2("open", tmp) > > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From simon.urbanek at r-project.org Thu Aug 13 20:47:32 2015 From: simon.urbanek at r-project.org (Simon Urbanek) Date: Thu, 13 Aug 2015 14:47:32 -0400 Subject: [R-SIG-Mac] Adobe viewer needed? In-Reply-To: <13A0759F-013E-4079-A89C-87DABCBAAA9C@gmail.com> References: <13A0759F-013E-4079-A89C-87DABCBAAA9C@gmail.com> Message-ID: <9CC0957A-BB78-4EF4-A21F-9686E9DB5455@r-project.org> Tim, I fear that it must be a setting on your Mac - the default is to show the PDF in-ine in the same window (which uses the Preview engine behind the scenes). I suspect that you must have installed the Adobe plugin at some point (or some Adobe software) - OS X doesn't know anything about Adobe until you install some of their products at which point it's actually really hard to reverse the changes their installers make. Cheers, Simon > On Aug 13, 2015, at 7:25 AM, Tim Bates wrote: > > Hi, > In R.app 3.2.0, doing > > ?function -> index -> vignettes -> pdf > > R.app requests a version of Adobe Reader. I don?t have this installed, but all OS X users have preview.app > > Could the help service be coded to either: > 1. just open pdfs (that way they?ll be in a stand alone app configured by the user. > 2. set preview.app as the default in-app viewer? > > > my version is > _ > platform x86_64-apple-darwin13.4.0 > arch x86_64 > os darwin13.4.0 > system x86_64, darwin13.4.0 > status > major 3 > minor 2.0 > year 2015 > month 04 > day 16 > svn rev 68180 > language R > version.string R version 3.2.0 (2015-04-16) > nickname Full of Ingredients >> > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac From timothy.c.bates at gmail.com Fri Aug 14 13:27:35 2015 From: timothy.c.bates at gmail.com (Tim Bates) Date: Fri, 14 Aug 2015 12:27:35 +0100 Subject: [R-SIG-Mac] Adobe viewer needed? In-Reply-To: <9CC0957A-BB78-4EF4-A21F-9686E9DB5455@r-project.org> References: <13A0759F-013E-4079-A89C-87DABCBAAA9C@gmail.com> <9CC0957A-BB78-4EF4-A21F-9686E9DB5455@r-project.org> Message-ID: <998259F9-4DA6-4D97-A525-2BA472E10D5F@gmail.com> bingo. Didn?t think of the plugin, as Safari and Chrome both open pdfs inline using Preview.app The Adobe detritus was here if anyone else has this problem. /Library/Internet Plug-ins/AdobePDFViewer.plugin thanks! t > On 13 Aug 2015, at 7:47 PM, Simon Urbanek wrote: > > Tim, > > I fear that it must be a setting on your Mac - the default is to show the PDF in-ine in the same window (which uses the Preview engine behind the scenes). I suspect that you must have installed the Adobe plugin at some point (or some Adobe software) - OS X doesn't know anything about Adobe until you install some of their products at which point it's actually really hard to reverse the changes their installers make. > > Cheers, > Simon > > >> On Aug 13, 2015, at 7:25 AM, Tim Bates wrote: >> >> Hi, >> In R.app 3.2.0, doing >> >> ?function -> index -> vignettes -> pdf >> >> R.app requests a version of Adobe Reader. I don?t have this installed, but all OS X users have preview.app >> >> Could the help service be coded to either: >> 1. just open pdfs (that way they?ll be in a stand alone app configured by the user. >> 2. set preview.app as the default in-app viewer? >> >> >> my version is >> _ >> platform x86_64-apple-darwin13.4.0 >> arch x86_64 >> os darwin13.4.0 >> system x86_64, darwin13.4.0 >> status >> major 3 >> minor 2.0 >> year 2015 >> month 04 >> day 16 >> svn rev 68180 >> language R >> version.string R version 3.2.0 (2015-04-16) >> nickname Full of Ingredients >>> >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac at r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > From bbolker at gmail.com Fri Aug 14 18:52:38 2015 From: bbolker at gmail.com (Ben Bolker) Date: Fri, 14 Aug 2015 16:52:38 +0000 Subject: [R-SIG-Mac] lme4/macos crossover question Message-ID: As pointed out in this lme4 issue: https://github.com/lme4/lme4/issues/302 , lme4 is behaving badly on Snow Leopard, failing to find an (apparently) exported function urlhead <- "https://www.r-project.org/nosvn/R.check/r-" urltail <- "/gamm4-00check.html" versions <- c("devel-osx-x86_64-clang", "release-osx-x86_64-mavericks", "release-osx-x86_64-snowleopard") checkfun <- function(ver) { uu <- paste0(urlhead,ver,urltail) rr <- readLines(url(uu,method="libcurl")) any(grepl("could not find function.*REMLcrit",rr)) } sapply(versions,checkfun) Here's the (broken to make Gmane happy) link to the bad case: https://www.r-project.org/nosvn/R.check/ r-release-osx-x86_64-snowleopard/gamm4-00check.html The REMLcrit function is exported, at least in all recent versions of the package (and we haven't been able to reproduce on any other platforms). Any ideas ... ? Possibly the Snow Leopard test build on CRAN is using an out-of-date version of lme4 ... ? thanks Ben Bolker From dwinsemius at comcast.net Fri Aug 14 22:58:42 2015 From: dwinsemius at comcast.net (David Winsemius) Date: Fri, 14 Aug 2015 13:58:42 -0700 Subject: [R-SIG-Mac] lme4/macos crossover question In-Reply-To: References: Message-ID: <788B6CC2-ADCA-4059-989D-B42D1CD4A1E9@comcast.net> On Aug 14, 2015, at 9:52 AM, Ben Bolker wrote: > > As pointed out in this lme4 issue: https://github.com/lme4/lme4/issues/302 , > lme4 is behaving badly on Snow Leopard, failing to find an > (apparently) exported function > > urlhead <- "https://www.r-project.org/nosvn/R.check/r-" > urltail <- "/gamm4-00check.html" > versions <- c("devel-osx-x86_64-clang", > "release-osx-x86_64-mavericks", > "release-osx-x86_64-snowleopard") > checkfun <- function(ver) { > uu <- paste0(urlhead,ver,urltail) > rr <- readLines(url(uu,method="libcurl")) > any(grepl("could not find function.*REMLcrit",rr)) > } > sapply(versions,checkfun) I could not get those to run with method="libcurl", possibly since I have not yet updated to 3.2.2? This did run: checkfun <- function(ver) { uu <- paste0(urlhead,ver, urltail) rr <- readLines(url(uu)) any(grepl("could not find function.*REMLcrit",rr)) } sapply(versions,checkfun) devel-osx-x86_64-clang release-osx-x86_64-mavericks FALSE FALSE release-osx-x86_64-snowleopard TRUE > > Here's the (broken to make Gmane happy) link to the bad case: > > https://www.r-project.org/nosvn/R.check/ > r-release-osx-x86_64-snowleopard/gamm4-00check.html > > The REMLcrit function is exported, at least in all recent versions of > the package (and we haven't been able to reproduce on any other > platforms). > > Any ideas ... ? Possibly the Snow Leopard test build on CRAN is > using an out-of-date version of lme4 ... ? > R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut" Platform: x86_64-apple-darwin10.8.0 (64-bit) > sessionInfo() R version 3.2.1 (2015-06-18) Platform: x86_64-apple-darwin10.8.0 (64-bit) Running under: OS X 10.7.5 (Lion) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grDevices utils datasets stats graphics grid methods base other attached packages: [1] lme4_1.1-8 Matrix_1.2-2 stringr_1.0.0 dplyr_0.4.2 [5] ada_2.0-3 rpart_4.1-10 MASS_7.3-43 digest_0.6.8 [9] segmented_0.5-1.1 rms_4.3-1 SparseM_1.6 Hmisc_3.16-0 [13] ggplot2_1.0.1 Formula_1.2-1 survival_2.38-3 sos_1.3-8 [17] brew_1.0-6 lattice_0.20-33 loaded via a namespace (and not attached): [1] Rcpp_0.12.0 nloptr_1.0.4 RColorBrewer_1.1-2 plyr_1.8.3 [5] tools_3.2.1 polspline_1.1.12 gtable_0.1.2 nlme_3.1-121 [9] DBI_0.3.1 parallel_3.2.1 mvtnorm_1.0-3 proto_0.3-10 [13] gridExtra_2.0.0 cluster_2.0.3 nnet_7.3-10 R6_2.1.0 [17] foreign_0.8-65 multcomp_1.4-1 minqa_1.2.4 latticeExtra_0.6-26 [21] TH.data_1.0-6 reshape2_1.4.1 magrittr_1.5 scales_0.2.5 [25] codetools_0.2-14 splines_3.2.1 assertthat_0.1 colorspace_1.2-6 [29] labeling_0.3 quantreg_5.11 sandwich_2.3-3 stringi_0.5-5 [33] acepack_1.3-3.3 lazyeval_0.1.10 munsell_0.4.2 zoo_1.7-12 [R.app GUI 1.66 (6956) x86_64-apple-darwin10.8.0] I installed today an updated macbinary version of lme4, lme4_1.1-8.tgz, which the GUI package installer did for me with all the many dependencies. That is the latest version at CRAN for SL: http://cran.cnr.berkeley.edu/bin/macosx/contrib/3.2/ Is that version "out of date"? I suppose it might be, since I see this at the top of the CRAN package check: ? using R version 3.2.0 Patched (2015-04-28 r68272) ? using platform: x86_64-apple-darwin10.8.0 (64-bit) ? using session charset: UTF-8 ? checking for file ?gamm4/DESCRIPTION? ... OK ? this is package ?gamm4? version ?0.2-3? I get this at the console: > require(lme4) Loading required package: lme4 Loading required package: Matrix > set.seed(0) > y <- rnorm(20) > x <- rnorm(20) > g <-factor(rep(1:2,10)) > REMLcrit(lmer(y~(1|g)+x)) [1] 57.98661 I'd be happy to remove and attempt reinstalling from source something else if that would be of any use to you wiser folk, who know what you are looking for and only need cannon fodder, er, willing test subjects. > thanks > Ben Bolker > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac David Winsemius Alameda, CA, USA From timothy.c.bates at gmail.com Sat Aug 15 15:22:15 2015 From: timothy.c.bates at gmail.com (Tim Bates) Date: Sat, 15 Aug 2015 14:22:15 +0100 Subject: [R-SIG-Mac] Two UI suggestions: 1. key bindings for help-page navigation buttons; 2: increase font-size of function status bar Message-ID: Hi, A couple of minor suggestions for the mac GUI. First, Help window back-forward buttons. Often when the user has opened help, they want to navigate back a page. Currently the back ( "?) buttons in the help window lack key bindings. So one has to use the mouse to navigate forward and back. Request: Could these keys be bound to "?-{" and "?-}" respectively? That would match how Safari handles this app (and many others that have followed it for history navigation). Second, The function help bar (bottom of the "R console? window) is very helpful, but perhaps in too small a font size. The font used is also smaller than Apple chooses to use for the comparable Finder folder-trail and selection status bars. Could the font size/bar height be upped a couple of points (or perhaps linked to the display font size? best, tim From bhh at xs4all.nl Sat Aug 15 16:57:13 2015 From: bhh at xs4all.nl (Berend Hasselman) Date: Sat, 15 Aug 2015 16:57:13 +0200 Subject: [R-SIG-Mac] Two UI suggestions: 1. key bindings for help-page navigation buttons; 2: increase font-size of function status bar In-Reply-To: References: Message-ID: > On 15-08-2015, at 15:22, Tim Bates wrote: > > Hi, > A couple of minor suggestions for the mac GUI. > > First, Help window back-forward buttons. > > Often when the user has opened help, they want to navigate back a page. > Currently the back ( "?) buttons in the help window lack key bindings. So one has to use the mouse to navigate forward and back. > > Request: Could these keys be bound to "?-{" and "?-}" respectively? That would match how Safari handles this app (and many others that have followed it for history navigation). > I haven?t assigned any keyboard shortcut for Safari, The keys mentioned in Safari for me are: ??-[" and ??-]? I would prefer ??-[" and ??-]? so that the Shift key is not necessary. Berend > Second, The function help bar (bottom of the "R console? window) is very helpful, but perhaps in too small a font size. > > The font used is also smaller than Apple chooses to use for the comparable Finder folder-trail and selection status bars. > > Could the font size/bar height be upped a couple of points (or perhaps linked to the display font size? > > best, tim > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac From timothy.c.bates at gmail.com Sat Aug 15 17:17:37 2015 From: timothy.c.bates at gmail.com (Tim Bates) Date: Sat, 15 Aug 2015 16:17:37 +0100 Subject: [R-SIG-Mac] Two UI suggestions: 1. key bindings for help-page navigation buttons; 2: increase font-size of function status bar In-Reply-To: References: Message-ID: <802D0E2F-A801-4D88-B819-4A06DAAB18E8@gmail.com> >> Request: Could back and forward navigation keys be bound to "?-{" and "?-}" respectively? That would match how Safari (and others) handle history navigation. > The keys mentioned in Safari for me are: ??-[" and ??-]? I would prefer ??-[" and ??-]? so that the Shift key is not necessary. Sorry? typo when i grabbed the ? character: you?re right, it?s the non-shifted square-brackets. > Second, The function help bar (bottom of the "R console? window) is very helpful, but perhaps in too small a font size. > The font used is also smaller than Apple chooses to use for the comparable Finder folder-trail and selection status bars. > Could the font size/bar height be upped a couple of points (or perhaps linked to the display font size? From dwinsemius at comcast.net Sat Aug 15 19:27:21 2015 From: dwinsemius at comcast.net (David Winsemius) Date: Sat, 15 Aug 2015 10:27:21 -0700 Subject: [R-SIG-Mac] Two UI suggestions: 1. key bindings for help-page navigation buttons; 2: increase font-size of function status bar In-Reply-To: References: Message-ID: On Aug 15, 2015, at 6:22 AM, Tim Bates wrote: > Hi, > A couple of minor suggestions for the mac GUI. > > First, Help window back-forward buttons. > > Often when the user has opened help, they want to navigate back a page. > Currently the back ( "?) buttons in the help window lack key bindings. So one has to use the mouse to navigate forward and back. On my machine OSX 10.7.5 with SL-vers of R 3.2.1, R.app GUI 1.66 (6956), the cmd-right-arrow and the cmd left arrow give forward and back behavior in the help page display. I see little value in assigning this also or instead of the current behavior. I discovered this by trial and error so it might be worth documenting in the OSX-FAQ document, although it seemed pretty intuitive and was the first thing I tried after seeing this request. (It's how Firefox is configured.) David. > > Request: Could these keys be bound to "?-{" and "?-}" respectively? That would match how Safari handles this app (and many others that have followed it for history navigation). > > Second, The function help bar (bottom of the "R console? window) is very helpful, but perhaps in too small a font size. > > The font used is also smaller than Apple chooses to use for the comparable Finder folder-trail and selection status bars. > > Could the font size/bar height be upped a couple of points (or perhaps linked to the display font size? > > best, tim > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac David Winsemius Alameda, CA, USA From timothy.c.bates at gmail.com Sat Aug 15 21:45:56 2015 From: timothy.c.bates at gmail.com (Tim Bates) Date: Sat, 15 Aug 2015 20:45:56 +0100 Subject: [R-SIG-Mac] Two UI suggestions: 1. key bindings for help-page navigation buttons; 2: increase font-size of function status bar In-Reply-To: References: Message-ID: <80060AB6-A354-43DB-A63C-175009A40C77@gmail.com> > On my machine OSX 10.7.5 with SL-vers of R 3.2.1, R.app GUI 1.66 (6956), the cmd-right-arrow and the cmd left arrow give forward and back behavior in help. So it is. Not having this in any menu (unlike, say, those same keys for back and forth in the graphics window) makes it hard to discover. Perhaps adding menu options for ?Back? and ?Forward? in the ?Windows? menu, showing they are bound to ?-[ and ?-] would enable discovery. Anyone have thoughts on the function-bar help size? t > I see little value in assigning this also or instead of the current behavior. I discovered this by trial and error so it might be worth documenting in the OSX-FAQ document, although it seemed pretty intuitive and was the first thing I tried after seeing this request. (It's how Firefox is configured.) > On Aug 15, 2015, at 6:22 AM, Tim Bates wrote: >> A couple of minor suggestions for the mac GUI. >> First, Could help navigation be bound to "{" and "?-}" respectively? >> >> Second, The function help bar (bottom of the "R console? window) is very helpful, but perhaps in too small a font size. >> The font used is also smaller than Apple chooses to use for the comparable Finder folder-trail and selection status bars. >> Could the font size/bar height be upped a couple of points (or perhaps linked to the display font size? From bhh at xs4all.nl Sat Aug 15 22:00:19 2015 From: bhh at xs4all.nl (Berend Hasselman) Date: Sat, 15 Aug 2015 22:00:19 +0200 Subject: [R-SIG-Mac] Two UI suggestions: 1. key bindings for help-page navigation buttons; 2: increase font-size of function status bar In-Reply-To: <80060AB6-A354-43DB-A63C-175009A40C77@gmail.com> References: <80060AB6-A354-43DB-A63C-175009A40C77@gmail.com> Message-ID: <49BBD663-76EE-47B8-BF99-089AE3B3DC44@xs4all.nl> > On 15-08-2015, at 21:45, Tim Bates wrote: > >> On my machine OSX 10.7.5 with SL-vers of R 3.2.1, R.app GUI 1.66 (6956), the cmd-right-arrow and the cmd left arrow give forward and back behavior in help. > > So it is. Not having this in any menu (unlike, say, those same keys for back and forth in the graphics window) makes it hard to discover. > > Perhaps adding menu options for ?Back? and ?Forward? in the ?Windows? menu, showing they are bound to ?-[ and ?-] would enable discovery. > > Anyone have thoughts on the function-bar help size? > Very small. I can only just about read it:-). But not always. I wouldn?t mind something larger. Berend > t > >> I see little value in assigning this also or instead of the current behavior. I discovered this by trial and error so it might be worth documenting in the OSX-FAQ document, although it seemed pretty intuitive and was the first thing I tried after seeing this request. (It's how Firefox is configured.) > >> On Aug 15, 2015, at 6:22 AM, Tim Bates wrote: >>> A couple of minor suggestions for the mac GUI. >>> First, Could help navigation be bound to "{" and "?-}" respectively? >>> >>> Second, The function help bar (bottom of the "R console? window) is very helpful, but perhaps in too small a font size. >>> The font used is also smaller than Apple chooses to use for the comparable Finder folder-trail and selection status bars. >>> Could the font size/bar height be upped a couple of points (or perhaps linked to the display font size? > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac From carl at witthoft.com Sun Aug 16 17:29:13 2015 From: carl at witthoft.com (Carl Witthoft) Date: Sun, 16 Aug 2015 11:29:13 -0400 Subject: [R-SIG-Mac] Help page key bindings In-Reply-To: References: Message-ID: <55D0AC49.1080004@witthoft.com> May I suggest an alternative? Since MacOS allows you to bind the keystroke of your choice to any menu item (on an app-specific basis), if the "help/forwards" and "help/backwards" were added to a menu, then everyone could set whatever bindings they prefer. -- Carl Witthoft carl at witthoft.com http://witthoft.com/resume From simon.urbanek at r-project.org Sun Aug 16 18:42:15 2015 From: simon.urbanek at r-project.org (Simon Urbanek) Date: Sun, 16 Aug 2015 12:42:15 -0400 Subject: [R-SIG-Mac] Two UI suggestions: 1. key bindings for help-page navigation buttons; 2: increase font-size of function status bar In-Reply-To: References: Message-ID: <7ACAEAF5-8438-4FD3-9B0E-DAD616D5C5C2@r-project.org> On Aug 15, 2015, at 1:27 PM, David Winsemius wrote: > > On Aug 15, 2015, at 6:22 AM, Tim Bates wrote: > >> Hi, >> A couple of minor suggestions for the mac GUI. >> >> First, Help window back-forward buttons. >> >> Often when the user has opened help, they want to navigate back a page. >> Currently the back ( "?) buttons in the help window lack key bindings. So one has to use the mouse to navigate forward and back. > > On my machine OSX 10.7.5 with SL-vers of R 3.2.1, R.app GUI 1.66 (6956), the cmd-right-arrow and the cmd left arrow give forward and back behavior in the help page display. I see little value in assigning this also or instead of the current behavior. I discovered this by trial and error so it might be worth documenting in the OSX-FAQ document, although it seemed pretty intuitive and was the first thing I tried after seeing this request. (It's how Firefox is configured.) > Yes, and is the default behavior in all browsers, including Safari. Since we simply use WebKit, we get that default, so it's consistent. Also not that it works in the absence of any buttons. The <[>/<]> in interesting - I have never used it and wasn't aware of it, since IMHO the more intuitive way above works. Given that we don't explicitly define any key equivalent, we could add those to the buttons if people are interested. The GUI has been designed so long ago, that all our helper windows share the same main menu, so we don't actually have menu items for individual navigation, so there is no good place where to put the information about the available key bindings. >> >> Request: Could these keys be bound to "?-{" and "?-}" respectively? That would match how Safari handles this app (and many others that have followed it for history navigation). >> >> Second, The function help bar (bottom of the "R console? window) is very helpful, but perhaps in too small a font size. >> >> The font used is also smaller than Apple chooses to use for the comparable Finder folder-trail and selection status bars. >> >> Could the font size/bar height be upped a couple of points (or perhaps linked to the display font size? >> It was deliberately chosen to be so small, as to fit two lines of help. However, you're right that the hardware has evolved since this was done in a way where the effective size becomes increasingly smaller, so it may make sense to increase the size of the status bar along with the font size. Cheers, Simon >> best, tim >> >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac at r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > David Winsemius > Alameda, CA, USA > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac From bhh at xs4all.nl Sun Aug 16 20:09:03 2015 From: bhh at xs4all.nl (Berend Hasselman) Date: Sun, 16 Aug 2015 20:09:03 +0200 Subject: [R-SIG-Mac] Two UI suggestions: 1. key bindings for help-page navigation buttons; 2: increase font-size of function status bar In-Reply-To: <7ACAEAF5-8438-4FD3-9B0E-DAD616D5C5C2@r-project.org> References: <7ACAEAF5-8438-4FD3-9B0E-DAD616D5C5C2@r-project.org> Message-ID: > On 16-08-2015, at 18:42, Simon Urbanek wrote: > > > On Aug 15, 2015, at 1:27 PM, David Winsemius wrote: > >> >> On Aug 15, 2015, at 6:22 AM, Tim Bates wrote: >> >>> Hi, >>> A couple of minor suggestions for the mac GUI. >>> >>> First, Help window back-forward buttons. >>> >>> Often when the user has opened help, they want to navigate back a page. >>> Currently the back ( "?) buttons in the help window lack key bindings. So one has to use the mouse to navigate forward and back. >> >> On my machine OSX 10.7.5 with SL-vers of R 3.2.1, R.app GUI 1.66 (6956), the cmd-right-arrow and the cmd left arrow give forward and back behavior in the help page display. I see little value in assigning this also or instead of the current behavior. I discovered this by trial and error so it might be worth documenting in the OSX-FAQ document, although it seemed pretty intuitive and was the first thing I tried after seeing this request. (It's how Firefox is configured.) >> > > > Yes, and is the default behavior in all browsers, including Safari. Since we simply use WebKit, we get that default, so it's consistent. Also not that it works in the absence of any buttons. > > The <[>/<]> in interesting - I have never used it and wasn't aware of it, since IMHO the more intuitive way above works. Given that we don't explicitly define any key equivalent, we could add those to the buttons if people are interested. > The Safari History menu displays those two key equivalents (and not the other above mentioned two). At least on my OS X and Safari. I wouldn?t mind those key equivalents. I find them less contorted than the and > The GUI has been designed so long ago, that all our helper windows share the same main menu, so we don't actually have menu items for individual navigation, so there is no good place where to put the information about the available key bindings. > > >>> >>> Request: Could these keys be bound to "?-{" and "?-}" respectively? That would match how Safari handles this app (and many others that have followed it for history navigation). >>> >>> Second, The function help bar (bottom of the "R console? window) is very helpful, but perhaps in too small a font size. >>> >>> The font used is also smaller than Apple chooses to use for the comparable Finder folder-trail and selection status bars. >>> >>> Could the font size/bar height be upped a couple of points (or perhaps linked to the display font size? >>> > > > It was deliberately chosen to be so small, as to fit two lines of help. However, you're right that the hardware has evolved since this was done in a way where the effective size becomes increasingly smaller, so it may make sense to increase the size of the status bar along with the font size. > That would be wonderful. Berend From roy.mendelssohn at noaa.gov Sun Aug 16 22:45:10 2015 From: roy.mendelssohn at noaa.gov (Roy Mendelssohn - NOAA Federal) Date: Sun, 16 Aug 2015 13:45:10 -0700 Subject: [R-SIG-Mac] Error on linking to R.3.2.2 package Message-ID: <050520FF-C679-4331-BDF5-D96C79124034@noaa.gov> If I go to the cran home page, and then to the Mac downloads and click on the "R-3.2.2.pkg? link I get: > Object not found! > > The requested URL was not found on this server. The link on the referring page seems to be wrong or outdated. Please inform the author ofthat page about the error. > > If you think this is a server error, please contact the webmaster. > > Error 404 Thanks for any help. -Roy ********************** "The contents of this message do not reflect any position of the U.S. Government or NOAA." ********************** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center ***Note new address and phone*** 110 Shaffer Road Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/ "Old age and treachery will overcome youth and skill." "From those who have been given much, much will be expected" "the arc of the moral universe is long, but it bends toward justice" -MLK Jr. From brandon.hurr at gmail.com Sun Aug 16 23:59:21 2015 From: brandon.hurr at gmail.com (Brandon Hurr) Date: Sun, 16 Aug 2015 14:59:21 -0700 Subject: [R-SIG-Mac] Error on linking to R.3.2.2 package In-Reply-To: <050520FF-C679-4331-BDF5-D96C79124034@noaa.gov> References: <050520FF-C679-4331-BDF5-D96C79124034@noaa.gov> Message-ID: I noticed this today too. It links to 3.2.1, but if you change the 1 to 2 you can download the correct package. Obviously not ideal, but something. B On Sun, Aug 16, 2015 at 1:45 PM, Roy Mendelssohn - NOAA Federal < roy.mendelssohn at noaa.gov> wrote: > If I go to the cran home page, and then to the Mac downloads and click on > the "R-3.2.2.pkg? link I get: > > > Object not found! > > > > The requested URL was not found on this server. The link on the > referring page seems to be wrong or outdated. Please inform the author > ofthat page about the error. > > > > If you think this is a server error, please contact the webmaster. > > > > Error 404 > > Thanks for any help. > > -Roy > > > ********************** > "The contents of this message do not reflect any position of the U.S. > Government or NOAA." > ********************** > Roy Mendelssohn > Supervisory Operations Research Analyst > NOAA/NMFS > Environmental Research Division > Southwest Fisheries Science Center > ***Note new address and phone*** > 110 Shaffer Road > Santa Cruz, CA 95060 > Phone: (831)-420-3666 > Fax: (831) 420-3980 > e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/ > > "Old age and treachery will overcome youth and skill." > "From those who have been given much, much will be expected" > "the arc of the moral universe is long, but it bends toward justice" -MLK > Jr. > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > [[alternative HTML version deleted]] From dwinsemius at comcast.net Mon Aug 17 00:11:35 2015 From: dwinsemius at comcast.net (David Winsemius) Date: Sun, 16 Aug 2015 15:11:35 -0700 Subject: [R-SIG-Mac] Error on linking to R.3.2.2 package In-Reply-To: <050520FF-C679-4331-BDF5-D96C79124034@noaa.gov> References: <050520FF-C679-4331-BDF5-D96C79124034@noaa.gov> Message-ID: <5F9F04A2-BE54-417A-82FB-3AEDE36FB8FB@comcast.net> On Aug 16, 2015, at 1:45 PM, Roy Mendelssohn - NOAA Federal wrote: > If I go to the cran home page, and then to the Mac downloads and click on the "R-3.2.2.pkg? link I get: I clicked on the generic Mac download link on the main page and it gave me R-3.2.2.pkg -- David. > >> Object not found! >> >> The requested URL was not found on this server. The link on the referring page seems to be wrong or outdated. Please inform the author ofthat page about the error. >> >> If you think this is a server error, please contact the webmaster. >> >> Error 404 > > Thanks for any help. > > -Roy > > > ********************** > "The contents of this message do not reflect any position of the U.S. Government or NOAA." > ********************** > Roy Mendelssohn > Supervisory Operations Research Analyst > NOAA/NMFS > Environmental Research Division > Southwest Fisheries Science Center > ***Note new address and phone*** > 110 Shaffer Road > Santa Cruz, CA 95060 > Phone: (831)-420-3666 > Fax: (831) 420-3980 > e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/ > > "Old age and treachery will overcome youth and skill." > "From those who have been given much, much will be expected" > "the arc of the moral universe is long, but it bends toward justice" -MLK Jr. > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac David Winsemius Alameda, CA, USA From roy.mendelssohn at noaa.gov Mon Aug 17 00:33:35 2015 From: roy.mendelssohn at noaa.gov (Roy Mendelssohn - NOAA Federal) Date: Sun, 16 Aug 2015 15:33:35 -0700 Subject: [R-SIG-Mac] Error on linking to R.3.2.2 package In-Reply-To: <5F9F04A2-BE54-417A-82FB-3AEDE36FB8FB@comcast.net> References: <050520FF-C679-4331-BDF5-D96C79124034@noaa.gov> <5F9F04A2-BE54-417A-82FB-3AEDE36FB8FB@comcast.net> Message-ID: yes now it downloads. Before it gave the error as shown. -Roy > On Aug 16, 2015, at 3:11 PM, David Winsemius wrote: > > > On Aug 16, 2015, at 1:45 PM, Roy Mendelssohn - NOAA Federal wrote: > >> If I go to the cran home page, and then to the Mac downloads and click on the "R-3.2.2.pkg? link I get: > > I clicked on the generic Mac download link on the main page and it gave me R-3.2.2.pkg > > -- > David. >> >>> Object not found! >>> >>> The requested URL was not found on this server. The link on the referring page seems to be wrong or outdated. Please inform the author ofthat page about the error. >>> >>> If you think this is a server error, please contact the webmaster. >>> >>> Error 404 >> >> Thanks for any help. >> >> -Roy >> >> >> ********************** >> "The contents of this message do not reflect any position of the U.S. Government or NOAA." >> ********************** >> Roy Mendelssohn >> Supervisory Operations Research Analyst >> NOAA/NMFS >> Environmental Research Division >> Southwest Fisheries Science Center >> ***Note new address and phone*** >> 110 Shaffer Road >> Santa Cruz, CA 95060 >> Phone: (831)-420-3666 >> Fax: (831) 420-3980 >> e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/ >> >> "Old age and treachery will overcome youth and skill." >> "From those who have been given much, much will be expected" >> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr. >> >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac at r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > David Winsemius > Alameda, CA, USA > ********************** "The contents of this message do not reflect any position of the U.S. Government or NOAA." ********************** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center ***Note new address and phone*** 110 Shaffer Road Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/ "Old age and treachery will overcome youth and skill." "From those who have been given much, much will be expected" "the arc of the moral universe is long, but it bends toward justice" -MLK Jr. From dwinsemius at comcast.net Mon Aug 17 01:05:37 2015 From: dwinsemius at comcast.net (David Winsemius) Date: Sun, 16 Aug 2015 16:05:37 -0700 Subject: [R-SIG-Mac] Error on linking to R.3.2.2 package In-Reply-To: <5F9F04A2-BE54-417A-82FB-3AEDE36FB8FB@comcast.net> References: <050520FF-C679-4331-BDF5-D96C79124034@noaa.gov> <5F9F04A2-BE54-417A-82FB-3AEDE36FB8FB@comcast.net> Message-ID: <1A88A7F1-0BF9-40C1-9077-65409FC8C2F6@comcast.net> Their is a higher probability (p < .0.05) of CRAN weirdness on weekends. -- David. On Aug 16, 2015, at 3:11 PM, David Winsemius wrote: > > On Aug 16, 2015, at 1:45 PM, Roy Mendelssohn - NOAA Federal wrote: > >> If I go to the cran home page, and then to the Mac downloads and click on the "R-3.2.2.pkg? link I get: > > I clicked on the generic Mac download link on the main page and it gave me R-3.2.2.pkg > > -- > David. >> >>> Object not found! >>> >>> The requested URL was not found on this server. The link on the referring page seems to be wrong or outdated. Please inform the author ofthat page about the error. >>> >>> If you think this is a server error, please contact the webmaster. >>> >>> Error 404 >> >> Thanks for any help. >> >> -Roy >> >> >> ********************** >> "The contents of this message do not reflect any position of the U.S. Government or NOAA." >> ********************** >> Roy Mendelssohn >> Supervisory Operations Research Analyst >> NOAA/NMFS >> Environmental Research Division >> Southwest Fisheries Science Center >> ***Note new address and phone*** >> 110 Shaffer Road >> Santa Cruz, CA 95060 >> Phone: (831)-420-3666 >> Fax: (831) 420-3980 >> e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/ >> >> "Old age and treachery will overcome youth and skill." >> "From those who have been given much, much will be expected" >> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr. >> >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac at r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > David Winsemius > Alameda, CA, USA > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac David Winsemius Alameda, CA, USA From simon.urbanek at r-project.org Mon Aug 17 04:20:55 2015 From: simon.urbanek at r-project.org (Simon Urbanek) Date: Sun, 16 Aug 2015 22:20:55 -0400 Subject: [R-SIG-Mac] Error on linking to R.3.2.2 package In-Reply-To: <1A88A7F1-0BF9-40C1-9077-65409FC8C2F6@comcast.net> References: <050520FF-C679-4331-BDF5-D96C79124034@noaa.gov> <5F9F04A2-BE54-417A-82FB-3AEDE36FB8FB@comcast.net> <1A88A7F1-0BF9-40C1-9077-65409FC8C2F6@comcast.net> Message-ID: On Aug 16, 2015, at 7:05 PM, David Winsemius wrote: > Their is a higher probability (p < .0.05) of CRAN weirdness on weekends. > Heh, in this case, just my bad - forgot to fix the href when releasing the binary yesterday - it was reported earlier today and fixed, but it takes a bit of time until things propagate. Cheers, Simon > -- > David. > On Aug 16, 2015, at 3:11 PM, David Winsemius wrote: > >> >> On Aug 16, 2015, at 1:45 PM, Roy Mendelssohn - NOAA Federal wrote: >> >>> If I go to the cran home page, and then to the Mac downloads and click on the "R-3.2.2.pkg? link I get: >> >> I clicked on the generic Mac download link on the main page and it gave me R-3.2.2.pkg >> >> -- >> David. >>> >>>> Object not found! >>>> >>>> The requested URL was not found on this server. The link on the referring page seems to be wrong or outdated. Please inform the author ofthat page about the error. >>>> >>>> If you think this is a server error, please contact the webmaster. >>>> >>>> Error 404 >>> >>> Thanks for any help. >>> >>> -Roy >>> >>> >>> ********************** >>> "The contents of this message do not reflect any position of the U.S. Government or NOAA." >>> ********************** >>> Roy Mendelssohn >>> Supervisory Operations Research Analyst >>> NOAA/NMFS >>> Environmental Research Division >>> Southwest Fisheries Science Center >>> ***Note new address and phone*** >>> 110 Shaffer Road >>> Santa Cruz, CA 95060 >>> Phone: (831)-420-3666 >>> Fax: (831) 420-3980 >>> e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/ >>> >>> "Old age and treachery will overcome youth and skill." >>> "From those who have been given much, much will be expected" >>> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr. >>> >>> _______________________________________________ >>> R-SIG-Mac mailing list >>> R-SIG-Mac at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> >> David Winsemius >> Alameda, CA, USA >> >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac at r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > David Winsemius > Alameda, CA, USA > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > From jefferis at gmail.com Tue Aug 18 00:13:11 2015 From: jefferis at gmail.com (Gregory Jefferis) Date: Mon, 17 Aug 2015 23:13:11 +0100 Subject: [R-SIG-Mac] keeping two patch level releases of the same minor release installed Message-ID: <638E44E3-2951-47F5-81CE-A08935A8B2B9@gmail.com> Hello, I use Rswitch in conjunction with CRAN installers to keep different minor releases series (e.g. 3.2.X vs 3.1.X) installed. Now I find that I want to install 3.2.2 and 3.2.1 at the same time, so I tried pkgutil --forget org.r-project.R.mavericks.fw.pkg on install, but 3.2.1 disappears, presumably because the contents of /Library/Frameworks/R.framework/Versions/ looks like this: 3.1 3.2 Current Can anyone suggest an easy way to keep and switch between the patch level releases? With many thanks, Greg. R.version _ platform x86_64-apple-darwin13.4.0 arch x86_64 os darwin13.4.0 system x86_64, darwin13.4.0 status major 3 minor 2.2 year 2015 month 08 day 14 svn rev 69053 language R version.string R version 3.2.2 (2015-08-14) nickname Fire Safety -- Gregory Jefferis, PhD Division of Neurobiology MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge, CB2 OQH, UK http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis http://jefferislab.org http://flybrain.stanford.edu From simon.urbanek at r-project.org Tue Aug 18 02:50:14 2015 From: simon.urbanek at r-project.org (Simon Urbanek) Date: Mon, 17 Aug 2015 20:50:14 -0400 Subject: [R-SIG-Mac] keeping two patch level releases of the same minor release installed In-Reply-To: <638E44E3-2951-47F5-81CE-A08935A8B2B9@gmail.com> References: <638E44E3-2951-47F5-81CE-A08935A8B2B9@gmail.com> Message-ID: <8FA3265C-6E20-4260-BC45-F4AE75C72768@r-project.org> On Aug 17, 2015, at 6:13 PM, Gregory Jefferis wrote: > Hello, > > I use Rswitch in conjunction with CRAN installers to keep different minor releases series (e.g. 3.2.X vs 3.1.X) installed. > > Now I find that I want to install 3.2.2 and 3.2.1 at the same time, so I tried > > pkgutil --forget org.r-project.R.mavericks.fw.pkg > > on install, but 3.2.1 disappears, presumably because the contents of /Library/Frameworks/R.framework/Versions/ looks like this: > > 3.1 3.2 Current > > Can anyone suggest an easy way to keep and switch between the patch level releases? > Idea: Install one, move it to to 3.2.1 instead of 3.2, then use --forget, install second one and move it to 3.2.2. Then always create a symlink from 3.2 to either 3.2.1 or 3.2.2 depending on what you want to use. It's the same trick as Current except one level deeper. Note that you'll still have separate package trees for better or worse. I didn't actually test it, but in principle it should work. Cheers, Simon > With many thanks, > > Greg. > > > R.version > _ > platform x86_64-apple-darwin13.4.0 > arch x86_64 > os darwin13.4.0 > system x86_64, darwin13.4.0 > status > major 3 > minor 2.2 > year 2015 > month 08 > day 14 > svn rev 69053 > language R > version.string R version 3.2.2 (2015-08-14) > nickname Fire Safety > > -- > Gregory Jefferis, PhD > Division of Neurobiology > MRC Laboratory of Molecular Biology > Francis Crick Avenue > Cambridge Biomedical Campus > Cambridge, CB2 OQH, UK > > http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis > http://jefferislab.org > http://flybrain.stanford.edu > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > From spencer.graves at prodsyse.com Tue Aug 18 02:54:34 2015 From: spencer.graves at prodsyse.com (Spencer Graves) Date: Mon, 17 Aug 2015 19:54:34 -0500 Subject: [R-SIG-Mac] R 3.2.2 install problems under OS X 10.10.3 Message-ID: <55D2824A.70103@prodsyse.com> Hello: After upgrading from R 3.2.1 to 3.2.2 under OS X 10.10.3, attempts to start the default R GUI fail with, "Problem Report for R: R cannot be opened because of a problem." "Problem Details and System Configuration" are copied below. (R 3.2.2 seems to work fine within RStudio 0.98.1103.) What do you suggest I do to fix this problem? Thanks, Spencer Graves Problem Details and System Configuration Process: R [569] Path: /Applications/R.app/Contents/MacOS/R Identifier: org.R-project.R Version: ??? Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: R [569] User ID: 501 Date/Time: 2015-08-17 19:46:47.942 -0500 OS Version: Mac OS X 10.10.3 (14D136) Report Version: 11 Anonymous UUID: 6621BCEA-EA0C-3D7A-AE0A-BFCE63A9A8B4 Sleep/Wake UUID: 9C8F92EE-E940-4B17-A64C-C0F470DFE449 Time Awake Since Boot: 2600 seconds Time Since Wake: 700 seconds Crashed Thread: 0 Exception Type: EXC_BREAKPOINT (SIGTRAP) Exception Codes: 0x0000000000000002, 0x0000000000000000 Application Specific Information: dyld: launch, loading dependent libraries Dyld Error Message: Library not loaded: /Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libR.dylib Referenced from: /Applications/R.app/Contents/MacOS/R Reason: image not found Binary Images: 0x7fff6b9f0000 - 0x7fff6ba26837 dyld (353.2.1) <65DCCB06-339C-3E25-9702-600A28291D0E> /usr/lib/dyld Model: MacBookPro11,3, BootROM MBP112.0138.B14, 4 processors, Intel Core i7, 2.8 GHz, 16 GB, SMC 2.19f12 Graphics: Intel Iris Pro, Intel Iris Pro, Built-In Graphics: NVIDIA GeForce GT 750M, NVIDIA GeForce GT 750M, PCIe, 2048 MB Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533641465238412D50422020 Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533641465238412D50422020 AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x134), Broadcom BCM43xx 1.0 (7.15.166.24.3) Bluetooth: Version 4.3.4f4 15601, 3 services, 27 devices, 1 incoming serial ports Network Service: Wi-Fi, AirPort, en0 Serial ATA Device: APPLE SSD SM1024F, 1 TB USB Device: Internal Memory Card Reader USB Device: BRCM20702 Hub USB Device: Bluetooth USB Host Controller USB Device: Apple Internal Keyboard / Trackpad Thunderbolt Bus: MacBook Pro, Apple Inc., 17.1 From pdalgd at gmail.com Tue Aug 18 11:25:08 2015 From: pdalgd at gmail.com (peter dalgaard) Date: Tue, 18 Aug 2015 11:25:08 +0200 Subject: [R-SIG-Mac] R 3.2.2 install problems under OS X 10.10.3 In-Reply-To: <55D2824A.70103@prodsyse.com> References: <55D2824A.70103@prodsyse.com> Message-ID: <4C7C22C5-625B-4853-B8D7-121BCB4B4BB3@gmail.com> On 18 Aug 2015, at 02:54 , Spencer Graves wrote: > Hello: > > > After upgrading from R 3.2.1 to 3.2.2 under OS X 10.10.3, attempts to start the default R GUI fail with, "Problem Report for R: R cannot be opened because of a problem." "Problem Details and System Configuration" are copied below. (R 3.2.2 seems to work fine within RStudio 0.98.1103.) > > > What do you suggest I do to fix this problem? > Dunno, it works fine for me, at least on Mavericks 10.9.5. However, the reference to Library/Frameworks/R.framework/Versions/3.1/... makes me suspect that you are somehow mixing versions. Perhaps clean up and reinstall? -pd > > Thanks, > Spencer Graves > > > Problem Details and System Configuration > > > Process: R [569] > Path: /Applications/R.app/Contents/MacOS/R > Identifier: org.R-project.R > Version: ??? > Code Type: X86-64 (Native) > Parent Process: ??? [1] > Responsible: R [569] > User ID: 501 > > Date/Time: 2015-08-17 19:46:47.942 -0500 > OS Version: Mac OS X 10.10.3 (14D136) > Report Version: 11 > Anonymous UUID: 6621BCEA-EA0C-3D7A-AE0A-BFCE63A9A8B4 > > Sleep/Wake UUID: 9C8F92EE-E940-4B17-A64C-C0F470DFE449 > > Time Awake Since Boot: 2600 seconds > Time Since Wake: 700 seconds > > Crashed Thread: 0 > > Exception Type: EXC_BREAKPOINT (SIGTRAP) > Exception Codes: 0x0000000000000002, 0x0000000000000000 > > Application Specific Information: > dyld: launch, loading dependent libraries > > Dyld Error Message: > Library not loaded: /Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libR.dylib > Referenced from: /Applications/R.app/Contents/MacOS/R > Reason: image not found > > Binary Images: > 0x7fff6b9f0000 - 0x7fff6ba26837 dyld (353.2.1) <65DCCB06-339C-3E25-9702-600A28291D0E> /usr/lib/dyld > > Model: MacBookPro11,3, BootROM MBP112.0138.B14, 4 processors, Intel Core i7, 2.8 GHz, 16 GB, SMC 2.19f12 > Graphics: Intel Iris Pro, Intel Iris Pro, Built-In > Graphics: NVIDIA GeForce GT 750M, NVIDIA GeForce GT 750M, PCIe, 2048 MB > Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533641465238412D50422020 > Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533641465238412D50422020 > AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x134), Broadcom BCM43xx 1.0 (7.15.166.24.3) > Bluetooth: Version 4.3.4f4 15601, 3 services, 27 devices, 1 incoming serial ports > Network Service: Wi-Fi, AirPort, en0 > Serial ATA Device: APPLE SSD SM1024F, 1 TB > USB Device: Internal Memory Card Reader > USB Device: BRCM20702 Hub > USB Device: Bluetooth USB Host Controller > USB Device: Apple Internal Keyboard / Trackpad > Thunderbolt Bus: MacBook Pro, Apple Inc., 17.1 > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com From spencer.graves at prodsyse.com Wed Aug 19 03:20:46 2015 From: spencer.graves at prodsyse.com (Spencer Graves) Date: Tue, 18 Aug 2015 20:20:46 -0500 Subject: [R-SIG-Mac] R 3.2.2 install problems under OS X 10.10.3 In-Reply-To: <4C7C22C5-625B-4853-B8D7-121BCB4B4BB3@gmail.com> References: <55D2824A.70103@prodsyse.com> <4C7C22C5-625B-4853-B8D7-121BCB4B4BB3@gmail.com> Message-ID: <55D3D9EE.5080608@prodsyse.com> Hi, Peter: On 8/18/2015 4:25 AM, peter dalgaard wrote: > On 18 Aug 2015, at 02:54 , Spencer Graves wrote: > >> Hello: >> >> >> After upgrading from R 3.2.1 to 3.2.2 under OS X 10.10.3, attempts to start the default R GUI fail with, "Problem Report for R: R cannot be opened because of a problem." "Problem Details and System Configuration" are copied below. (R 3.2.2 seems to work fine within RStudio 0.98.1103.) >> >> >> What do you suggest I do to fix this problem? >> > Dunno, it works fine for me, at least on Mavericks 10.9.5. > > However, the reference to Library/Frameworks/R.framework/Versions/3.1/... makes me suspect that you are somehow mixing versions. Perhaps clean up and reinstall? Thanks. Now I can't find a way to start R at all outside of RStudio after uninstalling and reinstalling. What do you suggest I try next? Thanks, Spencer p.s. To be precise, I ran the following as described in "4.2 Uninstalling under OS X" in "R Installation and Administration": ..$ sudo rm -rf /Library/Frameworks/R.framework ..$ sudo rm -rf /Applications/R.app ..$ sudo rm -rf /usr/bin/R ..$ sudo rm -rf /usr/bin/Rscript Then I double-clicked on "R-3.2.2.pkg" in Downloads. R seemed to install, and R 3.2.2 started as expected under RStudio, but I couldn't find stand-alone R icons. So I upgraded to 10.10.5 and double-clicked again on "R-3.2.2.pkg". That didn't help. FYI, from within RStudio, I get the following: > sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.5 (Yosemite) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_3.2.2 > -pd > > >> Thanks, >> Spencer Graves >> >> >> Problem Details and System Configuration >> >> >> Process: R [569] >> Path: /Applications/R.app/Contents/MacOS/R >> Identifier: org.R-project.R >> Version: ??? >> Code Type: X86-64 (Native) >> Parent Process: ??? [1] >> Responsible: R [569] >> User ID: 501 >> >> Date/Time: 2015-08-17 19:46:47.942 -0500 >> OS Version: Mac OS X 10.10.3 (14D136) >> Report Version: 11 >> Anonymous UUID: 6621BCEA-EA0C-3D7A-AE0A-BFCE63A9A8B4 >> >> Sleep/Wake UUID: 9C8F92EE-E940-4B17-A64C-C0F470DFE449 >> >> Time Awake Since Boot: 2600 seconds >> Time Since Wake: 700 seconds >> >> Crashed Thread: 0 >> >> Exception Type: EXC_BREAKPOINT (SIGTRAP) >> Exception Codes: 0x0000000000000002, 0x0000000000000000 >> >> Application Specific Information: >> dyld: launch, loading dependent libraries >> >> Dyld Error Message: >> Library not loaded: /Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libR.dylib >> Referenced from: /Applications/R.app/Contents/MacOS/R >> Reason: image not found >> >> Binary Images: >> 0x7fff6b9f0000 - 0x7fff6ba26837 dyld (353.2.1) <65DCCB06-339C-3E25-9702-600A28291D0E> /usr/lib/dyld >> >> Model: MacBookPro11,3, BootROM MBP112.0138.B14, 4 processors, Intel Core i7, 2.8 GHz, 16 GB, SMC 2.19f12 >> Graphics: Intel Iris Pro, Intel Iris Pro, Built-In >> Graphics: NVIDIA GeForce GT 750M, NVIDIA GeForce GT 750M, PCIe, 2048 MB >> Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533641465238412D50422020 >> Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533641465238412D50422020 >> AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x134), Broadcom BCM43xx 1.0 (7.15.166.24.3) >> Bluetooth: Version 4.3.4f4 15601, 3 services, 27 devices, 1 incoming serial ports >> Network Service: Wi-Fi, AirPort, en0 >> Serial ATA Device: APPLE SSD SM1024F, 1 TB >> USB Device: Internal Memory Card Reader >> USB Device: BRCM20702 Hub >> USB Device: Bluetooth USB Host Controller >> USB Device: Apple Internal Keyboard / Trackpad >> Thunderbolt Bus: MacBook Pro, Apple Inc., 17.1 >> >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac at r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac From simon.urbanek at r-project.org Wed Aug 19 03:37:31 2015 From: simon.urbanek at r-project.org (Simon Urbanek) Date: Tue, 18 Aug 2015 21:37:31 -0400 Subject: [R-SIG-Mac] R 3.2.2 install problems under OS X 10.10.3 In-Reply-To: <55D3D9EE.5080608@prodsyse.com> References: <55D2824A.70103@prodsyse.com> <4C7C22C5-625B-4853-B8D7-121BCB4B4BB3@gmail.com> <55D3D9EE.5080608@prodsyse.com> Message-ID: <197B6686-5DBA-4CE2-899C-2E79AFE2D172@r-project.org> Spencer, use open -a R in Terminal or use Spotlight to look for R (the application) - you have probably moved it someplace non-default and unfortunately Apple's Installer is doing a really good job in upgrading the R.app that you have assigned last and apparently it's not the one in Applications. Cheers, Simon On Aug 18, 2015, at 9:20 PM, Spencer Graves wrote: > Hi, Peter: > > > On 8/18/2015 4:25 AM, peter dalgaard wrote: >> On 18 Aug 2015, at 02:54 , Spencer Graves wrote: >> >>> Hello: >>> >>> >>> After upgrading from R 3.2.1 to 3.2.2 under OS X 10.10.3, attempts to start the default R GUI fail with, "Problem Report for R: R cannot be opened because of a problem." "Problem Details and System Configuration" are copied below. (R 3.2.2 seems to work fine within RStudio 0.98.1103.) >>> >>> >>> What do you suggest I do to fix this problem? >>> >> Dunno, it works fine for me, at least on Mavericks 10.9.5. >> >> However, the reference to Library/Frameworks/R.framework/Versions/3.1/... makes me suspect that you are somehow mixing versions. Perhaps clean up and reinstall? > > > Thanks. Now I can't find a way to start R at all outside of RStudio after uninstalling and reinstalling. > > > What do you suggest I try next? > > > Thanks, > Spencer > > > p.s. To be precise, I ran the following as described in "4.2 Uninstalling under OS X" in "R Installation and Administration": > > > ..$ sudo rm -rf /Library/Frameworks/R.framework > ..$ sudo rm -rf /Applications/R.app > ..$ sudo rm -rf /usr/bin/R > ..$ sudo rm -rf /usr/bin/Rscript > > > Then I double-clicked on "R-3.2.2.pkg" in Downloads. R seemed to install, and R 3.2.2 started as expected under RStudio, but I couldn't find stand-alone R icons. So I upgraded to 10.10.5 and double-clicked again on "R-3.2.2.pkg". That didn't help. FYI, from within RStudio, I get the following: > > > > sessionInfo() > R version 3.2.2 (2015-08-14) > Platform: x86_64-apple-darwin13.4.0 (64-bit) > Running under: OS X 10.10.5 (Yosemite) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_3.2.2 > >> -pd >> >> >>> Thanks, >>> Spencer Graves >>> >>> >>> Problem Details and System Configuration >>> >>> >>> Process: R [569] >>> Path: /Applications/R.app/Contents/MacOS/R >>> Identifier: org.R-project.R >>> Version: ??? >>> Code Type: X86-64 (Native) >>> Parent Process: ??? [1] >>> Responsible: R [569] >>> User ID: 501 >>> >>> Date/Time: 2015-08-17 19:46:47.942 -0500 >>> OS Version: Mac OS X 10.10.3 (14D136) >>> Report Version: 11 >>> Anonymous UUID: 6621BCEA-EA0C-3D7A-AE0A-BFCE63A9A8B4 >>> >>> Sleep/Wake UUID: 9C8F92EE-E940-4B17-A64C-C0F470DFE449 >>> >>> Time Awake Since Boot: 2600 seconds >>> Time Since Wake: 700 seconds >>> >>> Crashed Thread: 0 >>> >>> Exception Type: EXC_BREAKPOINT (SIGTRAP) >>> Exception Codes: 0x0000000000000002, 0x0000000000000000 >>> >>> Application Specific Information: >>> dyld: launch, loading dependent libraries >>> >>> Dyld Error Message: >>> Library not loaded: /Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libR.dylib >>> Referenced from: /Applications/R.app/Contents/MacOS/R >>> Reason: image not found >>> >>> Binary Images: >>> 0x7fff6b9f0000 - 0x7fff6ba26837 dyld (353.2.1) <65DCCB06-339C-3E25-9702-600A28291D0E> /usr/lib/dyld >>> >>> Model: MacBookPro11,3, BootROM MBP112.0138.B14, 4 processors, Intel Core i7, 2.8 GHz, 16 GB, SMC 2.19f12 >>> Graphics: Intel Iris Pro, Intel Iris Pro, Built-In >>> Graphics: NVIDIA GeForce GT 750M, NVIDIA GeForce GT 750M, PCIe, 2048 MB >>> Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533641465238412D50422020 >>> Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533641465238412D50422020 >>> AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x134), Broadcom BCM43xx 1.0 (7.15.166.24.3) >>> Bluetooth: Version 4.3.4f4 15601, 3 services, 27 devices, 1 incoming serial ports >>> Network Service: Wi-Fi, AirPort, en0 >>> Serial ATA Device: APPLE SSD SM1024F, 1 TB >>> USB Device: Internal Memory Card Reader >>> USB Device: BRCM20702 Hub >>> USB Device: Bluetooth USB Host Controller >>> USB Device: Apple Internal Keyboard / Trackpad >>> Thunderbolt Bus: MacBook Pro, Apple Inc., 17.1 >>> >>> _______________________________________________ >>> R-SIG-Mac mailing list >>> R-SIG-Mac at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > From bhh at xs4all.nl Sun Aug 23 21:43:39 2015 From: bhh at xs4all.nl (Berend Hasselman) Date: Sun, 23 Aug 2015 21:43:39 +0200 Subject: [R-SIG-Mac] "Layout still needs update ..." in R.app on OS X Yosemite Message-ID: I?m running R version 3.2.2 Patched (2015-08-14 r69078) -- "Fire Safety? [R.app GUI 1.66 (6996) x86_64-apple-darwin13.4.0] on OS X Yosemite 10.10.5. This is the Mavericks build. After starting R.app and issuing CMD+, to access the Preferences. and closing the preferences window I get this error message (coloured red): 2015-08-23 21:31:21.633 R[2079:87205] Layout still needs update after calling -[NSScrollView layout]. NSScrollView or one of its superclasses may have overridden -layout without calling super. Or, something may have dirtied layout in the middle of updating it. Both are programming errors in Cocoa Autolayout. The former is pretty likely to arise if some pre-Cocoa Autolayout class had a method called layout, but it should be fixed. The message is not issued again when repeating the above procedure but is issued if I access preferences after issuing a valid R command. Could someone throw some light on this? Berend From kevinushey at gmail.com Wed Aug 26 00:37:51 2015 From: kevinushey at gmail.com (Kevin Ushey) Date: Tue, 25 Aug 2015 15:37:51 -0700 Subject: [R-SIG-Mac] R-devel on http://r.research.att.com/ is stale Message-ID: The page lists R-devel as r69167, but r69078 is instead delivered from http://r.research.att.com/mavericks/R-devel/R-devel-mavericks-signed.pkg. This seems to be the case for R-patched and friends as well. Best, Kevin From simon.urbanek at r-project.org Wed Aug 26 16:22:50 2015 From: simon.urbanek at r-project.org (Simon Urbanek) Date: Wed, 26 Aug 2015 09:22:50 -0500 Subject: [R-SIG-Mac] R-devel on http://r.research.att.com/ is stale In-Reply-To: References: Message-ID: <0792429D-FB01-4CB2-9A79-9431DF568629@r-project.org> Kevin, On Aug 25, 2015, at 5:37 PM, Kevin Ushey wrote: > The page lists R-devel as r69167, but r69078 is instead delivered from > http://r.research.att.com/mavericks/R-devel/R-devel-mavericks-signed.pkg. > This seems to be the case for R-patched and friends as well. > there was a problem with disks on that machine that has been fixed yesterday - I think that should have also fixed the issue you're describing. Thanks, Simon From brandon.hurr at gmail.com Wed Aug 26 19:48:12 2015 From: brandon.hurr at gmail.com (Brandon Hurr) Date: Wed, 26 Aug 2015 10:48:12 -0700 Subject: [R-SIG-Mac] arguments lookup is disabled while R is busy Message-ID: The code hints appear to be not working properly for me. In both the editor window and in R GUI I see the subject line in parentheses rather than the usual helpful text indicating what variables are acceptable in a particular function. Tab autocompletion is also non-functioning. Any pointers? Thanks, Brandon https://i.imgur.com/QiAq0W9.png > devtools::session_info() Session info ---------------------------------------------------------------------------------- setting value version R version 3.2.2 (2015-08-14) system x86_64, darwin13.4.0 ui AQUA language (EN) collate en_US.UTF-8 tz America/Los_Angeles date 2015-08-26 Packages -------------------------------------------------------------------------------------- package * version date source assertthat 0.1 2013-12-06 CRAN (R 3.2.0) colorspace 1.2-6 2015-03-11 CRAN (R 3.2.0) DBI 0.3.1 2014-09-24 CRAN (R 3.2.0) devtools * 1.9.0 2015-08-25 Github (hadley/devtools at 76ada1d) digest 0.6.8 2014-12-31 CRAN (R 3.2.0) dplyr * 0.4.2.9002 2015-08-25 Github (hadley/dplyr at 70b74de) ggplot2 * 1.0.1.9003 2015-08-25 Github (hadley/ggplot2 at e023c24) gtable 0.1.2 2012-12-05 CRAN (R 3.2.0) labeling 0.3 2014-08-23 CRAN (R 3.2.0) lazyeval 0.1.10.9000 2015-05-26 Github (hadley/lazyeval at ecb8dc0) magrittr 1.5 2014-11-22 CRAN (R 3.2.0) memoise 0.2.1 2014-04-22 CRAN (R 3.2.0) munsell 0.4.2 2013-07-11 CRAN (R 3.2.0) plyr 1.8.3 2015-06-12 CRAN (R 3.2.0) R6 2.1.0 2015-07-04 CRAN (R 3.2.0) Rcpp 0.12.0 2015-07-25 CRAN (R 3.2.0) readxl * 0.1.0.9000 2015-08-25 Github (hadley/readxl at 7c7f66b) reshape2 1.4.1 2014-12-06 CRAN (R 3.2.0) rstudioapi 0.3.1 2015-04-07 CRAN (R 3.2.0) scales 0.3.0.9000 2015-08-25 Github (hadley/scales at 7fc502c) stringi 0.5-5 2015-06-29 CRAN (R 3.2.0) stringr 1.0.0 2015-04-30 CRAN (R 3.2.0) From simon.urbanek at r-project.org Fri Aug 28 04:34:22 2015 From: simon.urbanek at r-project.org (Simon Urbanek) Date: Thu, 27 Aug 2015 22:34:22 -0400 Subject: [R-SIG-Mac] arguments lookup is disabled while R is busy In-Reply-To: References: Message-ID: <1D9C9971-6EAF-482F-9558-42840E5E0D0B@r-project.org> Yes, that is expected, since you need R to obtain those (it requires R code to run) and R is single-threaded, so you get all those hints only when R is not busy. Cheers, Simon On Aug 26, 2015, at 1:48 PM, Brandon Hurr wrote: > The code hints appear to be not working properly for me. In both the > editor window and in R GUI I see the subject line in parentheses > rather than the usual helpful text indicating what variables are > acceptable in a particular function. > Tab autocompletion is also non-functioning. > > Any pointers? > > Thanks, > Brandon > > https://i.imgur.com/QiAq0W9.png > >> devtools::session_info() > Session info ---------------------------------------------------------------------------------- > setting value > version R version 3.2.2 (2015-08-14) > system x86_64, darwin13.4.0 > ui AQUA > language (EN) > collate en_US.UTF-8 > tz America/Los_Angeles > date 2015-08-26 > > Packages -------------------------------------------------------------------------------------- > package * version date source > assertthat 0.1 2013-12-06 CRAN (R 3.2.0) > colorspace 1.2-6 2015-03-11 CRAN (R 3.2.0) > DBI 0.3.1 2014-09-24 CRAN (R 3.2.0) > devtools * 1.9.0 2015-08-25 Github (hadley/devtools at 76ada1d) > digest 0.6.8 2014-12-31 CRAN (R 3.2.0) > dplyr * 0.4.2.9002 2015-08-25 Github (hadley/dplyr at 70b74de) > ggplot2 * 1.0.1.9003 2015-08-25 Github (hadley/ggplot2 at e023c24) > gtable 0.1.2 2012-12-05 CRAN (R 3.2.0) > labeling 0.3 2014-08-23 CRAN (R 3.2.0) > lazyeval 0.1.10.9000 2015-05-26 Github (hadley/lazyeval at ecb8dc0) > magrittr 1.5 2014-11-22 CRAN (R 3.2.0) > memoise 0.2.1 2014-04-22 CRAN (R 3.2.0) > munsell 0.4.2 2013-07-11 CRAN (R 3.2.0) > plyr 1.8.3 2015-06-12 CRAN (R 3.2.0) > R6 2.1.0 2015-07-04 CRAN (R 3.2.0) > Rcpp 0.12.0 2015-07-25 CRAN (R 3.2.0) > readxl * 0.1.0.9000 2015-08-25 Github (hadley/readxl at 7c7f66b) > reshape2 1.4.1 2014-12-06 CRAN (R 3.2.0) > rstudioapi 0.3.1 2015-04-07 CRAN (R 3.2.0) > scales 0.3.0.9000 2015-08-25 Github (hadley/scales at 7fc502c) > stringi 0.5-5 2015-06-29 CRAN (R 3.2.0) > stringr 1.0.0 2015-04-30 CRAN (R 3.2.0) > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > From brandon.hurr at gmail.com Fri Aug 28 05:12:35 2015 From: brandon.hurr at gmail.com (Brandon Hurr) Date: Thu, 27 Aug 2015 20:12:35 -0700 Subject: [R-SIG-Mac] arguments lookup is disabled while R is busy In-Reply-To: <1D9C9971-6EAF-482F-9558-42840E5E0D0B@r-project.org> References: <1D9C9971-6EAF-482F-9558-42840E5E0D0B@r-project.org> Message-ID: At the time I wasn't doing anything. The editor window was open and the GUI window was waiting for input. It was working fine in Rstudio so I switched briefly, and now after a few power cycles it's like it was. Not sure what I did, but I guess it's ok. On Thu, Aug 27, 2015 at 7:34 PM, Simon Urbanek wrote: > Yes, that is expected, since you need R to obtain those (it requires R code to run) and R is single-threaded, so you get all those hints only when R is not busy. > > Cheers, > Simon > > > On Aug 26, 2015, at 1:48 PM, Brandon Hurr wrote: > >> The code hints appear to be not working properly for me. In both the >> editor window and in R GUI I see the subject line in parentheses >> rather than the usual helpful text indicating what variables are >> acceptable in a particular function. >> Tab autocompletion is also non-functioning. >> >> Any pointers? >> >> Thanks, >> Brandon >> >> https://i.imgur.com/QiAq0W9.png >> >>> devtools::session_info() >> Session info ---------------------------------------------------------------------------------- >> setting value >> version R version 3.2.2 (2015-08-14) >> system x86_64, darwin13.4.0 >> ui AQUA >> language (EN) >> collate en_US.UTF-8 >> tz America/Los_Angeles >> date 2015-08-26 >> >> Packages -------------------------------------------------------------------------------------- >> package * version date source >> assertthat 0.1 2013-12-06 CRAN (R 3.2.0) >> colorspace 1.2-6 2015-03-11 CRAN (R 3.2.0) >> DBI 0.3.1 2014-09-24 CRAN (R 3.2.0) >> devtools * 1.9.0 2015-08-25 Github (hadley/devtools at 76ada1d) >> digest 0.6.8 2014-12-31 CRAN (R 3.2.0) >> dplyr * 0.4.2.9002 2015-08-25 Github (hadley/dplyr at 70b74de) >> ggplot2 * 1.0.1.9003 2015-08-25 Github (hadley/ggplot2 at e023c24) >> gtable 0.1.2 2012-12-05 CRAN (R 3.2.0) >> labeling 0.3 2014-08-23 CRAN (R 3.2.0) >> lazyeval 0.1.10.9000 2015-05-26 Github (hadley/lazyeval at ecb8dc0) >> magrittr 1.5 2014-11-22 CRAN (R 3.2.0) >> memoise 0.2.1 2014-04-22 CRAN (R 3.2.0) >> munsell 0.4.2 2013-07-11 CRAN (R 3.2.0) >> plyr 1.8.3 2015-06-12 CRAN (R 3.2.0) >> R6 2.1.0 2015-07-04 CRAN (R 3.2.0) >> Rcpp 0.12.0 2015-07-25 CRAN (R 3.2.0) >> readxl * 0.1.0.9000 2015-08-25 Github (hadley/readxl at 7c7f66b) >> reshape2 1.4.1 2014-12-06 CRAN (R 3.2.0) >> rstudioapi 0.3.1 2015-04-07 CRAN (R 3.2.0) >> scales 0.3.0.9000 2015-08-25 Github (hadley/scales at 7fc502c) >> stringi 0.5-5 2015-06-29 CRAN (R 3.2.0) >> stringr 1.0.0 2015-04-30 CRAN (R 3.2.0) >> >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac at r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> > From simon.urbanek at r-project.org Fri Aug 28 17:02:19 2015 From: simon.urbanek at r-project.org (Simon Urbanek) Date: Fri, 28 Aug 2015 11:02:19 -0400 Subject: [R-SIG-Mac] arguments lookup is disabled while R is busy In-Reply-To: References: <1D9C9971-6EAF-482F-9558-42840E5E0D0B@r-project.org> Message-ID: <6273AB2C-52DF-4269-984B-9E69A9E01B07@r-project.org> > On Aug 27, 2015, at 11:12 PM, Brandon Hurr wrote: > > At the time I wasn't doing anything. The editor window was open and > the GUI window was waiting for input. It was working fine in Rstudio > so I switched briefly, and now after a few power cycles it's like it > was. Not sure what I did, but I guess it's ok. > Maybe I was not parsing your e-mail correctly - the title says "arguments lookup is disabled while R is busy" which is expected. So how to reproduce what you describe? Thanks, Simon > On Thu, Aug 27, 2015 at 7:34 PM, Simon Urbanek > wrote: >> Yes, that is expected, since you need R to obtain those (it requires R code to run) and R is single-threaded, so you get all those hints only when R is not busy. >> >> Cheers, >> Simon >> >> >> On Aug 26, 2015, at 1:48 PM, Brandon Hurr wrote: >> >>> The code hints appear to be not working properly for me. In both the >>> editor window and in R GUI I see the subject line in parentheses >>> rather than the usual helpful text indicating what variables are >>> acceptable in a particular function. >>> Tab autocompletion is also non-functioning. >>> >>> Any pointers? >>> >>> Thanks, >>> Brandon >>> >>> https://i.imgur.com/QiAq0W9.png >>> >>>> devtools::session_info() >>> Session info ---------------------------------------------------------------------------------- >>> setting value >>> version R version 3.2.2 (2015-08-14) >>> system x86_64, darwin13.4.0 >>> ui AQUA >>> language (EN) >>> collate en_US.UTF-8 >>> tz America/Los_Angeles >>> date 2015-08-26 >>> >>> Packages -------------------------------------------------------------------------------------- >>> package * version date source >>> assertthat 0.1 2013-12-06 CRAN (R 3.2.0) >>> colorspace 1.2-6 2015-03-11 CRAN (R 3.2.0) >>> DBI 0.3.1 2014-09-24 CRAN (R 3.2.0) >>> devtools * 1.9.0 2015-08-25 Github (hadley/devtools at 76ada1d) >>> digest 0.6.8 2014-12-31 CRAN (R 3.2.0) >>> dplyr * 0.4.2.9002 2015-08-25 Github (hadley/dplyr at 70b74de) >>> ggplot2 * 1.0.1.9003 2015-08-25 Github (hadley/ggplot2 at e023c24) >>> gtable 0.1.2 2012-12-05 CRAN (R 3.2.0) >>> labeling 0.3 2014-08-23 CRAN (R 3.2.0) >>> lazyeval 0.1.10.9000 2015-05-26 Github (hadley/lazyeval at ecb8dc0) >>> magrittr 1.5 2014-11-22 CRAN (R 3.2.0) >>> memoise 0.2.1 2014-04-22 CRAN (R 3.2.0) >>> munsell 0.4.2 2013-07-11 CRAN (R 3.2.0) >>> plyr 1.8.3 2015-06-12 CRAN (R 3.2.0) >>> R6 2.1.0 2015-07-04 CRAN (R 3.2.0) >>> Rcpp 0.12.0 2015-07-25 CRAN (R 3.2.0) >>> readxl * 0.1.0.9000 2015-08-25 Github (hadley/readxl at 7c7f66b) >>> reshape2 1.4.1 2014-12-06 CRAN (R 3.2.0) >>> rstudioapi 0.3.1 2015-04-07 CRAN (R 3.2.0) >>> scales 0.3.0.9000 2015-08-25 Github (hadley/scales at 7fc502c) >>> stringi 0.5-5 2015-06-29 CRAN (R 3.2.0) >>> stringr 1.0.0 2015-04-30 CRAN (R 3.2.0) >>> >>> _______________________________________________ >>> R-SIG-Mac mailing list >>> R-SIG-Mac at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >> > From brandon.hurr at gmail.com Fri Aug 28 17:32:41 2015 From: brandon.hurr at gmail.com (Brandon Hurr) Date: Fri, 28 Aug 2015 08:32:41 -0700 Subject: [R-SIG-Mac] arguments lookup is disabled while R is busy In-Reply-To: <6273AB2C-52DF-4269-984B-9E69A9E01B07@r-project.org> References: <1D9C9971-6EAF-482F-9558-42840E5E0D0B@r-project.org> <6273AB2C-52DF-4269-984B-9E69A9E01B07@r-project.org> Message-ID: Simon, Wires crossed methinks. I took a photo (imgur link in first message). In it you can see the bottom of the editor window which says, "(arguments lookup is disabled while R is busy)". While in the GUI window, it is the prompt ">". When I switched to the GUI window, it would say that in the bottom of the GUI window. The hints and autocomplete weren't working. My point is that it wasn't busy doing anything and yet it insisted it was. I closed and reopened R a few times and nothing changed. Then I went to Rstudio, in which the code hints and autocomplete was working. After a few reboots, it no longer does this and I can not get it to reproduce using similar code ( I no longer have the original code I was working with because I changed it too much). The only thing I can think of is that during this session, I updated from R 3.2.1 to 3.2.2 and also updated a lot of packages. Perhaps a reboot was in order? Sorry for the noise. Brandon On Fri, Aug 28, 2015 at 8:02 AM, Simon Urbanek wrote: > >> On Aug 27, 2015, at 11:12 PM, Brandon Hurr wrote: >> >> At the time I wasn't doing anything. The editor window was open and >> the GUI window was waiting for input. It was working fine in Rstudio >> so I switched briefly, and now after a few power cycles it's like it >> was. Not sure what I did, but I guess it's ok. >> > > Maybe I was not parsing your e-mail correctly - the title says "arguments lookup is disabled while R is busy" which is expected. So how to reproduce what you describe? > > Thanks, > Simon > > > >> On Thu, Aug 27, 2015 at 7:34 PM, Simon Urbanek >> wrote: >>> Yes, that is expected, since you need R to obtain those (it requires R code to run) and R is single-threaded, so you get all those hints only when R is not busy. >>> >>> Cheers, >>> Simon >>> >>> >>> On Aug 26, 2015, at 1:48 PM, Brandon Hurr wrote: >>> >>>> The code hints appear to be not working properly for me. In both the >>>> editor window and in R GUI I see the subject line in parentheses >>>> rather than the usual helpful text indicating what variables are >>>> acceptable in a particular function. >>>> Tab autocompletion is also non-functioning. >>>> >>>> Any pointers? >>>> >>>> Thanks, >>>> Brandon >>>> >>>> https://i.imgur.com/QiAq0W9.png >>>> >>>>> devtools::session_info() >>>> Session info ---------------------------------------------------------------------------------- >>>> setting value >>>> version R version 3.2.2 (2015-08-14) >>>> system x86_64, darwin13.4.0 >>>> ui AQUA >>>> language (EN) >>>> collate en_US.UTF-8 >>>> tz America/Los_Angeles >>>> date 2015-08-26 >>>> >>>> Packages -------------------------------------------------------------------------------------- >>>> package * version date source >>>> assertthat 0.1 2013-12-06 CRAN (R 3.2.0) >>>> colorspace 1.2-6 2015-03-11 CRAN (R 3.2.0) >>>> DBI 0.3.1 2014-09-24 CRAN (R 3.2.0) >>>> devtools * 1.9.0 2015-08-25 Github (hadley/devtools at 76ada1d) >>>> digest 0.6.8 2014-12-31 CRAN (R 3.2.0) >>>> dplyr * 0.4.2.9002 2015-08-25 Github (hadley/dplyr at 70b74de) >>>> ggplot2 * 1.0.1.9003 2015-08-25 Github (hadley/ggplot2 at e023c24) >>>> gtable 0.1.2 2012-12-05 CRAN (R 3.2.0) >>>> labeling 0.3 2014-08-23 CRAN (R 3.2.0) >>>> lazyeval 0.1.10.9000 2015-05-26 Github (hadley/lazyeval at ecb8dc0) >>>> magrittr 1.5 2014-11-22 CRAN (R 3.2.0) >>>> memoise 0.2.1 2014-04-22 CRAN (R 3.2.0) >>>> munsell 0.4.2 2013-07-11 CRAN (R 3.2.0) >>>> plyr 1.8.3 2015-06-12 CRAN (R 3.2.0) >>>> R6 2.1.0 2015-07-04 CRAN (R 3.2.0) >>>> Rcpp 0.12.0 2015-07-25 CRAN (R 3.2.0) >>>> readxl * 0.1.0.9000 2015-08-25 Github (hadley/readxl at 7c7f66b) >>>> reshape2 1.4.1 2014-12-06 CRAN (R 3.2.0) >>>> rstudioapi 0.3.1 2015-04-07 CRAN (R 3.2.0) >>>> scales 0.3.0.9000 2015-08-25 Github (hadley/scales at 7fc502c) >>>> stringi 0.5-5 2015-06-29 CRAN (R 3.2.0) >>>> stringr 1.0.0 2015-04-30 CRAN (R 3.2.0) >>>> >>>> _______________________________________________ >>>> R-SIG-Mac mailing list >>>> R-SIG-Mac at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>> >>> >> > From vincent.moriarty at csun.edu Fri Aug 7 02:23:17 2015 From: vincent.moriarty at csun.edu (Moriarty,Vincent W) Date: Fri, 07 Aug 2015 00:23:17 -0000 Subject: [R-SIG-Mac] R GUI is freezing Message-ID: <24CD9158-FB32-4B83-BC1F-850C73BDE244@csun.edu> Hi Christopher, I just came across your post online concerning R freezing. I?ve been having this same problem for many months now over multiple machines. Did you ever find a satisfactory answer for this issue? Cheers, Vincent From cfcastilloster at gmail.com Mon Aug 24 02:25:35 2015 From: cfcastilloster at gmail.com (Carlos) Date: Mon, 24 Aug 2015 00:25:35 -0000 Subject: [R-SIG-Mac] =?utf-8?q?Error_in_untar2=28tarfile=2C_files=2C_list?= =?utf-8?b?LCBleGRpcikgOiB1bnN1cHBvcnRlZCBlbnRyeSB0eXBlIOKAmHjigJk=?= References: Message-ID: After a while serching in google found out that: sudo apt-get install r-base-dev fixed the issue From jeelsens at ncsu.edu Sun Aug 30 01:28:27 2015 From: jeelsens at ncsu.edu (Johanna Elsensohn) Date: Sat, 29 Aug 2015 23:28:27 -0000 Subject: [R-SIG-Mac] Error loading packages Message-ID: Hello, I'm not having any luck loading two packages, ggplot2 and psych so I'm not sure if this is Mac specific or Rapp specific. When trying to load the packages, I get the below error messages, highlighted in bold. I have tried installing and loading the package asked for (in this case 'munsell'), but the same error message will appear, with a new/different package name. I have uninstalled and reinstalled R and the packages themselves, and from several different mirrors. I had the same issue on R v3.2.1. I'm not sure what else to try, or how many other packages are affected. Thanks for any help you can give me. My script and session info are below. For R "Fire Safety", v3.2.2. > rm(list=ls()) > library(plyr) > library(ggplot2) *Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : * * there is no package called ?munsell?* *Error: package or namespace load failed for ?ggplot2?* > library(reshape2) > library(psych) *Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : * * there is no package called ?mnormt?* *Error: package or namespace load failed for ?psych?* > sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.2 (Yosemite) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] reshape2_1.4.1 plyr_1.8.3 loaded via a namespace (and not attached): [1] magrittr_1.5 tools_3.2.2 gtable_0.1.2 Rcpp_0.12.0 stringi_0.5-5 grid_3.2.2 stringr_1.0.0 digest_0.6.8 [9] proto_0.3-10 > -- Johanna [[alternative HTML version deleted]] From grubio at mat.upv.es Mon Aug 10 17:11:40 2015 From: grubio at mat.upv.es (Gregorio Rubio Navarro) Date: Mon, 10 Aug 2015 15:11:40 -0000 Subject: [R-SIG-Mac] problems to open files and changing directory Message-ID: <38495D6A-F8B1-4769-9792-097FFFB42E9A@mat.upv.es> Hi, Very often R.app crashes when I try to open a file or to change directory. The problem started with Maverick and remains with Yosemite. What can I do? Thanks Gregorio