On Fri, Jan 14, 2011 at 10:09 AM, Diya v <diya_2208@yahoo.co.in> wrote:
>
> Hello All,
>
Hello Diya.

> Firstly I would like to introduce myself as Diya.
>
Nice to meet you. Would you mind not posting in HTML?

> I am trying to install a software on Ubuntu and it's giving me an error which I trying to do the make command. I tried to google the error but there were not many posts related to this. I am guessing that it may be a compilation and gc++ issue. Could any one help me to resolve this error.
>
> Below is the error message.
>
> /usr/bin/ld: cannot find -lbam
> collect2: ld returned 1 exit status
> make[2]: *** [prep_reads] Error 1
> make[2]: Leaving directory `/home/diya/tophat-1.1.0/src'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/home/diya/tophat-1.1.0'
> make: *** [all] Error 2
>

This means that the libraries and/or library directories you supplied
to make for linking do not include one called 'libbam.a' or
'libbam.so'. You need to find out where that library is and include
the appropriate -l or -L option for your ld.

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Hi Nils,

Thank you so much for the help. I could now install the software. But when I am trying to run the test data to see if everything worked well I have a list of errors.

Below is the list.
diya@ubuntu:~/test_data$ sudo tophat -r 20 test_ref reads_1.fq reads_2.fq

[Fri Jan 14 12:23:13 2011] Beginning TopHat run (v1.1.0)
-----------------------------------------------
[Fri Jan 14 12:23:13 2011] Preparing output location ./tophat_out/
[Fri Jan 14 12:23:13 2011] Checking for Bowtie index files
[Fri Jan 14 12:23:13 2011] Checking for reference FASTA file
[Fri Jan 14 12:23:13 2011] Checking for Bowtie
*** Bowtie version:*** *** *** *0.12.7.0
[Fri Jan 14 12:23:13 2011] Checking for Samtools
Traceback (most recent call last):
* File
"/usr/local/bin/tophat", line 2174, in <module>
*** sys.exit(main())
* File "/usr/local/bin/tophat", line 2088, in main
*** check_samtools()
* File "/usr/local/bin/tophat", line 850, in check_samtools
*** samtools_version = get_samtools_version()
* File "/usr/local/bin/tophat", line 837, in get_samtools_version
*** samtools_version = [int(x.split('-')[0]) for x in version_val.split('.')]
ValueError: invalid literal for int() with base 10: '12a'

Could you please tell me what this error mean?

Thanks in advance.

Diya


--- On Sat, 15/1/11, Nils Kassube <kassube@gmx.net> wrote:

From: Nils Kassube <kassube@gmx.net>
Subject: Re: Problem in installing software on ubuntu
To:
ubuntu-users@lists.ubuntu.com
Date: Saturday, 15 January, 2011, 12:09 AM

Diya v wrote:
> I am trying to install a software on Ubuntu and it's giving me an
> error which I trying to do the make command.

> Below is the error message.

> /usr/bin/ld: cannot find -lbam

I think the message means that the loader can't find the bam library.
You should install the package "libbam-dev", if your application has
something to do with "manipulates nucleotide sequence alignments in BAM
or SAM format" (that's what the package is used for).


Nils

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Hi

Thank you so much for the help. I could now install the software. But when I am trying to run the test data to see if everything worked well I have a list of errors.

Below is the list.
diya@ubuntu:~/test_data$ sudo tophat -r 20 test_ref reads_1.fq reads_2.fq

[Fri Jan 14 12:23:13 2011] Beginning TopHat run (v1.1.0)
-----------------------------------------------
[Fri Jan 14 12:23:13 2011] Preparing output location ./tophat_out/
[Fri Jan 14 12:23:13 2011] Checking for Bowtie index files
[Fri Jan 14 12:23:13 2011] Checking for reference FASTA file
[Fri Jan 14 12:23:13 2011] Checking for
Bowtie
*** Bowtie version:*** *** *** *0.12.7.0
[Fri Jan 14 12:23:13 2011] Checking for Samtools
Traceback (most recent call last):
* File
"/usr/local/bin/tophat", line 2174, in <module>
*** sys.exit(main())
* File "/usr/local/bin/tophat", line 2088, in main
*** check_samtools()
* File "/usr/local/bin/tophat", line 850, in check_samtools
*** samtools_version = get_samtools_version()
* File "/usr/local/bin/tophat", line 837, in get_samtools_version
*** samtools_version = [int(x.split('-')[0]) for x in version_val.split('.')]
ValueError: invalid literal for int() with base 10: '12a'

The sam version that I installed is samtools-0.1.12a

Could you please tell me what this error mean?

Thanks in advance.

Diya


--- On Sat, 15/1/11, Nils Kassube <kassube@gmx.net> wrote:

From: Nils Kassube <kassube@gmx.net>
Subject: Re: Problem
in installing software on ubuntu
To:
ubuntu-users@lists.ubuntu.com
Date: Saturday, 15 January, 2011, 12:09 AM

Diya v wrote:
> I am trying to install a software on Ubuntu and it's giving me an
> error which I trying to do the make command.

> Below is the error message.

> /usr/bin/ld: cannot find -lbam

I think the message means that the loader can't find the bam library.
You should install the package "libbam-dev", if your application has
something to do with "manipulates nucleotide sequence alignments in BAM
or SAM format" (that's what the package is used for).


Nils

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Diya v wrote:
> Thank you so much for the help. I could now install the software.

Great!

> But
> when I am trying to run the test data to see if everything worked
> well I have a list of errors.
>
> Below is the list.
[...]
> [Fri Jan 14 12:23:13 2011] Checking for Samtools
> Traceback (most recent call last):
> File "/usr/local/bin/tophat", line 2174, in <module>
> sys.exit(main())
> File "/usr/local/bin/tophat", line 2088, in main
> check_samtools()
> File "/usr/local/bin/tophat", line 850, in check_samtools
> samtools_version = get_samtools_version()
> File "/usr/local/bin/tophat", line 837, in get_samtools_version
> samtools_version = [int(x.split('-')[0]) for x in
> version_val.split('.')] ValueError: invalid literal for int() with
> base 10: '12a'

I'm not so sure what it means - after all I don't know anything about
that tophat software. But I would guess that either your software
expects a different version of samtools or you don't have those samtools
installed. Searching for samtools in synaptic reveals two possible
packages: "samtools" and "libbio-samtools-perl". Maybe you need them
both installed. If that doesn't help, have a look at the source
directory of your application and check if there is a file "README" or
"INSTALL" which might give a hint which version is needed and check if
you have that version is installed.


Nils

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