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Question: Can not install deSolve
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gravatar for geparada88
8 months ago by
geparada8810
geparada8810 wrote:

Hello,

I updated R, and now I can not install deSolve. I am getting a compilation error:
 

install.packages("deSolve")
trying URL 'https://cran.rstudio.com/src/contrib/deSolve_1.14.tar.gz'
Content type 'application/x-gzip' length 2341489 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

* installing *source* package ‘deSolve’ ...
** package ‘deSolve’ successfully unpacked and MD5 sums checked
** libs
clang -I/Users/gp7/miniconda2/lib/R/include -DNDEBUG  -I/Users/gp7/miniconda2/include    -fPIC  -I/Users/gp7/miniconda2/include  -c DLLutil.c -o DLLutil.o
clang -I/Users/gp7/miniconda2/lib/R/include -DNDEBUG  -I/Users/gp7/miniconda2/include    -fPIC  -I/Users/gp7/miniconda2/include  -c R_init_deSolve.c -o R_init_deSolve.o
clang -I/Users/gp7/miniconda2/lib/R/include -DNDEBUG  -I/Users/gp7/miniconda2/include    -fPIC  -I/Users/gp7/miniconda2/include  -c brent.c -o brent.o
clang -I/Users/gp7/miniconda2/lib/R/include -DNDEBUG  -I/Users/gp7/miniconda2/include    -fPIC  -I/Users/gp7/miniconda2/include  -c call_daspk.c -o call_daspk.o
clang -I/Users/gp7/miniconda2/lib/R/include -DNDEBUG  -I/Users/gp7/miniconda2/include    -fPIC  -I/Users/gp7/miniconda2/include  -c call_euler.c -o call_euler.o
clang -I/Users/gp7/miniconda2/lib/R/include -DNDEBUG  -I/Users/gp7/miniconda2/include    -fPIC  -I/Users/gp7/miniconda2/include  -c call_iteration.c -o call_iteration.o
clang -I/Users/gp7/miniconda2/lib/R/include -DNDEBUG  -I/Users/gp7/miniconda2/include    -fPIC  -I/Users/gp7/miniconda2/include  -c call_lsoda.c -o call_lsoda.o
clang -I/Users/gp7/miniconda2/lib/R/include -DNDEBUG  -I/Users/gp7/miniconda2/include    -fPIC  -I/Users/gp7/miniconda2/include  -c call_radau.c -o call_radau.o
clang -I/Users/gp7/miniconda2/lib/R/include -DNDEBUG  -I/Users/gp7/miniconda2/include    -fPIC  -I/Users/gp7/miniconda2/include  -c call_rk4.c -o call_rk4.o
clang -I/Users/gp7/miniconda2/lib/R/include -DNDEBUG  -I/Users/gp7/miniconda2/include    -fPIC  -I/Users/gp7/miniconda2/include  -c call_rkAuto.c -o call_rkAuto.o
clang -I/Users/gp7/miniconda2/lib/R/include -DNDEBUG  -I/Users/gp7/miniconda2/include    -fPIC  -I/Users/gp7/miniconda2/include  -c call_rkFixed.c -o call_rkFixed.o
clang -I/Users/gp7/miniconda2/lib/R/include -DNDEBUG  -I/Users/gp7/miniconda2/include    -fPIC  -I/Users/gp7/miniconda2/include  -c call_rkImplicit.c -o call_rkImplicit.o
clang -I/Users/gp7/miniconda2/lib/R/include -DNDEBUG  -I/Users/gp7/miniconda2/include    -fPIC  -I/Users/gp7/miniconda2/include  -c call_zvode.c -o call_zvode.o
gfortran   -fPIC  -I/Users/gp7/miniconda2/include -L/Users/gp7/miniconda2/lib  -c daux.f -o daux.o
make: gfortran: No such file or directory
make: *** [daux.o] Error 1
ERROR: compilation failed for package ‘deSolve’
* removing ‘/Users/gp7/miniconda2/lib/R/library/deSolve’
Warning in install.packages :
  installation of package ‘deSolve’ had non-zero exit status

The downloaded source packages are in
    ‘/private/var/folders/0h/z3ycz6gx4rj5_frl6r5wnvbw000g0g/T/RtmpGaoXm9/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done

This is my R setup:

 

R.Version ()
$platform
[1] "x86_64-apple-darwin11.4.2"

$arch
[1] "x86_64"

$os
[1] "darwin11.4.2"

$system
[1] "x86_64, darwin11.4.2"

$status
[1] ""

$major
[1] "3"

$minor
[1] "3.2"

$year
[1] "2016"

$month
[1] "10"

$day
[1] "31"

$`svn rev`
[1] "71607"

$language
[1] "R"

$version.string
[1] "R version 3.3.2 (2016-10-31)"

$nickname
[1] "Sincere Pumpkin Patch"

 

 

Any help will be really appreciated!

 

ADD COMMENTlink modified 8 months ago by Martin Morgan ♦♦ 20k • written 8 months ago by geparada8810
2
gravatar for Martin Morgan
8 months ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

Not a Bioconductor package so not strictly relevant here, but you need to install a gfortran compiler following instructions to install 'mandatory tools' and in the and MacOS FAQ.

ADD COMMENTlink written 8 months ago by Martin Morgan ♦♦ 20k

Thank you Martin,
I realised this after posting the question. I'll be more careful next time.

ADD REPLYlink written 8 months ago by geparada8810
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