Re: [Fink-beginners] phase compiling: fcgi-pm5124-0.74-1 failed

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/w

Re: [Fink-beginners] phase compiling: fcgi-pm5124-0.74-1 failed

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/w

Re: [Fink-beginners] can't get started

Dr. Hansen, Thanks. But keep in mind this is a beginner's forum. Nothing at Oracle says JDK (or Java Development Kit). If I search on Java Development Kit I get hits, but not from sites I know to trust. Wikipedia's description of JDK indicates 3 alternatives: Java SE, Java EE, Java ME. It

Re: [Fink-beginners] problem with Fink reinstallation after Yosemite update

Removing Fink completely and reinstalling worked fine. Thanks! On Fri, Nov 28, 2014 at 3:35 PM, Alexander Hansen < alexanderk.han...@gmail.com> wrote: > > > On Nov 28, 2014, at 12:31 PM, Jessilyn Dunn > wrote: > > What now jessilyndunn in fink-0.38.2? $ $(test -x /usr/bin/gcc) && echo > "gcc OK"

Re: [Fink-beginners] can't get started

Don’t use the JREl which is completely and utterly useless for our purposes. Use the JDK, because Fink needs to build against Java.. We’ll try to make that more clear, but Java on OS X is a giant mess. And apologies for the websites that we _have absolutely no control over_, but we try to do

Re: [Fink-beginners] can't get started

I just started fink to ask the exact same question. After fighting this in circles for about an hour and a half I think my request for help might have been a little more laden with frustration. I can test the JRE installation and can see it in the associated web pages test link. I can also see t

[Fink-beginners] can't get started

Following instructions at Download Fink Source Release at finkproject.org , when I get to ./bootstrap, after prompt to use root privileges, picking sudo and entering password, I get: Please install Java SDK before re-attempting fink bootstrap and a pop-up telling me I

Re: [Fink-beginners] problem with Fink reinstallation after Yosemite update

> On Nov 28, 2014, at 12:31 PM, Jessilyn Dunn wrote: > > What now jessilyndunn in fink-0.38.2? $ $(test -x /usr/bin/gcc) && echo "gcc > OK" > gcc OK > What now jessilyndunn in fink-0.38.2? $ $(test -x /usr/bin/make) && echo > "make OK" > make OK > What now jessilyndunn in fink-0.38.2? $ $(tes

Re: [Fink-beginners] problem with Fink reinstallation after Yosemite update

What now jessilyndunn in fink-0.38.2? $ $(test -x /usr/bin/gcc) && echo "gcc OK" gcc OK What now jessilyndunn in fink-0.38.2? $ $(test -x /usr/bin/make) && echo "make OK" make OK What now jessilyndunn in fink-0.38.2? $ $(test -d /usr/include) && echo "/usr/include OK" /usr/include OK On Fri,

Re: [Fink-beginners] problem with Fink reinstallation after Yosemite update

> On Nov 28, 2014, at 12:19 PM, Jessilyn Dunn wrote: > > > thanks. I get 0 files and the following folders: > total 0 > drwxr-xr-x 1058 root wheel 35972 Nov 28 12:29 bin > drwxr-xr-x 257 root wheel 8738 Nov 28 12:22 include > drwxr-xr-x 281 root wheel 9554 Nov 28 14:26 lib > drwxr

Re: [Fink-beginners] problem with Fink reinstallation after Yosemite update

thanks. I get 0 files and the following folders: total 0 drwxr-xr-x 1058 root wheel 35972 Nov 28 12:29 bin drwxr-xr-x 257 root wheel 8738 Nov 28 12:22 include drwxr-xr-x 281 root wheel 9554 Nov 28 14:26 lib drwxr-xr-x 172 root wheel 5848 Nov 28 12:35 libexec drwxr-xr-x13

Re: [Fink-beginners] problem with Fink reinstallation after Yosemite update

> On Nov 28, 2014, at 12:15 PM, Jessilyn Dunn wrote: > > yes, it exists and contains 1248 files. Is there any file in particular > needed here? > No. The test is literally just whether that is a directory. For completeness, what do you get from ls -l /usr ? -- Alexander Hansen, Ph.D.

Re: [Fink-beginners] problem with Fink reinstallation after Yosemite update

yes, it exists and contains 1248 files. Is there any file in particular needed here? On Fri, Nov 28, 2014 at 3:11 PM, Alexander Hansen < alexanderk.han...@gmail.com> wrote: > > On Nov 28, 2014, at 11:59 AM, Jessilyn Dunn > wrote: > > Thanks, I get: > $ ./fink-virtual-pkgs --debug > -bash: ./fink

Re: [Fink-beginners] problem with Fink reinstallation after Yosemite update

> On Nov 28, 2014, at 11:59 AM, Jessilyn Dunn wrote: > > Thanks, I get: > $ ./fink-virtual-pkgs --debug > -bash: ./fink-virtual-pkgs: No such file or directory > > but the fink-virtual-pkgs is there: > ls -l fink-virt* > -rwxr-xr-x@ 1 jessilyndunn staff 6223 Oct 29 14:33 fink-virtual-pkgs.in

Re: [Fink-beginners] problem with Fink reinstallation after Yosemite update

Thanks, I get: $ ./fink-virtual-pkgs --debug -bash: ./fink-virtual-pkgs: No such file or directory but the fink-virtual-pkgs is there: ls -l fink-virt* -rwxr-xr-x@ 1 jessilyndunn staff 6223 Oct 29 14:33 fink-virtual-pkgs.in On Fri, Nov 28, 2014 at 2:51 PM, Alexander Hansen < alexanderk.han.

Re: [Fink-beginners] problem with Fink reinstallation after Yosemite update

> On Nov 28, 2014, at 11:45 AM, Jessilyn Dunn wrote: > > Thanks, and sorry about that. For gcc version, I get: > Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr > --with-gxx-include-dir=/usr/include/c++/4.2.1 > Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5s

Re: [Fink-beginners] problem with Fink reinstallation after Yosemite update

Thanks, and sorry about that. For gcc version, I get: Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn) Target: x86_64-apple-darwin14.0.0 Thread model: posix What

Re: [Fink-beginners] problem with Fink reinstallation after Yosemite update

> On Nov 28, 2014, at 11:29 AM, Jessilyn Dunn wrote: > > Thank you very much! It appears that I have both make and gcc: > > -rwxr-xr-x 1 root wheel 14160 Sep 26 22:06 /usr/bin/make > -rwxr-xr-x 1 root wheel 14160 Sep 26 22:06 /usr/bin/gcc > > GNU Make 3.81 > Copyright (C) 2006 Free Soft

Re: [Fink-beginners] problem with Fink reinstallation after Yosemite update

Thank you very much! It appears that I have both make and gcc: -rwxr-xr-x 1 root wheel 14160 Sep 26 22:06 /usr/bin/make -rwxr-xr-x 1 root wheel 14160 Sep 26 22:06 /usr/bin/gcc GNU Make 3.81 Copyright (C) 2006 Free Software Foundation, Inc. This is free software; see the source for copy

Re: [Fink-beginners] problem with Fink reinstallation after Yosemite update

> On Nov 28, 2014, at 10:05 AM, Jessilyn Dunn wrote: > > Hello, > I am having some trouble getting Fink reinstalled. I had previously used Fink > on Mavericks before updating to Yosemite, but after updating to Yosemite, > Fink also appears to need an update (I used the documentation to remove

[Fink-beginners] problem with Fink reinstallation after Yosemite update

Hello, I am having some trouble getting Fink reinstalled. I had previously used Fink on Mavericks before updating to Yosemite, but after updating to Yosemite, Fink also appears to need an update (I used the documentation to remove the old Fink and am now attempting to reinstall using the first time

Re: [Fink-beginners] phase compiling: fcgi-pm5124-0.74-1 failed

On Nov 26, 2014, at 6:38 PM, Prabhjeet Basra 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

Re: [Fink-beginners] phase compiling: fcgi-pm5124-0.74-1 failed

> On Nov 26, 2014, at 6:38 PM, Prabhjeet Basra > wrote: > > Hi > > 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

[Fink-beginners] phase compiling: fcgi-pm5124-0.74-1 failed

Hi 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 "/usr/bin/arch" -x86_64 perl5.12.4 FCGI.PL FCGI.pm R