Re: [circos] troubles installing ...on my mac

[Paulo Nuin]

Hi Camilla

Can you post the output for the make, with the error? Also, where are you getting this error (which library)?

Thanks
Paulo


On 2012-06-12, at 2:14 PM, Camilla LN wrote:

> Heia,
> I am trying to follow the instructions on this page
> http://zientzilaria.heroku.com/blog/2012/06/03/installing-circos-on-os-x/
>
> I keep getting the error message "Launch of "make" failed: the PowerPC architecture is no longer supported." when I do the make command.
> Any suggestions as to what I should do?
> I am running mac osx 10.74
>
> Thanks,
> Camilla
>
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[Camilla LN]

Heia,
Yes I get this message everytime I do make.
This is what I get:
misschandra-lt:src cnesbo$ make

Launch of "make" failed: the PowerPC architecture is no longer supported.

Camilla

On Tuesday, June 12, 2012 1:07:20 PM UTC-6, nuin wrote:

Hi Camilla

Can you post the output for the make, with the error? Also, where are you getting this error (which library)?

Thanks
Paulo


On 2012-06-12, at 2:14 PM, Camilla LN wrote:

> Heia,
> I am trying to follow the instructions on this page
> http://zientzilaria.heroku.com/blog/2012/06/03/installing-circos-on-os-x/
>
> I keep getting the error message "Launch of "make" failed: the PowerPC architecture is no longer supported."  when I do the make command.
> Any suggestions as to what I should do?
> I am running mac osx 10.74
>
> Thanks,
> Camilla
>
> --
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[Paulo Nuin]

You seem to have an old version of Xcode running, can you try updating it? What OS X version are you using?

Cheers
Paulo

On 2012-06-13, at 12:04 PM, Camilla LN wrote:

> Heia,
> Yes I get this message everytime I do make.
> This is what I get:
> misschandra-lt:src cnesbo$ make
> Launch of "make" failed: the PowerPC architecture is no longer supported.
>
> Camilla
>
> On Tuesday, June 12, 2012 1:07:20 PM UTC-6, nuin wrote:
> Hi Camilla
>
> Can you post the output for the make, with the error? Also, where are you getting this error (which library)?
>
> Thanks
> Paulo
>
>
> On 2012-06-12, at 2:14 PM, Camilla LN wrote:
>
> > Heia,
> > I am trying to follow the instructions on this page
> > http://zientzilaria.heroku.com/blog/2012/06/03/installing-circos-on-os-x/
> >
> > I keep getting the error message "Launch of "make" failed: the PowerPC architecture is no longer supported." when I do the make command.
> > Any suggestions as to what I should do?
> > I am running mac osx 10.74
> >
> > Thanks,
> > Camilla
> >
> > --
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[Martin Krzywinski]

Is your Mac an old model which uses the PowerPC chip?

I am a late arrival into the Mac os x world, so I am not sure whether Xcode, the Mac os x dev addon contains the developers tools for PowerPC. Its version of make may require intel.

Martin Krzywinski

http://mkweb.bcgsc.ca

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[Camilla LN]

No - my mac is almost brand new. I am running MacOS X 10.7.4

[Paulo Nuin]

Hi

Try checking which make you have

>which make

and try updating your Xcode (if not updated yet).

Let us know

Cheers
Paulo

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[Camilla LN]

I hope that sorted out my problem.
I did which

misschandra-lt:src cnesbo$ make
Launch of "make" failed: the PowerPC architecture is no longer supported.

misschandra-lt:src cnesbo$ which make
/sw/bin/make
misschandra-lt:src cnesbo$ which Xcode
misschandra-lt:src cnesbo$

It looks like I have no Xcode so I am installing that now.

Thanks a million.
Camilla

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[Paulo Nuin]

Hi

This make that you have might not be the right one. Usually, it's installed

/usr/bin/make

maybe it was installed with something else.

You won't see Xcode by using which, as it's only a command line app checker. If you don't have a directory "Developer" in our installation, installing Xcode is the right choice.

Let me know how it goes.

Cheers
Paulo

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[Camilla LN]

Heia,
I am back to installing again. I installed Xcode. (it might already have been there I guess)
But my make is still not right.
The error message is the same:
biosci-pc:srctemp cnesbo$ make

Launch of "make" failed: the PowerPC architecture is no longer supported.

biosci-pc:srctemp cnesbo$ which make
/sw/bin/make
biosci-pc:srctemp cnesbo$

How do I get the right make?
Thanks a million for your help with this!!
Camilla

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[Paulo Nuin]

Try finding any other make

>sudo find / -name make

and report here.

Paulo

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[Camilla LN]

I cant see anyother make
this is what  got: (a lot of Permission denied)

biosci-pc:srctemp cnesbo$ >sudo find / -name make
find: /.DocumentRevisions-V100: Permission denied
find: /.Spotlight-V100: Permission denied
find: /.Trashes: Permission denied

find: /dev/fd/3: Not a directory
find: /dev/fd/4: Not a directory
find: /Library/Application Support/Apple/ParentalControls/Users: Permission denied
find: /Library/Application Support/BOINC Data/locale: Permission denied
find: /Library/Application Support/BOINC Data/skins: Permission denied
find: /Library/Application Support/BOINC Data/switcher: Permission denied
find: /Library/Caches/com.google.UpdateEngine.Framework.0: Permission denied
find: /Library/Server/Mail/Data/mta: Permission denied
find: /Library/Server/Mail/Data/spool/active: Permission denied
find: /Library/Server/Mail/Data/spool/bounce: Permission denied
find: /Library/Server/Mail/Data/spool/corrupt: Permission denied
find: /Library/Server/Mail/Data/spool/defer: Permission denied
find: /Library/Server/Mail/Data/spool/deferred: Permission denied
find: /Library/Server/Mail/Data/spool/flush: Permission denied
find: /Library/Server/Mail/Data/spool/hold: Permission denied
find: /Library/Server/Mail/Data/spool/incoming: Permission denied
find: /Library/Server/Mail/Data/spool/maildrop: Permission denied
find: /Library/Server/Mail/Data/spool/private: Permission denied
find: /Library/Server/Mail/Data/spool/public: Permission denied
find: /Library/Server/Mail/Data/spool/saved: Permission denied
find: /Library/Server/Mail/Data/spool/trace: Permission denied
find: /private/etc/cups/certs: Permission denied
find: /private/tmp/launchd-423.jD5sA3: Permission denied
find: /private/var/agentx: Permission denied
find: /private/var/amavis: Permission denied
find: /private/var/at/tabs: Permission denied
find: /private/var/at/tmp: Permission denied
find: /private/var/audit: Permission denied
find: /private/var/backups: Permission denied
find: /private/var/db/dhcpclient: Permission denied
find: /private/var/db/dslocal/nodes/Default: Permission denied
find: /private/var/db/krb5kdc: Permission denied
find: /private/var/db/launchd.db/com.apple.launchd.peruser.0: Permission denied
find: /private/var/db/launchd.db/com.apple.launchd.peruser.1: Permission denied
find: /private/var/db/launchd.db/com.apple.launchd.peruser.212: Permission denied
find: /private/var/db/launchd.db/com.apple.launchd.peruser.222: Permission denied
find: /private/var/db/launchd.db/com.apple.launchd.peruser.26: Permission denied
find: /private/var/db/launchd.db/com.apple.launchd.peruser.4294967294: Permission denied
find: /private/var/db/launchd.db/com.apple.launchd.peruser.89: Permission denied
find: /private/var/db/launchd.db/com.apple.launchd.peruser.92: Permission denied
find: /private/var/db/launchd.db/com.apple.launchd.peruser.97: Permission denied
find: /private/var/db/sudo: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/0/com.apple.revisiond.temp: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/C: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/Cleanup At Startup: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n000003800000t/C: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n000003800000t/T: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n0000084000021/C: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n0000084000021/T: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n00000b400002s/C: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n00000b400002s/T: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n00000bh00002w/C: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n00000bh00002w/T: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n00000c4000031/C: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n00000c4000031/T: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n00000s0000068/C: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n00000s0000068/T: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n00000s800006_/T: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n00000sm00006d/C: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n00000sm00006d/T: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n00000th00006m/C: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n00000th00006m/T: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n00000tm00006n/T: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n00000vr00006y/C: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_n00000vr00006y/T: Permission denied
find: /private/var/folders/zz/zyxvpxvq6csfxvn_ngzzzzzvzzzzzy/C: Permission denied
find: /private/var/jabberd: Permission denied
find: /private/var/log/krb5kdc: Permission denied
find: /private/var/pgsql_socket: Permission denied
find: /private/var/root: Permission denied
find: /private/var/run/mds: Permission denied
find: /private/var/spool/cups: Permission denied
find: /private/var/spool/fax: Permission denied
find: /private/var/spool/mqueue: Permission denied
find: /private/var/tmp/launchd: Permission denied
find: /private/var/virusmails: Permission denied
find: /sw/var/mysql/mysql: Permission denied
find: /sw/var/mysql/test: Permission denied
find: /System/Library/DirectoryServices/DefaultLocalDB/Default: Permission denied
find: /System/Library/User Template: Permission denied
find: /Users/cnesbo/.cpan/build/HTML-Template-2.8/blib/temp_cache_dir: Permission denied
find: /Volumes/Geneious_mac64_5_6_4/.Trashes: Permission denied
biosci-pc:srctemp cnesbo$

[Paulo Nuin]

Strange that with sudo you got all this. I will have to think about a solution for you.

I let you know

Paulo

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[Camilla LN]

Ok Thanks! I am at ASM now - will get back to installing when I return back,
Camilla

[Martin Krzywinski]

Looks like your make is being taken from a Fink install

http://www.finkproject.org/

See this thread -

https://discussions.apple.com/thread/3199064?start=0&tstart=0

Remove /sw from your PATH. The canonical make should be from

/usr/bin/make

Martin Krzywinski

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[Paulo Nuin]

Sounds reasonable I guess. I haven't though of Fink, maybe the last time I used it was still OS X Tiger.

Paulo

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Paulo Nuin

[Camilla LN]

Thanks for the suggestion Martin. Could you tell me how I remove /sw?
I am just not very computer-litterat and dont want to completely destroy my mca.
Thank you so much for your help,
Camilla

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[Paulo Nuin]

Just try removing from your path, at .bashrc, or .bash_profile. You should find another make on /usr/bin. Or just run make with

/usr/bin/make

You have to restart terminal for your new path to be enabled.

Paulo

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[Camilla LN]

Thanks for getting back to me.
Sorry to be so stupid, but I am not sure how to remove a path.
Do I type rm something ?

If I want to run make with /usr/bin/make - what do I type to do that?
Thanks again
Camilla

[Paulo Nuin]

On 2012-06-21, at 12:54 PM, Camilla LN wrote:

Thanks for getting back to me.
Sorry to be so stupid, but I am not sure how to remove a path.
Do I type rm something ?

You have to edit the PATH variable in the file .bash_profile, or .bashrc.

If I want to run make with /usr/bin/make - what do I type to do that?

You type just that

/usr/bin/make

as long as make is that location.

Paulo

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[Martin Krzywinski]

Or at the terminal, prefix your current PATH with /usr/bin

# your current path - presumably, /sw is in there somewhere

> echo $PATH

/Users/martink/Library/Application Support/GoodSync:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin

# add /usr/bin to the front, so that it supersedes any other directory

> export PATH=/usr/bin/:$PATH

> which make

/usr/bin/make

This will work only for your current login session.

This is better than deleting /sw. 

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

[Camilla LN]

hmm I tried to do that ... but I dont think it worked (?)

This is what I get

dhcp184-48-38-46:srctemp cnesbo$ echo $PATH
/sw/bin:/sw/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/X11R6/bin
dhcp184-48-38-46:srctemp cnesbo$ export PATH=/usr/bin/:$PATH
dhcp184-48-38-46:srctemp cnesbo$ which make
/sw/bin/make

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[Camilla LN]

Heia,
I tried to run make like you suggested .. but got
dhcp184-48-38-46:srctemp cnesbo$ /usr/bin/make
-bash: /usr/bin/make: No such file or directory

On Thursday, June 21, 2012 10:27:39 AM UTC-6, nuin wrote:

[Paulo Nuin]

/usr/bin, /usr/local/bin are already in your path, but /sw/bin is taking precedence. Just run make with

/usr/bin/make

and see what happens.

Paulo

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[Paulo Nuin]

Ok, I just wrote about that. It seems that you haven't installed Xcode and accessories correctly.

Try running

gcc -v

and let us know.


Cheers
Paulo

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[Martin Krzywinski]

Do you have make anywhere else on your system?

> locate make | grep make$

/usr/bin/automake

/usr/bin/gmake

/usr/bin/imake

/usr/bin/make

...

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

[Camilla LN]

Really...! I tried installing it - but I guess something went wrong.
This is what I got fro your command:
dhcp184-48-38-46:srctemp cnesbo$ gcc -v
-bash: gcc: command not found

[Camilla LN]

...I got this
dhcp184-48-38-46:srctemp cnesbo$ locate make | grep make$

WARNING: The locate database (/var/db/locate.database) does not exist.
To create the database, run the following command:

  sudo launchctl load -w /System/Library/LaunchDaemons/com.apple.locate.plist

Please be aware that the database can take some time to generate; once
the database has been created, this message will no longer appear.

Should I make the database?

I am ready to give this up soon :)

[Paulo Nuin]

Yes, make the database. Or try

sudo find / -name make

Cheers
Paulo

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[Martin Krzywinski]

If you can't find gcc, then something went wrong with the xcode installation.

Can you try to install again? Do so off your Mac OS X distribution DVD.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Paulo Nuin]

Or you can download from the AppStore

http://itunes.apple.com/us/app/xcode/id497799835?ls=1&mt=12

What remind me, if you just downloaded from the AppStore you actually need to install it after downloading, it's not just downloading as most Apps. Open the Launchpad and try to find the icon for Xcode install and click on it.

Cheers
Paulo

[Camilla LN]

I did do the install - not just download. And it keeps telling me its installed.
There must be something utterly wrong with my Mac.
I will try installing on the Mac in the lab and see if I can get it working there ....

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[Martin Krzywinski]

Check for make in

/Developer/usr/bin/make

/Applications/Xcode.app/Contents/Developer/usr/bin

http://stackoverflow.com/questions/6767481/where-can-i-find-make-program-for-mac-os-x-lion

Martin Krzywinski

science + art

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[Camilla LN]

My applications - and Xcode are not in 'my' users directory - but on the 'Harddrive' directory .. could that be a problem?
Make is in the Xcode directory in Applications ..

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[Martin Krzywinski]

Add the directory where make resides to the front of your PATH and you're good to go.

Martin Krzywinski

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[Camilla LN]

Heia,
I finally found out what the problem with make was. In Xcode I had to go and 'install command line tools' in preferences.
But I am still having issues.
I have followed the recipe here "http://zientzilaria.heroku.com/blog/2012/06/03/installing-circos-on-os-x/"

but when I run for instance " install Config::General" I get this:

cpan[1]> install Config::General
Going to read '/Users/cnesbo/.cpan/Metadata'
  Database was generated on Sun, 15 Jul 2012 09:51:03 GMT
Running install for module 'Config::General'
Running make for T/TL/TLINDEN/Config-General-2.50.tar.gz
Checksum for /Users/cnesbo/.cpan/sources/authors/id/T/TL/TLINDEN/Config-General-2.50.tar.gz ok
Scanning cache /Users/cnesbo/.cpan/build for sizes
..............................................................I have neither the -x permission nor the permission to change the permission; can only partially estimate disk usage of 'temp_cache_dir'
Can't cd to (/Users/cnesbo/.cpan/build/HTML-Template-2.8/blib/) temp_cache_dir: Permission denied
 at /System/Library/Perl/5.12/CPAN/CacheMgr.pm line 136
..............DONE

  CPAN.pm: Going to build T/TL/TLINDEN/Config-General-2.50.tar.gz

Checking if your kit is complete...
Looks good
Writing Makefile for Config::General

Launch of "make" failed: the PowerPC architecture is no longer supported.

  TLINDEN/Config-General-2.50.tar.gz
  /sw/bin/make -- NOT OK
'YAML' not installed, will not store persistent state
Running make test
  Can't test without successful make
Running make install
  Make had returned bad status, install seems impossible
Failed during this command:
 TLINDEN/Config-General-2.50.tar.gz           : make NO

Other things worked, so what I have now is:
Camillas-MacBook-Pro:bin cnesbo$ ./test.modules
ok   Carp
fail Clone is not usable (it or a sub-module is missing)
fail Config::General is not usable (it or a sub-module is missing)
ok   Cwd
ok   Data::Dumper
ok   Digest::MD5
ok   File::Basename
ok   File::Spec::Functions
ok   File::Temp
ok   FindBin
fail Font::TTF::Font is not usable (it or a sub-module is missing)
ok   GD
ok   GD::Image
ok   GD::Polyline
ok   Getopt::Long
ok   IO::File
ok   List::MoreUtils
ok   List::Util
fail Math::Bezier is not usable (it or a sub-module is missing)
ok   Math::BigFloat
fail Math::Round is not usable (it or a sub-module is missing)
fail Math::VecStat is not usable (it or a sub-module is missing)
ok   Memoize
ok   POSIX
fail Params::Validate is not usable (it or a sub-module is missing)
ok   Pod::Usage
fail Readonly is not usable (it or a sub-module is missing)
ok   Regexp::Common
fail Set::IntSpan is not usable (it or a sub-module is missing)
ok   Storable
ok   Sys::Hostname
ok   Text::Balanced
fail Text::Format is not usable (it or a sub-module is missing)
ok   Time::HiRes

Do you have any advice as to how I can get the other modules instaled?
Thanks
Camilla

[Martin Krzywinski]

> Launch of "make" failed: the PowerPC architecture is no longer supported.

> TLINDEN/Config-General-2.50.tar.gz
>  /sw/bin/make -- NOT OK

Your system is still reading make from /sw. It should be using the make installed from Xcode.

Now that the right Xcode bits are installed, you should have more instances of make (e.g. in /usr/bin)

> locate make | grep make$

Make sure that the /usr/bin/make is visible in your path before /sw/bin. 

If you're not using /sw, remove it from your PATH or put it at the end.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

Camilla

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[Camilla LN]

Heia,
When I do which make I get this:
Camillas-MacBook-Pro:bin cnesbo$ which make
/usr/bin/make

Is it because of the cpan that it cannot use the make?
Can I get the modules from elsewhere and do the make 'manually' ?

Camilla

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