CIRCOS Installation Issue

Jessica Jessie

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Jan 24, 2024, 3:42:10 PMJan 24

to Circos

Hello,

I'm unable to install CIRCOS with both Ubuntu and perl.
Screenshot (354).png

Paulo Nuin

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Jan 24, 2024, 3:51:17 PMJan 24

to circos-data-...@googlegroups.com

Hi

You don’t seem to have Linux installed, you have WSL but no distribution installed in it.

Take a look at this https://github.com/MicrosoftDocs/WSL/blob/main/WSL/install.md and go from there.

Cheers

Paulo

On Jan 24, 2024, at 8:36 AM, Jessica Jessie <jessicaj...@gmail.com> wrote:

Hello,

I'm unable to install CIRCOS with both Ubuntu and perl.

<Screenshot (354).png><Screenshot (355).png>

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<Screenshot (355).png><Screenshot (354).png>

Jessica Jessie

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Apr 3, 2024, 4:53:30 PMApr 3

to Circos

Hi

Thank you for your guidance. That issue has been resolved. I got another issue (unable to install GD and GD::Polyline in circos modules) , please have a look at it.

mouryapraharshabobbili@Mouryas-MBP bin % perl circos -modules

ok 1.50 Carp

ok 0.45 Clone

ok 2.65 Config::General

ok 3.78 Cwd

ok 2.174 Data::Dumper

ok 2.55 Digest::MD5

ok 2.85 File::Basename

ok 3.78 File::Spec::Functions

ok 0.2309 File::Temp

ok 1.51 FindBin

ok 0.39 Font::TTF::Font

missing GD

missing GD::Polyline

ok 2.5 Getopt::Long

ok 1.40 IO::File

ok 0.428 List::MoreUtils

ok 1.5 List::Util

ok 0.01 Math::Bezier

ok 1.999816 Math::BigFloat

ok 0.07 Math::Round

ok 0.08 Math::VecStat

ok 1.03_01 Memoize

ok 1.88 POSIX

ok 1.29 Params::Validate

ok 1.69 Pod::Usage

ok 2.05 Readonly

ok 2017060201 Regexp::Common

ok 2.87 SVG

ok 1.19 Set::IntSpan

ok 1.6611 Statistics::Basic

ok 3.15 Storable

ok 1.22 Sys::Hostname

ok 2.03 Text::Balanced

ok 0.62 Text::Format

ok 1.976 Time::HiRes

mouryapraharshabobbili@Mouryas-MBP bin % ls

circos circos.exe compile.bat compile.make gddiag list.modules test.modules

mouryapraharshabobbili@Mouryas-MBP bin % perl -MCPAN -e shell

Terminal does not support AddHistory.

To fix enter> install Term::ReadLine::Perl

cpan shell -- CPAN exploration and modules installation (v2.22)

Enter 'h' for help.

cpan[1]> install GD GD::Polyline

Reading '/Users/mouryapraharshabobbili/.cpan/Metadata'

Database was generated on Wed, 03 Apr 2024 19:54:04 GMT

Running install for module 'GD'

Checksum for /Users/mouryapraharshabobbili/.cpan/sources/authors/id/R/RU/RURBAN/GD-2.78.tar.gz ok

Scanning cache /Users/mouryapraharshabobbili/.cpan/build for sizes

............................................................................DONE

---- Unsatisfied dependencies detected during ----

---- RURBAN/GD-2.78.tar.gz ----

ExtUtils::PkgConfig [build_requires]

Running install for module 'ExtUtils::PkgConfig'

Checksum for /Users/mouryapraharshabobbili/.cpan/sources/authors/id/X/XA/XAOC/ExtUtils-PkgConfig-1.16.tar.gz ok

Configuring X/XA/XAOC/ExtUtils-PkgConfig-1.16.tar.gz with Makefile.PL

***

*** ExtUtils::PkgConfig requires the pkg-config utility, but it doesn't

*** seem to be in your PATH. Is it correctly installed?

*** PATH=/Users/mouryapraharshabobbili/perl5/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin

***

No 'Makefile' created XAOC/ExtUtils-PkgConfig-1.16.tar.gz

/usr/bin/perl Makefile.PL -- NOT OK

RURBAN/GD-2.78.tar.gz

Has already been unwrapped into directory /Users/mouryapraharshabobbili/.cpan/build/GD-2.78-2

Warning: Prerequisite 'ExtUtils::PkgConfig => 0' for 'RURBAN/GD-2.78.tar.gz' failed when processing 'XAOC/ExtUtils-PkgConfig-1.16.tar.gz' with 'writemakefile => NO -- No 'Makefile' created

'. Continuing, but chances to succeed are limited.

Configuring R/RU/RURBAN/GD-2.78.tar.gz with Makefile.PL

Notice: Type perl Makefile.PL -h for command-line option summary.

Can't locate ExtUtils/PkgConfig.pm in @INC (you may need to install the ExtUtils::PkgConfig module) (@INC contains: /Users/mouryapraharshabobbili/perl5/lib/perl5/darwin-thread-multi-2level /Users/mouryapraharshabobbili/perl5/lib/perl5 /Library/Perl/5.30/darwin-thread-multi-2level /Library/Perl/5.30 /Network/Library/Perl/5.30/darwin-thread-multi-2level /Network/Library/Perl/5.30 /Library/Perl/Updates/5.30.3 /System/Library/Perl/5.30/darwin-thread-multi-2level /System/Library/Perl/5.30 /System/Library/Perl/Extras/5.30/darwin-thread-multi-2level /System/Library/Perl/Extras/5.30 .) at Makefile.PL line 555.

Warning: No success on command[/usr/bin/perl Makefile.PL]

RURBAN/GD-2.78.tar.gz

/usr/bin/perl Makefile.PL -- NOT OK

Running install for module 'GD::Polyline'

RURBAN/GD-2.78.tar.gz

Has already been unwrapped into directory /Users/mouryapraharshabobbili/.cpan/build/GD-2.78-2

RURBAN/GD-2.78.tar.gz

'/usr/bin/perl Makefile.PL' returned status 512, not re-running

Failed during this command:

RURBAN/GD-2.78.tar.gz : writemakefile NO '/usr/bin/perl Makefile.PL' returned status 512

XAOC/ExtUtils-PkgConfig-1.16.tar.gz : writemakefile NO -- No 'Makefile' created

cpan[2]> install ExtUtils::PkgConfig

Running install for module 'ExtUtils::PkgConfig'

XAOC/ExtUtils-PkgConfig-1.16.tar.gz

Has already been unwrapped into directory /Users/mouryapraharshabobbili/.cpan/build/ExtUtils-PkgConfig-1.16-2

XAOC/ExtUtils-PkgConfig-1.16.tar.gz

No 'Makefile' created

, not re-running

cpan[3]>

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