Re: [R-SIG-Mac] [Rd] R CMD build looking for texi2dvi in the wrong place (R-devel)
Ah, there was no announcement other than the discussions on requiring texinfo 5.1+ in R-devel and the NEWS: • ‘configure’ requires the ‘texi2any’ script from ‘texinfo’ 5.1 or later, in place of the ‘makeinfo’ program. Since OS X ships with old texinfo we have to use a custom build. FWIW all this should really be on R-SIG-Mac - moving there. Cheers, Simon On Jan 12, 2015, at 9:26 PM, Dan Tenenbaum wrote: > > > - Original Message - >> From: "Simon Urbanek" >> To: "Dan Tenenbaum" >> Cc: "R-devel" >> Sent: Monday, January 12, 2015 5:50:35 PM >> Subject: Re: [Rd] R CMD build looking for texi2dvi in the wrong place >> (R-devel) >> >> Dan, >> >> On Jan 12, 2015, at 7:50 PM, Dan Tenenbaum >> wrote: >> >>> R CMD build fails with recent R-devel because it is looking for >>> texi2dvi in /usr/local/bin, but on this system, MacTex has >>> installed it in /usr/bin. >>> >> >> No, you're looking at the wrong package - texi2dvi comes from texinfo >> which is now mandatory in version 5.2+ located in /usr/local since >> OS X comes with an old version. You should install it from >> >> http://r.research.att.com/libs/texinfo-5.2-darwin10.tar.gz >> > > Thanks, was there an announcement that I missed about this and if so, where > was it? > > Dan > > > >> Cheers, >> Simon >> >> >> >>> $ R CMD build IRanges >>> * checking for file 'IRanges/DESCRIPTION' ... OK >>> * preparing 'IRanges': >>> * checking DESCRIPTION meta-information ... OK >>> * cleaning src >>> * installing the package to build vignettes >>> * creating vignettes ... ERROR >>> [...] >>> Warning in sub(object$syntax$docexpr, val, chunk[pos[1L]]) : >>> argument 'replacement' has length > 1 and only the first element >>> will be used >>> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = >>> quiet, : >>> Running 'texi2dvi' on 'IRangesOverview.tex' failed. >>> Messages: >>> sh: /usr/local/bin/texi2dvi: No such file or directory >>> Calls: -> texi2pdf -> texi2dvi >>> Execution halted >>> >>> That's with: >>> >>> R Under development (unstable) (2015-01-11 r67421) >>> Platform: x86_64-apple-darwin13.4.0 (64-bit) >>> Running under: OS X 10.9.5 (Mavericks) >>> >>> 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 >>> >>> The same command works without error on: >>> >>> R Under development (unstable) (2014-11-11 r66970) >>> Platform: x86_64-apple-darwin13.4.0 (64-bit) >>> >>> 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 >>> >>> Setting >>> options(texi2dvi='/usr/bin/texi2dvi') >>> >>> in my ~/.Rprofile did not help, I suspect because R CMD build runs >>> buildVignettes() in a subprocess started with --vanilla. Creating >>> a symlink from /usr/bin/texi2dvi to /usr/local/bin/texi2dvi gave >>> me a "too many levels of symbolic links" error. Making it a hard >>> link works, but seems like a real hack (what if the executable was >>> not relocatable?). >>> >>> Thanks in advance, >>> Dan >>> >>> __ >>> r-de...@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-devel >>> >> >> > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Installing from source on OSX 10.10.1 and R 3.2 (devel version)
I downgraded my gfortran to 4.8 and things seem to be working again. Thanks
for the hint. Bryan
> On Jan 12, 2015, at 3:36 PM, Bryan Hanson wrote:
>
> Hi Simon… I never compiled R myself, I just got R-devel-mavericks.pkg from
> http://r.research.att.com/ (this morning, though I had the same experience
> about 3 weeks ago, and gave up, hoping it was something which would go
> away…). I did update gcc back in December, this is what I have installed:
>
>> gcc --version
> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
> --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/c++/4.2.1
> Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn)
> Target: x86_64-apple-darwin14.0.0
> Thread model: posix
>
> which I notice has an even newer target.
>
> Bryan
>
>
>> On Jan 12, 2015, at 3:29 PM, Simon Urbanek
>> wrote:
>>
>> Bryan,
>>
>> it means that you have a mismatch between the Fortran compiler used to build
>> R and the one you are using to build packages. Did you remove and/or update
>> Fortran between compiling R and the packages?
>>
>> Cheers,
>> Simon
>>
>>
>>> On Jan 12, 2015, at 2:20 PM, Bryan Hanson wrote:
>>>
>>> I’m trying to get R 3.2 working fully so I can test my packages before
>>> sending to CRAN. R 3.2 appears to work OK in general terms. However, when
>>> I try to install some packages I need, I run into errors with the libraries
>>> that the install process desires. I get the same or very similar messages
>>> from several packages. Let’s use amap as an example:
>>>
>>> install.packages("amap", type = "source")
>>> […]
>>> ld: warning: directory not found for option
>>> '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
>>> ld: library not found for -lgfortran
>>> clang: error: linker command failed with exit code 1 (use -v to see
>>> invocation)
>>> make: *** [amap.so] Error 1
>>> ERROR: compilation failed for package ‘amap’
>>> * removing ‘/Users/bryanhanson/Library/R/3.2/library/amap’
>>> * restoring previous ‘/Users/bryanhanson/Library/R/3.2/library/amap’
>>>
>>> The full output is appended after this message. The problem here is clear
>>> in one sense: there no directory on my machine by that name, since on
>>> Yosemite it is darwin13.4.0 and gcc is at 4.9.2. xcode and xquartz have
>>> been updated. I don’t know if this is a problem with a symlink on my
>>> system or an issue with the amap package not yet being fully updated for R
>>> 3.2 or a problem with R 3.2 or a mangled gcc install. All suggestions
>>> welcome, there’s a good chance I’m being simple-minded here.
>>>
>>> Thank you. Bryan
>>>
>>> === dir listing
>>>
pwd
>>> /usr/local/lib/gcc/x86_64-apple-darwin13.4.0
ls -l
>>> total 16
>>> lrwxr-xr-x 1 bryanhanson wheel67 Dec 12 14:29 4.8.2 ->
>>> ../../../Cellar/gcc48/4.8.3/lib/gcc/x86_64-apple-darwin13.4.0/4.8.3
>>> lrwxr-xr-x 1 bryanhanson wheel67 Dec 12 14:22 4.8.3 ->
>>> ../../../Cellar/gcc48/4.8.3/lib/gcc/x86_64-apple-darwin13.4.0/4.8.3
>>> drwxr-xr-x 66 bryanhanson wheel 2244 Dec 20 10:36 4.9.2
>>>
>>> === SessionInfo()
>>>
>>> R Under development (unstable) (2015-01-11 r67421)
>>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>>> Running under: OS X 10.10.1 (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] sos_1.3-8 brew_1.0-6
>>>
>>> loaded via a namespace (and not attached):
>>> [1] tools_3.2.0
>>>
>>> === Full output from install.packages
>>>
>>> install.packages("amap", type = "source")
>>> Installing package into ‘/Users/bryanhanson/Library/R/3.2/library’
>>> (as ‘lib’ is unspecified)
>>> trying URL 'http://cran.at.r-project.org/src/contrib/amap_0.8-14.tar.gz'
>>> Content type 'application/x-gzip' length 259358 bytes (253 KB)
>>> opened URL
>>> ==
>>> downloaded 253 KB
>>>
>>>
>>> Loading Bryan's .Rprofile
>>>
>>> Loading required package: brew
>>>
>>> Completed Bryan's .Rprofile GET TO WORK!
>>>
>>> * installing *source* package ‘amap’ ...
>>> ** package ‘amap’ successfully unpacked and MD5 sums checked
>>> checking for gcc... gcc
>>> checking for C compiler default output file name... a.out
>>> checking whether the C compiler works... yes
>>> checking whether we are cross compiling... no
>>> checking for suffix of executables... checking for suffix of object
>>> files... o
>>> checking whether we are using the GNU C compiler... yes
>>> checking whether gcc accepts -g... yes
>>> checking for gcc option to accept ANSI C... none needed
>>> checking for pthread_create in -lpthread... yes
>>> configure: creating ./config.status
>>> config.status: creating src/Makevars
>>> **
Re: [R-SIG-Mac] hangs on Open Dialog
Carl, > On Jan 12, 2015, at 5:43 PM, Carl Witthoft wrote: > > Updated info: I installed the latest patch version of R from > research.att.com , > and there are several things behaving differently. Now I do not get any > files opened when I open R, whereas previously all files open when I quit R > re-opened (even if I'd used quit() and had a normal end of session). > In addition, the Window menu no longer displays windows (such as files being > edited) which had been closed earlier in my R session. > > BUT: I torture-tested by opening about 50 files inside R. I then force-quit > R, and then on restart, R tries to re-open all the files again! I'm guessing > this is desired behavior, to recover any lost work, but it's a bit unnerving. > At the very least, can you advise if there's a config file somewhere that I > could delete to avoid this recovery mode? > Send all thanks to Apple - this is how the OS behave now - I find it extremely annoying, but AFAIK the app has no control over it, because they come as regular open request to the app. That said, nothing really changed on the R side - we didn't touch the R.app for almost a year, so whatever you may be seeing has to do wither with your OS or the build you picked. Cheers, Simon > >> -- >> >> Message: 4 >> Date: Mon, 12 Jan 2015 17:20:03 -0500 >> From: Carl Witthoft >> To: "r-sig-mac@r-project.org" >> Subject: [R-SIG-Mac] Still have hangs on Open Dialog Box >> Message-ID: <54b44893.9040...@witthoft.com> >> Content-Type: text/plain; charset=utf-8; format=flowed >> >> I thought this problem had gone away, but it's still hitting me. >> >> Yosemite on a dual-core iMac, R 3.1.2 GUI 1.65 Mavericks build (6833). >> I've verified Permissions and Disk, using DiskUtility. >> >> What happens is: I select "Open" from the menu to try to open a new file >> inside R, and I get the OpenDialog window, but the contents of the >> current directory never fill the window; just spinning beachball of >> death. I thought turning off DefaultFolder helped, but it didn't. I >> have to force-quit R and delete the file "com.apple.finder.plist" from >> my Library/Preferences directory to be able to successfully open a file >> from inside R (as opposed to double-clicking on a Finder window's file >> icon) the next time I open R.app GUI . >> >> The only other thing I noticed is that, when R starts up, a whole pile >> of previously-opened files are displayed and then disappear. WHen I hit >> the Mac OSX "F10" function key to display all current windows >> belonging to R, I got a strange (at least to me) display. All the >> current windows are displayed but ALSO a long row of mini-icons >> representing previously open (and closed) document windows. I posted a >> screen shot at https://app.box.com/s/qutc86rujitb49geur8c ; this >> appears to match my "Recent" doc list in the File Menu. >> I don't know what causes that -- Microsoft Office apps don't do this, >> but TextWrangler and GraphicConverter(for two examples) do. I don't >> know whether it is related to R's misbehavior on my machine. All I >> know for certain is that no other application I've tried ever hangs on >> Open dialog boxes. >> >> Any ideas? >> >> Carl >> > > -- > > Sent from a parallel universe almost, but not entirely, > nothing at all like this one. > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] hangs on Open Dialog
Updated info: I installed the latest patch version of R from research.att.com , and there are several things behaving differently. Now I do not get any files opened when I open R, whereas previously all files open when I quit R re-opened (even if I'd used quit() and had a normal end of session). In addition, the Window menu no longer displays windows (such as files being edited) which had been closed earlier in my R session. BUT: I torture-tested by opening about 50 files inside R. I then force-quit R, and then on restart, R tries to re-open all the files again! I'm guessing this is desired behavior, to recover any lost work, but it's a bit unnerving. At the very least, can you advise if there's a config file somewhere that I could delete to avoid this recovery mode? -- Message: 4 Date: Mon, 12 Jan 2015 17:20:03 -0500 From: Carl Witthoft To: "r-sig-mac@r-project.org" Subject: [R-SIG-Mac] Still have hangs on Open Dialog Box Message-ID: <54b44893.9040...@witthoft.com> Content-Type: text/plain; charset=utf-8; format=flowed I thought this problem had gone away, but it's still hitting me. Yosemite on a dual-core iMac, R 3.1.2 GUI 1.65 Mavericks build (6833). I've verified Permissions and Disk, using DiskUtility. What happens is: I select "Open" from the menu to try to open a new file inside R, and I get the OpenDialog window, but the contents of the current directory never fill the window; just spinning beachball of death. I thought turning off DefaultFolder helped, but it didn't. I have to force-quit R and delete the file "com.apple.finder.plist" from my Library/Preferences directory to be able to successfully open a file from inside R (as opposed to double-clicking on a Finder window's file icon) the next time I open R.app GUI . The only other thing I noticed is that, when R starts up, a whole pile of previously-opened files are displayed and then disappear. WHen I hit the Mac OSX "F10" function key to display all current windows belonging to R, I got a strange (at least to me) display. All the current windows are displayed but ALSO a long row of mini-icons representing previously open (and closed) document windows. I posted a screen shot at https://app.box.com/s/qutc86rujitb49geur8c ; this appears to match my "Recent" doc list in the File Menu. I don't know what causes that -- Microsoft Office apps don't do this, but TextWrangler and GraphicConverter(for two examples) do. I don't know whether it is related to R's misbehavior on my machine. All I know for certain is that no other application I've tried ever hangs on Open dialog boxes. Any ideas? Carl -- Sent from a parallel universe almost, but not entirely, nothing at all like this one. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Still have hangs on Open Dialog Box
I thought this problem had gone away, but it's still hitting me. Yosemite on a dual-core iMac, R 3.1.2 GUI 1.65 Mavericks build (6833). I've verified Permissions and Disk, using DiskUtility. What happens is: I select "Open" from the menu to try to open a new file inside R, and I get the OpenDialog window, but the contents of the current directory never fill the window; just spinning beachball of death. I thought turning off DefaultFolder helped, but it didn't. I have to force-quit R and delete the file "com.apple.finder.plist" from my Library/Preferences directory to be able to successfully open a file from inside R (as opposed to double-clicking on a Finder window's file icon) the next time I open R.app GUI . The only other thing I noticed is that, when R starts up, a whole pile of previously-opened files are displayed and then disappear. WHen I hit the Mac OSX "F10" function key to display all current windows belonging to R, I got a strange (at least to me) display. All the current windows are displayed but ALSO a long row of mini-icons representing previously open (and closed) document windows. I posted a screen shot at https://app.box.com/s/qutc86rujitb49geur8c ; this appears to match my "Recent" doc list in the File Menu. I don't know what causes that -- Microsoft Office apps don't do this, but TextWrangler and GraphicConverter(for two examples) do. I don't know whether it is related to R's misbehavior on my machine. All I know for certain is that no other application I've tried ever hangs on Open dialog boxes. Any ideas? Carl -- Sent from a parallel universe almost, but not entirely, nothing at all like this one. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Installing from source on OSX 10.10.1 and R 3.2 (devel version)
Hi Simon… I never compiled R myself, I just got R-devel-mavericks.pkg from
http://r.research.att.com/ (this morning, though I had the same experience
about 3 weeks ago, and gave up, hoping it was something which would go away…).
I did update gcc back in December, this is what I have installed:
> gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
--with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/c++/4.2.1
Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin14.0.0
Thread model: posix
which I notice has an even newer target.
Bryan
> On Jan 12, 2015, at 3:29 PM, Simon Urbanek
> wrote:
>
> Bryan,
>
> it means that you have a mismatch between the Fortran compiler used to build
> R and the one you are using to build packages. Did you remove and/or update
> Fortran between compiling R and the packages?
>
> Cheers,
> Simon
>
>
>> On Jan 12, 2015, at 2:20 PM, Bryan Hanson wrote:
>>
>> I’m trying to get R 3.2 working fully so I can test my packages before
>> sending to CRAN. R 3.2 appears to work OK in general terms. However, when
>> I try to install some packages I need, I run into errors with the libraries
>> that the install process desires. I get the same or very similar messages
>> from several packages. Let’s use amap as an example:
>>
>> install.packages("amap", type = "source")
>> […]
>> ld: warning: directory not found for option
>> '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
>> ld: library not found for -lgfortran
>> clang: error: linker command failed with exit code 1 (use -v to see
>> invocation)
>> make: *** [amap.so] Error 1
>> ERROR: compilation failed for package ‘amap’
>> * removing ‘/Users/bryanhanson/Library/R/3.2/library/amap’
>> * restoring previous ‘/Users/bryanhanson/Library/R/3.2/library/amap’
>>
>> The full output is appended after this message. The problem here is clear
>> in one sense: there no directory on my machine by that name, since on
>> Yosemite it is darwin13.4.0 and gcc is at 4.9.2. xcode and xquartz have
>> been updated. I don’t know if this is a problem with a symlink on my system
>> or an issue with the amap package not yet being fully updated for R 3.2 or
>> a problem with R 3.2 or a mangled gcc install. All suggestions welcome,
>> there’s a good chance I’m being simple-minded here.
>>
>> Thank you. Bryan
>>
>> === dir listing
>>
>>> pwd
>> /usr/local/lib/gcc/x86_64-apple-darwin13.4.0
>>> ls -l
>> total 16
>> lrwxr-xr-x 1 bryanhanson wheel67 Dec 12 14:29 4.8.2 ->
>> ../../../Cellar/gcc48/4.8.3/lib/gcc/x86_64-apple-darwin13.4.0/4.8.3
>> lrwxr-xr-x 1 bryanhanson wheel67 Dec 12 14:22 4.8.3 ->
>> ../../../Cellar/gcc48/4.8.3/lib/gcc/x86_64-apple-darwin13.4.0/4.8.3
>> drwxr-xr-x 66 bryanhanson wheel 2244 Dec 20 10:36 4.9.2
>>
>> === SessionInfo()
>>
>> R Under development (unstable) (2015-01-11 r67421)
>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>> Running under: OS X 10.10.1 (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] sos_1.3-8 brew_1.0-6
>>
>> loaded via a namespace (and not attached):
>> [1] tools_3.2.0
>>
>> === Full output from install.packages
>>
>> install.packages("amap", type = "source")
>> Installing package into ‘/Users/bryanhanson/Library/R/3.2/library’
>> (as ‘lib’ is unspecified)
>> trying URL 'http://cran.at.r-project.org/src/contrib/amap_0.8-14.tar.gz'
>> Content type 'application/x-gzip' length 259358 bytes (253 KB)
>> opened URL
>> ==
>> downloaded 253 KB
>>
>>
>> Loading Bryan's .Rprofile
>>
>> Loading required package: brew
>>
>> Completed Bryan's .Rprofile GET TO WORK!
>>
>> * installing *source* package ‘amap’ ...
>> ** package ‘amap’ successfully unpacked and MD5 sums checked
>> checking for gcc... gcc
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables... checking for suffix of object files...
>> o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc accepts -g... yes
>> checking for gcc option to accept ANSI C... none needed
>> checking for pthread_create in -lpthread... yes
>> configure: creating ./config.status
>> config.status: creating src/Makevars
>> ** libs
>> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> -I/usr/local/include/ -I/usr/local/include -I/usr/local/include/freetype2
>> -I/opt/X11/include-fPIC -Wall -mtune=core2 -g -O2 -c acprob.cpp -o
>> acprob.o
>> clang -I/Library/Frameworks/R.framework/Res
Re: [R-SIG-Mac] Installing from source on OSX 10.10.1 and R 3.2 (devel version)
Bryan,
it means that you have a mismatch between the Fortran compiler used to build R
and the one you are using to build packages. Did you remove and/or update
Fortran between compiling R and the packages?
Cheers,
Simon
> On Jan 12, 2015, at 2:20 PM, Bryan Hanson wrote:
>
> I’m trying to get R 3.2 working fully so I can test my packages before
> sending to CRAN. R 3.2 appears to work OK in general terms. However, when I
> try to install some packages I need, I run into errors with the libraries
> that the install process desires. I get the same or very similar messages
> from several packages. Let’s use amap as an example:
>
> install.packages("amap", type = "source")
> […]
> ld: warning: directory not found for option
> '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
> ld: library not found for -lgfortran
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> make: *** [amap.so] Error 1
> ERROR: compilation failed for package ‘amap’
> * removing ‘/Users/bryanhanson/Library/R/3.2/library/amap’
> * restoring previous ‘/Users/bryanhanson/Library/R/3.2/library/amap’
>
> The full output is appended after this message. The problem here is clear in
> one sense: there no directory on my machine by that name, since on Yosemite
> it is darwin13.4.0 and gcc is at 4.9.2. xcode and xquartz have been updated.
> I don’t know if this is a problem with a symlink on my system or an issue
> with the amap package not yet being fully updated for R 3.2 or a problem
> with R 3.2 or a mangled gcc install. All suggestions welcome, there’s a good
> chance I’m being simple-minded here.
>
> Thank you. Bryan
>
> === dir listing
>
>> pwd
> /usr/local/lib/gcc/x86_64-apple-darwin13.4.0
>> ls -l
> total 16
> lrwxr-xr-x 1 bryanhanson wheel67 Dec 12 14:29 4.8.2 ->
> ../../../Cellar/gcc48/4.8.3/lib/gcc/x86_64-apple-darwin13.4.0/4.8.3
> lrwxr-xr-x 1 bryanhanson wheel67 Dec 12 14:22 4.8.3 ->
> ../../../Cellar/gcc48/4.8.3/lib/gcc/x86_64-apple-darwin13.4.0/4.8.3
> drwxr-xr-x 66 bryanhanson wheel 2244 Dec 20 10:36 4.9.2
>
> === SessionInfo()
>
> R Under development (unstable) (2015-01-11 r67421)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X 10.10.1 (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] sos_1.3-8 brew_1.0-6
>
> loaded via a namespace (and not attached):
> [1] tools_3.2.0
>
> === Full output from install.packages
>
> install.packages("amap", type = "source")
> Installing package into ‘/Users/bryanhanson/Library/R/3.2/library’
> (as ‘lib’ is unspecified)
> trying URL 'http://cran.at.r-project.org/src/contrib/amap_0.8-14.tar.gz'
> Content type 'application/x-gzip' length 259358 bytes (253 KB)
> opened URL
> ==
> downloaded 253 KB
>
>
> Loading Bryan's .Rprofile
>
> Loading required package: brew
>
> Completed Bryan's .Rprofile GET TO WORK!
>
> * installing *source* package ‘amap’ ...
> ** package ‘amap’ successfully unpacked and MD5 sums checked
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables... checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking for pthread_create in -lpthread... yes
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include/ -I/usr/local/include -I/usr/local/include/freetype2
> -I/opt/X11/include-fPIC -Wall -mtune=core2 -g -O2 -c acprob.cpp -o
> acprob.o
> clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include/ -I/usr/local/include -I/usr/local/include/freetype2
> -I/opt/X11/include-fPIC -Wall -mtune=core2 -g -O2 -c burt.c -o burt.o
> clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include/ -I/usr/local/include -I/usr/local/include/freetype2
> -I/opt/X11/include-fPIC -Wall -mtune=core2 -g -O2 -c diss.c -o diss.o
> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include/ -I/usr/local/include -I/usr/local/include/freetype2
> -I/opt/X11/include-fPIC -Wall -mtune=core2 -g -O2 -c distance.cpp -o
> distance.o
> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include/ -I/usr/local/include -I/usr/local/include/freetype2
> -I/opt/X11/include-fPIC -Wall -mtune=core2 -g -O2 -c hclust.cpp -o
> hclus
[R-SIG-Mac] Installing from source on OSX 10.10.1 and R 3.2 (devel version)
I’m trying to get R 3.2 working fully so I can test my packages before sending
to CRAN. R 3.2 appears to work OK in general terms. However, when I try to
install some packages I need, I run into errors with the libraries that the
install process desires. I get the same or very similar messages from several
packages. Let’s use amap as an example:
install.packages("amap", type = "source")
[…]
ld: warning: directory not found for option
'-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [amap.so] Error 1
ERROR: compilation failed for package ‘amap’
* removing ‘/Users/bryanhanson/Library/R/3.2/library/amap’
* restoring previous ‘/Users/bryanhanson/Library/R/3.2/library/amap’
The full output is appended after this message. The problem here is clear in
one sense: there no directory on my machine by that name, since on Yosemite it
is darwin13.4.0 and gcc is at 4.9.2. xcode and xquartz have been updated. I
don’t know if this is a problem with a symlink on my system or an issue with
the amap package not yet being fully updated for R 3.2 or a problem with R 3.2
or a mangled gcc install. All suggestions welcome, there’s a good chance I’m
being simple-minded here.
Thank you. Bryan
=== dir listing
> pwd
/usr/local/lib/gcc/x86_64-apple-darwin13.4.0
> ls -l
total 16
lrwxr-xr-x 1 bryanhanson wheel67 Dec 12 14:29 4.8.2 ->
../../../Cellar/gcc48/4.8.3/lib/gcc/x86_64-apple-darwin13.4.0/4.8.3
lrwxr-xr-x 1 bryanhanson wheel67 Dec 12 14:22 4.8.3 ->
../../../Cellar/gcc48/4.8.3/lib/gcc/x86_64-apple-darwin13.4.0/4.8.3
drwxr-xr-x 66 bryanhanson wheel 2244 Dec 20 10:36 4.9.2
=== SessionInfo()
R Under development (unstable) (2015-01-11 r67421)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.1 (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] sos_1.3-8 brew_1.0-6
loaded via a namespace (and not attached):
[1] tools_3.2.0
=== Full output from install.packages
install.packages("amap", type = "source")
Installing package into ‘/Users/bryanhanson/Library/R/3.2/library’
(as ‘lib’ is unspecified)
trying URL 'http://cran.at.r-project.org/src/contrib/amap_0.8-14.tar.gz'
Content type 'application/x-gzip' length 259358 bytes (253 KB)
opened URL
==
downloaded 253 KB
Loading Bryan's .Rprofile
Loading required package: brew
Completed Bryan's .Rprofile GET TO WORK!
* installing *source* package ‘amap’ ...
** package ‘amap’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for pthread_create in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include/ -I/usr/local/include -I/usr/local/include/freetype2
-I/opt/X11/include-fPIC -Wall -mtune=core2 -g -O2 -c acprob.cpp -o
acprob.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include/ -I/usr/local/include -I/usr/local/include/freetype2
-I/opt/X11/include-fPIC -Wall -mtune=core2 -g -O2 -c burt.c -o burt.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include/ -I/usr/local/include -I/usr/local/include/freetype2
-I/opt/X11/include-fPIC -Wall -mtune=core2 -g -O2 -c diss.c -o diss.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include/ -I/usr/local/include -I/usr/local/include/freetype2
-I/opt/X11/include-fPIC -Wall -mtune=core2 -g -O2 -c distance.cpp -o
distance.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include/ -I/usr/local/include -I/usr/local/include/freetype2
-I/opt/X11/include-fPIC -Wall -mtune=core2 -g -O2 -c hclust.cpp -o
hclust.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include/ -I/usr/local/include -I/usr/local/include/freetype2
-I/opt/X11/include-fPIC -Wall -mtune=core2 -g -O2 -c kmeans.cpp -o
kmeans.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
-I/usr/local/include/ -I/usr/local/include -I/usr/local/include/freetype2
-I/opt/X11/include-fPIC -Wall -mtune=core2 -g -O2 -c matrice.cpp -o
matrice.o
gfortran-4.8 -fPIC -g -O2
