[R-SIG-Mac] R 3.4.0 problem

Simon Urbanek simon.urbanek at r-project.org
Sat May 27 14:33:37 CEST 2017 

> On May 26, 2017, at 11:57 PM, David Winsemius <dwinsemius at comcast.net> wrote:
> 
> 
>> On May 26, 2017, at 7:13 PM, Simon Urbanek <simon.urbanek at r-project.org> wrote:
>> 
>> 
>>> On May 16, 2017, at 4:01 PM, David Winsemius <dwinsemius at comcast.net> wrote:
>>> 
>>> 
>>>> On Apr 24, 2017, at 11:49 PM, catalin roibu <catalinroibu at 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?
> 

Yes, maybe I wasn't clear enough - the error says that the permissions on /usr could not be set - which is to be expected since Apple no longer allows root to change permissions so there is no way to avoid that. There were no other errors so it was as successful as can be on your system - that's what I was trying to convey.

Cheers,
Simon




> 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/>
>>>> 
>>>> 
>>>> 
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>>>> <#>
>>>> 
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>>>> 
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>>> 
>>> David Winsemius
>>> Alameda, CA, USA
>>> 
>>> _______________________________________________
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>> 
> 
> David Winsemius
> Alameda, CA, USA
>

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