[R] Cannot find ldfortran (R on Cygwin)

Duncan Murdoch murdoch.duncan at gmail.com
Thu Apr 11 14:05:53 CEST 2013

On 13-04-11 2:57 AM, Lalitha Viswanathan wrote:
> Hi
> I am new to Cygwin and Linux.
> I installed R under Cygwin as part of the setup
> I chose "All" during installation, for all packages. So I have the FULL
> installlation of cygwin up and running, including gfortran.
> *Under Cygwin, how do I check and configure the path to the various
> libraries?*

We don't support Cygwin, and the R version distributed with Cygwin 
(produced by someone else) doesn't pass the tests.  I recommend that you 
avoid it.  Use the Windows native version instead; it's the one we support.

Duncan Murdoch

>   I am trying below command and it says, cannot find "lgfortran"
> But I have installed gfortran from "All" and "Libs" during setup
> I access R as below
> 1) R
> 2) install.pacakges('vegan')
> 3) After choosing mirror, here is the output I get
> * installing *source* package ‘vegan’ ...
> ** package ‘vegan’ successfully unpacked and MD5 sums checked
> ** libs
> gfortran     -g -O2 -pipe   -c cepin.f -o cepin.o
> gcc -I/usr/lib/R/include -DNDEBUG        -g -O2 -pipe  -std=gnu99  -c
> data2hill.c -o data2hill.o
> gfortran     -g -O2 -pipe   -c decorana.f -o decorana.o
> gcc -I/usr/lib/R/include -DNDEBUG        -g -O2 -pipe  -std=gnu99  -c
> goffactor.c -o goffactor.o
> gfortran     -g -O2 -pipe   -c monoMDS.f -o monoMDS.o
> gcc -I/usr/lib/R/include -DNDEBUG        -g -O2 -pipe  -std=gnu99  -c
> nestedness.c -o nestedness.o
> gfortran     -g -O2 -pipe   -c ordering.f -o ordering.o
> gcc -I/usr/lib/R/include -DNDEBUG        -g -O2 -pipe  -std=gnu99  -c
> pnpoly.c -o pnpoly.o
> gcc -I/usr/lib/R/include -DNDEBUG        -g -O2 -pipe  -std=gnu99  -c
> stepacross.c -o stepacross.o
> gcc -I/usr/lib/R/include -DNDEBUG        -g -O2 -pipe  -std=gnu99  -c
> vegdist.c -o vegdist.o
> *gcc -shared -o vegan.dll cepin.o data2hill.o decorana.o goffactor.o
> monoMDS.o nestedness.o ordering.o pnpoly.o stepacross.o vegdist.o
> -lgfortran -lcygwin -luser32 -lkernel32 -ladvapi32 -lshell32
> -L/usr/lib/R/lib -lR /usr/lib/libintl.dll.a -L/usr/lib/ncursesw
> /usr/lib/libiconv.dll.a
> /usr/lib/../lib/gcc/i686-pc-cygwin/4.5.3/../../../../i686-pc-cygwin/bin/ld:
> cannot find -lgfortran
> *collect2: ld returned 1 exit status
> /usr/lib/R/share/make/shlib.mk:6: recipe for target `vegan.dll' failed
> make: *** [vegan.dll] Error 1
> ERROR: compilation failed for package ‘vegan’
> * removing ‘/usr/lib/R/site-library/vegan’
> The downloaded source packages are in
>          ‘/tmp/RtmpLmqud4/downloaded_packages’
> Warning message:
> In install.packages("vegan") :
>    installation of package ‘vegan’ had non-zero exit status
> 	[[alternative HTML version deleted]]
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