> On 27 May 2017, at 05:57 , David Winsemius <dwinsem...@comcast.net> wrote: > >> >> On May 26, 2017, at 7:13 PM, Simon Urbanek <simon.urba...@r-project.org> >> wrote: >> >> >>> On May 16, 2017, at 4:01 PM, David Winsemius <dwinsem...@comcast.net> wrote: >>> >>> >>>> On Apr 24, 2017, at 11:49 PM, catalin roibu <catalinro...@gmail.com> wrote: >>>> >>>> Dear all, >>>> >>>> I have a problem with the newest R version. I'm trying to install a >>>> specific package dplR who need the gpm package and I have this error on my >>>> macbook (OS Sierra): >>> >>> Generally one reads the error messages. Often, and this is one of those >>> cases, the first error message tells what the problem might be. You either >>> do not have the system package GMP or it is installed in a location where >>> the R package 'gmp' cannot find it. >>> >>> I had difficulties attempting to test the advice I found by (re-)installing >>> the GNU GMP package from CRAN/r.research.att.com: >>> >>> http://r.research.att.com/libs/gmp-6.0.0-darwin.13-x86_64.tar.gz >>> >>> I got: >>> ~ davidwinsemius$ sudo tar fvxz ~/gmp-6.0.0-darwin.13-x86_64.tar.gz -C / >>> x usr/: Can't set user=0/group=0 for usrCan't update time for usr >>> x usr/local/ >>> x usr/local/include/ >>> x usr/local/lib/ >>> x usr/local/share/ >>> x usr/local/share/info/ >>> x usr/local/share/info/dir >>> x usr/local/share/info/gmp.info >>> x usr/local/share/info/gmp.info-1 >>> x usr/local/share/info/gmp.info-2 >>> x usr/local/lib/libgmp.a >>> x usr/local/lib/libgmp.la >>> x usr/local/include/gmp.h >>> tar: Error exit delayed from previous errors. >>> >>> Search on the "Can't update time for usr"-error brought up a bunch of stuff >>> about 'XSAN' that I didn't really understand fully but did not seem >>> terribly relevant ... >>> >> >> FWIW that simply tells you that macOS is refusing even root to modify >> permissions and time for /usr which is deliberate by Apple for security >> reasons. Since El Capitan even root doesn't have privileges to modify /usr >> and its subdirectories other than /usr/local. So, yes, that error is beign. > > I did know that Apple had locked down /usr/ subdirectories. I'm not sure what > your conclusion implies, however. I generally assume that an error message > implies lack of success. Was the effort at installation of gmp from > gmp-6.0.0-darwin.13-x86_64.tar.gz actually completed? (Which means my > subsequent installation using gmp-6.1.2.tar.bz2 was not necessary, but I > guessing also not harmful?
The pragmatic way to find out would be to compare "tar tvfz ..." with what actually ended up in /usr/local. These are just straight unpacks, there is no postprocessing involved. -pd > > Best; > David. > >> >> Cheers, >> Simon >> >> >>> .... but the package 'gmp-6.1.2.tar.bz2' at gmplib.org expanded and >>> compiled without difficulty usign the switches recommended at the bottom of: >>> >>> http://r.research.att.com/libs/ >>> >>> davidwinsemius$ sudo tar fvxz >>> /Users/davidwinsemius/Downloads/gmp-6.1.2.tar.bz2 -C / >>> >>> (I'm not on Sierra, since Apple has classified my MacPro as "obsolete".) >>> >>> -- >>> >>> David >>> [R.app GUI 1.70 (7338) x86_64-apple-darwin15.6.0] >>> >>>> >>> >>> >>>>> install.packages("dplR") >>>> also installing the dependency ‘gmp’ >>>> >>>> Packages which are only available in source form, and may >>>> need compilation of C/C++/Fortran: ‘gmp’ ‘dplR’ >>>> Do you want to attempt to install these from sources? >>>> y/n: y >>>> installing the source packages ‘gmp’, ‘dplR’ >>>> >>>> trying URL 'https://cran.rstudio.com/src/contrib/gmp_0.5-13.1.tar.gz' >>>> Content type 'application/x-gzip' length 131321 bytes (128 KB) >>>> ================================================== >>>> downloaded 128 KB >>>> >>>> trying URL 'https://cran.rstudio.com/src/contrib/dplR_1.6.5.tar.gz' >>>> Content type 'application/x-gzip' length 1672999 bytes (1.6 MB) >>>> ================================================== >>>> downloaded 1.6 MB >>>> >>>> * installing *source* package ‘gmp’ ... >>>> ** package ‘gmp’ successfully unpacked and MD5 sums checked >>>> creating cache ./config.cache >>>> checking for __gmpz_ui_sub in -lgmp... no >>>> configure: error: GNU MP not found, or not 4.1.4 or up, see >>>> http://gmplib.org >>>> ERROR: configuration failed for package ‘gmp’ >>>> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/ >>>> Resources/library/gmp’ >>>> Warning in install.packages : >>>> installation of package ‘gmp’ had non-zero exit status >>>> ERROR: dependency ‘gmp’ is not available for package ‘dplR’ >>>> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/ >>>> Resources/library/dplR’ >>>> Warning in install.packages : >>>> installation of package ‘dplR’ had non-zero exit status >>>> >>>> The downloaded source packages are in >>>> ‘/private/var/folders/c5/6g4vbk5x55586m8ky2v_6pbc0000gn/T/RtmprYzSE8/ >>>> downloaded_packages’ >>>> >>>> >>>> All the other packages work in good conditions. >>>> Please help me to solve this annoying situation. >>>> >>>> Best regards! >>>> >>>> CR >>>> >>>> >>>> -- >>>> >>>> - >>>> - >>>> Catalin-Constantin ROIBU >>>> >>>> Lecturer PhD, Forestry engineer >>>> Forestry Faculty of Suceava >>>> Str. Universitatii no. 13, Suceava, 720229, Romania >>>> office phone +4 0230 52 29 78, ext. 531 >>>> mobile phone +4 0745 53 18 01 >>>> FAX: +4 0230 52 16 64 >>>> silvic.usv.ro <http://www.usv.ro/> >>>> >>>> >>>> >>>> <https://mailtrack.io/> Sent with Mailtrack >>>> <https://mailtrack.io/install?source=signature&lang=en&referral=catalinro...@gmail.com&idSignature=22> >>>> <#> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> R-SIG-Mac mailing list >>>> R-SIG-Mac@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@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@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....@cbs.dk Priv: pda...@gmail.com _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
