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Issues with installation instructions under OSX #2

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bguiastr opened this issue Dec 6, 2016 · 2 comments
Closed

Issues with installation instructions under OSX #2

bguiastr opened this issue Dec 6, 2016 · 2 comments

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@bguiastr
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bguiastr commented Dec 6, 2016

In the Installing_nlmixr.pdf file they are a couple issues for the OSX instructions:

  1. Is it currently not possible to copy and paste commands in R from the online pdf version on github > Suggest to change to an HTML format
  2. To install packages from github I believe that the syntax should be: devtools::install_github('nlmixrdevelopment/nlmixr ') not devtools::install_github('nlmixrdevelopment/nlmixr', repos = NULL, type = 'source') which gave erros. The same thing applies to the RxODE.
  3. For RxODE I got the following error even though I have gfortran (v.6.1) installed.
* installing *source* package ‘RxODE’ ...
** libs
** arch - 
echo "make libodeaux.a in ode/ ..."
make libodeaux.a in ode/ ...
(cd ode; make CC="`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CC`" FC="`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config FC`" CFLAGS="`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CFLAGS` -fPIC" FFLAGS="`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config FFLAGS` -fPIC" libodeaux.a)
gfortran-4.8 -g -O2 -fPIC  -c -o opkda2.o opkda2.f
make[1]: gfortran-4.8: No such file or directory
make[1]: *** [opkda2.o] Error 1
make: *** [libodeaux] Error 2
ERROR: compilation failed for package ‘RxODE’

I was able to solve the issue using this StackOverflow post.

  1. I just came to realize that RxODE is now available on CRAN and this should be mentioned in the instructions it would prevent the installation issues.
@RikSchoemaker
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Dear Benjamin,

Thank you for sharing your experience in installing on OS X! I have updated the installation instructions, mentioning that RxODE is now available on CRAN (make sure you get the version after 1 December), and I have added an rtf version of the installation document as well to make copying commands easier.

Kind regards,

Rik

@bguiastr
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bguiastr commented Dec 7, 2016

Great thanks !

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