[R-SIG-Mac] how to install RODBC on macOS Sierra 10.12.4?

[Spencer Graves]

Hello:


  I recently upgraded to R 3.4.0, and I've so far been unable to 
"install.packages('RODBC')" or "R CMD INSTALL RODBC_1.3-15.tar.gz". Both 
end with the following:



configure: error: "ODBC headers sql.h and sqlext.h not found"
ERROR: configuration failed for package ‘RODBC’


  I had RODBC installed in R 3.3, but that was before I upgraded to 
macOS Sierra 10.12.4.   I've tried to RTFM, but I don't know which FMTR, 
and I can't decrypt the documentation I've found that seem relevant.  I 
couldn't find the answer in Ripley's "ODBC Connectivity" vignette.



  "iodbc-42.5/iodbc/README.MACOSX" says, "You first need to install 
the latest Mac OS X Developer Packages, which can be found at 
"http://developer.apple.com/tools;.  I think I've done that, but I don't 
know how to check it.



  "iodbc-42.5/iodbc/README.MACOSX" continues, "Then, you can open 
the Xcode Project Builder files under mac/iODBCinst, mac/iODBC, 
mac/iODBCtest and mac/iODBCtestw,".  I don't know how find any of 
these.  It further continues, "or execute the following commands from a 
terminal session to build all the frameworks and demo applications:



$ cd mac
$ make"


  I just did "$ cd mac" and got, "-bash: cd: mac: No such file or 
directory".  Evidently, I need to substitute something for "mac" here, 
but I don't know what.




  Suggestions?  Thanks,
  Spencer Graves

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Re: [R-SIG-Mac] missing module when compiling R pkg:rms or external package SYMPHONY (in support of Bioc pkg symphony)

[David Winsemius]

> On May 5, 2017, at 12:13 AM, Berend Hasselman  wrote:
> 
> 
>> On 5 May 2017, at 03:12, David Winsemius  wrote:
>> 
>> Failing to get current rms package to compile (and appears that the CRAN 
>> build machine fails as well). The penultimate version of rms succeeds.
>> 
>> Both from console and cmd-line I get this response in R 3.4.0 (just 
>> installed today) running El Cap 10.11.6 with Xcode Version 8.2.1 (8C1002):
>> 
>> trying URL 'https://cran.cnr.berkeley.edu/src/contrib/rms_5.1-1.tar.gz'
>> Content type 'application/x-gzip' length 521311 bytes (509 KB)
>> ==
>> downloaded 509 KB
>> 
>> Loading required package: lattice
>> Loading required package: sos
>> Loading required package: brew
>> Loading required package: rms
>> Loading required package: Hmisc
>> Loading required package: survival
>> Loading required package: Formula
>> Loading required package: stats
>> Loading required package: ggplot2
>> 
>> Attaching package: ‘Hmisc’
>> 
>> The following objects are masked from ‘package:base’:
>> 
>>  format.pval, round.POSIXt, trunc.POSIXt, units
>> 
>> Loading required package: SparseM
>> 
>> Attaching package: ‘SparseM’
>> 
>> The following object is masked from ‘package:base’:
>> 
>>  backsolve
>> 
>> ##-- 2017-05-04 --##
>> Loading required package: graphics
>> 
>> Attaching package: ‘graphics’
>> 
>> The following object is masked from ‘package:SparseM’:
>> 
>>  image
>> 
>> * installing *source* package ‘rms’ ...
>> ** package ‘rms’ successfully unpacked and MD5 sums checked
>> ** libs
>> clang -I/Library/Frameworks/R.framework/Resources/include  
>> -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
>> gfortran   -fPIC  -g -O2  -c lrmfit.f -o lrmfit.o
>> gfortran   -fPIC  -g -O2  -c mlmats.f -o mlmats.o
>> gfortran   -fPIC  -g -O2  -c ormuv.f -o ormuv.o
>> gfortran   -fPIC  -g -O2  -c robcovf.f -o robcovf.o
>> clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup 
>> -single_module -multiply_defined suppress 
>> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rms.so 
>> init.o lrmfit.o mlmats.o ormuv.o robcovf.o 
>> -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 
>> -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm 
>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework 
>> -Wl,CoreFoundation
>> installing to 
>> /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs
>> ** R
>> ** demo
>> ** inst
>> ** preparing package for lazy loading
>> ** help
>> *** installing help indices
>> ** building package indices
>> ** testing if installed package can be loaded
>> Loading required package: lattice
>> Loading required package: sos
>> Loading required package: brew
>> Loading required package: rms
>> Loading required package: Hmisc
>> Loading required package: survival
>> Loading required package: Formula
>> Loading required package: stats
>> Loading required package: ggplot2
>> 
>> Attaching package: ‘Hmisc’
>> 
>> The following objects are masked from ‘package:base’:
>> 
>>  format.pval, round.POSIXt, trunc.POSIXt, units
>> 
>> Loading required package: SparseM
>> 
>> Attaching package: ‘SparseM’
>> 
>> The following object is masked from ‘package:base’:
>> 
>>  backsolve
>> 
>> Error: package or namespace load failed for ‘rms’ in dyn.load(file, DLLpath 
>> = DLLpath, ...):
>> unable to load shared object 
>> '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so':
>> dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so,
>>  6): Symbol not found: ___addtf3
>> Referenced from: /usr/local/lib/libquadmath.0.dylib
>> Expected in: /usr/local/lib/libgcc_s.1.dylib
>> in /usr/local/lib/libquadmath.0.dylib
>> ##-- 2017-05-04 --##
>> Loading required package: graphics
>> 
>> Attaching package: ‘graphics’
>> 
>> The following object is masked from ‘package:SparseM’:
>> 
>>  image
>> 
>> Error: package or namespace load failed for ‘rms’ in dyn.load(file, DLLpath 
>> = DLLpath, ...):
>> unable to load shared object 
>> '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so':
>> dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so,
>>  6): Symbol not found: ___addtf3
>> Referenced from: /usr/local/lib/libquadmath.0.dylib
>> Expected in: /usr/local/lib/libgcc_s.1.dylib
>> in /usr/local/lib/libquadmath.0.dylib
>> Error: loading failed
>> Execution halted
>> 
>> The downloaded source packages are in
>>  
>> ‘/private/var/folders/yq/m3j1jqtj6hq6s5mq_v0jn3s8gn/T/Rtmpplg8Th/downloaded_packages’
>> 
>> (WARNING: partial output only, ask package author to use Rprintf instead!)
>> ERROR: loading failed
>> * removing 
>> ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms’
>> * restoring previous 
>> ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms’
>> 
>> I get 

Re: [R-SIG-Mac] missing module when compiling R pkg:rms or external package SYMPHONY (in support of Bioc pkg symphony)

[Berend Hasselman]

> On 5 May 2017, at 03:12, David Winsemius  wrote:
> 
> Failing to get current rms package to compile (and appears that the CRAN 
> build machine fails as well). The penultimate version of rms succeeds.
> 
> Both from console and cmd-line I get this response in R 3.4.0 (just installed 
> today) running El Cap 10.11.6 with Xcode Version 8.2.1 (8C1002):
> 
> trying URL 'https://cran.cnr.berkeley.edu/src/contrib/rms_5.1-1.tar.gz'
> Content type 'application/x-gzip' length 521311 bytes (509 KB)
> ==
> downloaded 509 KB
> 
> Loading required package: lattice
> Loading required package: sos
> Loading required package: brew
> Loading required package: rms
> Loading required package: Hmisc
> Loading required package: survival
> Loading required package: Formula
> Loading required package: stats
> Loading required package: ggplot2
> 
> Attaching package: ‘Hmisc’
> 
> The following objects are masked from ‘package:base’:
> 
>   format.pval, round.POSIXt, trunc.POSIXt, units
> 
> Loading required package: SparseM
> 
> Attaching package: ‘SparseM’
> 
> The following object is masked from ‘package:base’:
> 
>   backsolve
> 
> ##-- 2017-05-04 --##
> Loading required package: graphics
> 
> Attaching package: ‘graphics’
> 
> The following object is masked from ‘package:SparseM’:
> 
>   image
> 
> * installing *source* package ‘rms’ ...
> ** package ‘rms’ successfully unpacked and MD5 sums checked
> ** libs
> clang -I/Library/Frameworks/R.framework/Resources/include  
> -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
> gfortran   -fPIC  -g -O2  -c lrmfit.f -o lrmfit.o
> gfortran   -fPIC  -g -O2  -c mlmats.f -o mlmats.o
> gfortran   -fPIC  -g -O2  -c ormuv.f -o ormuv.o
> gfortran   -fPIC  -g -O2  -c robcovf.f -o robcovf.o
> clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup 
> -single_module -multiply_defined suppress 
> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rms.so 
> init.o lrmfit.o mlmats.o ormuv.o robcovf.o 
> -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 
> -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm 
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework 
> -Wl,CoreFoundation
> installing to 
> /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs
> ** R
> ** demo
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> Loading required package: lattice
> Loading required package: sos
> Loading required package: brew
> Loading required package: rms
> Loading required package: Hmisc
> Loading required package: survival
> Loading required package: Formula
> Loading required package: stats
> Loading required package: ggplot2
> 
> Attaching package: ‘Hmisc’
> 
> The following objects are masked from ‘package:base’:
> 
>   format.pval, round.POSIXt, trunc.POSIXt, units
> 
> Loading required package: SparseM
> 
> Attaching package: ‘SparseM’
> 
> The following object is masked from ‘package:base’:
> 
>   backsolve
> 
> Error: package or namespace load failed for ‘rms’ in dyn.load(file, DLLpath = 
> DLLpath, ...):
> unable to load shared object 
> '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so':
> dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so,
>  6): Symbol not found: ___addtf3
> Referenced from: /usr/local/lib/libquadmath.0.dylib
> Expected in: /usr/local/lib/libgcc_s.1.dylib
> in /usr/local/lib/libquadmath.0.dylib
> ##-- 2017-05-04 --##
> Loading required package: graphics
> 
> Attaching package: ‘graphics’
> 
> The following object is masked from ‘package:SparseM’:
> 
>   image
> 
> Error: package or namespace load failed for ‘rms’ in dyn.load(file, DLLpath = 
> DLLpath, ...):
> unable to load shared object 
> '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so':
> dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so,
>  6): Symbol not found: ___addtf3
> Referenced from: /usr/local/lib/libquadmath.0.dylib
> Expected in: /usr/local/lib/libgcc_s.1.dylib
> in /usr/local/lib/libquadmath.0.dylib
> Error: loading failed
> Execution halted
> 
> The downloaded source packages are in
>   
> ‘/private/var/folders/yq/m3j1jqtj6hq6s5mq_v0jn3s8gn/T/Rtmpplg8Th/downloaded_packages’
> 
> (WARNING: partial output only, ask package author to use Rprintf instead!)
> ERROR: loading failed
> * removing 
> ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms’
> * restoring previous 
> ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms’
> 
> I get the same result with this (minus the request "to use Rprinf instead!"
> 
> $ R CMD INSTALL /Users/davidwinsemius/Downloads/rms_5.1-1.tar.gz 
> 
> Reported to Frank but he has seen no problems in his Linux