Hi,
I am having a similar problem installing Bioperl (I used $ fink install
bioperl-pm5162)

and received the error:

Failed: phase compiling: fcgi-pm5162-0.74-1 failed

(before this error, everything seemed to be running smoothly... see below)

New package:
dists/stable/main/binary-darwin-x86_64/web/libtidyp-dev_1.04-1_darwin-x86_64.deb

New package:
dists/stable/main/binary-darwin-x86_64/web/libtidyp-shlibs_1.04-1_darwin-x86_64.deb

New package:
dists/stable/main/binary-darwin-x86_64/web/tidyp_1.04-1_darwin-x86_64.deb

New package:
dists/stable/main/binary-darwin-x86_64/x11/xdg-base_0.8-2_darwin-x86_64.deb

For further details, my system information is:
Package manager version: 0.38.2
Distribution version: selfupdate-rsync Fri Nov 28 18:47:48 2014, 10.10,
x86_64
Trees: local/main stable/main stable/crypto
Xcode.app: 6.1
Xcode command-line tools: 6.1.0.0.1.1413057044
Max. Fink build jobs:  4

Thank you!
Jessilyn

On Fri, Nov 28, 2014 at 1:41 PM, Daniel Macks <dma...@netspace.org> wrote:

>      On Nov 26, 2014, at 6:38 PM, Prabhjeet Basra
> <prabhjeetba...@cmail.carleton.ca> wrote:
> >
> >  I am using:
> >
> >  Package manager version: 0.38.2
> >  Distribution version: selfupdate-rsync Wed Nov 26 20:33:40 2014,
> > 10.9, x86_64
> >  Trees: local/main stable/main
> >  Xcode.app: 6.1​
> >
> >  And I'm trying to install BioPerl and I keep getting this error
> >
> >  <snip>
> >
> >       Generating FCGI.pm  cp FCGI.pm blib/arch/FCGI.pm
> >  "/usr/bin/arch" -x86_64 perl5.12.4 -x86_64 perl5.12.4 "-Iblib/arch"
> > "-Iblib/lib" FCGI.XL FCGI.xs
> >  "/usr/bin/arch" -x86_64 perl5.12.4 -x86_64 perl5.12.4 "-Iblib/arch"
> > "-Iblib/lib" echo.PL echo.fpl
> >  "/usr/bin/arch" -x86_64 perl5.12.4 -x86_64 perl5.12.4 "-Iblib/arch"
> > "-Iblib/lib" remote.PL remote.fpl
> >  Can't open perl script "perl5.12.4": No such file or directory
> >  Can't open perl script "perl5.12.4": No such file or directory
> >  Can't open perl script "perl5.12.4": No such file or directory
>
>    >
> >  <snip>
> >
> >       Failed: phase compiling: fcgi-pm5124-0.74-1 failed
>
>   On Fri, 28 Nov 2014 10:15:29 -0800, Alexander Hansen
> <alexanderk.han...@gmail.com> wrote:
>   >
> >  I don’t reproduce this.  On my own 10.9/Xcode 6.1 setup I get:
> >
> >  Generating FCGI.pm
> >  cp FCGI.pm blib/arch/FCGI.pm
> >  /usr/bin/arch -x86_64 perl5.12.4 "-Iblib/arch" "-Iblib/lib" FCGI.XL
> FCGI.xs
>
>   Prabhjeet: was your computer previously running OS X 10.8 and then
> you updated it to 10.9?
>
>   dan
>
>   --
> Daniel Macks
> dma...@netspace.org
>
>
>
>
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