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Re: [S3tools-bugs] Bug report
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From: Pedamallu C. S. <pcs...@gm...> - 2014-01-23 20:08:08
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Hi Matt,
Thank you very much.
Now it is working.
I am getting the following warning
s3cmd get --recursive --force s3://LP6005408-DNA_B12111 .
s3://LP6005408-DNA_B12111/all.reads.fq1_1.fastq.gz ->
./all.reads.fq1_1.fastq.gz [1 of 50]
157814381 of 157814381 100% in 4s 36.03 MB/s done
WARNING: MD5 signatures do not match:
computed=43d2fccaec9c55d70ca326f8d0dc88bf,
received="695705a37a7a1084e4850a6db15e8a34-11"
s3://LP6005408-DNA_B12111/all.reads.fq1_10.fastq.gz ->
./all.reads.fq1_10.fastq.gz [2 of 50]
0 of 0 0% in 0s 0.00 B/s failed
WARNING: Retrying failed request: /all.reads.fq1_10.fastq.gz ()
WARNING: Waiting 3 sec...
Thanks
Chandra
On Wed, Jan 22, 2014 at 8:49 PM, Matt Domsch <ma...@do...> wrote:
> python 2.6.9 is your default - probably because it's installed into
> /usr/local/bin/ and that's first in your PATH environment variable.
>
> For s3cmd though, you don't want python 2.6.9 (/usr/local/bin/python),
> you want python 2.5.1 (/usr/bin/python). the easiest way is to just
> change the first line of the s3cmd you downloaded, so it reads
> #!/usr/bin/python, instead of #!/usr/bin/env python. The latter is finding
> the python 2.6.9, which isn't what you want.
>
>
>
>
>
> On Wed, Jan 22, 2014 at 5:03 PM, Pedamallu Chandra Sekhar <
> pcs...@gm...> wrote:
>
>> Hi Matt,
>>
>> Here is what i am getting when i run /user/bin/python
>>
>> Python 2.5.1 (r251:54863, Jul 10 2008, 17:25:56)
>> [GCC 4.1.2 20070925 (Red Hat 4.1.2-33)] on linux2
>>
>> When i run python
>>
>> Python 2.6.9 (unknown, Jan 22 2014, 15:39:18)
>> [GCC 4.1.2 20070925 (Red Hat 4.1.2-33)] on linux2
>> Type "help", "copyright", "credits" or "license" for more information.
>> >>> quit()
>>
>> How to make the Python2.6.9 as default?
>>
>> Thanks
>> Chandra
>>
>>
>> On Wed, Jan 22, 2014 at 5:59 PM, Matt Domsch <ma...@do...> wrote:
>>
>>> The version of python you have installed (2.6.9) is not the version of
>>> python that is packaged with Fedora 8. Fedora 8 has python-2.5.1-15.fc8 in
>>> the base repository, python-2.5.1-26.fc8 in updates. _This_ version of
>>> python does in fact have httplib bundled in, and httplib.HTTPSConnection()
>>> does exist there.
>>>
>>> You have python 2.6.9 installed - from where, I do not know, but I
>>> presume someone built it and put it in /usr/local/bin. If it was built
>>> without having first installed a set of SSL libraries, and pointed the
>>> Python build at those SSL libraries, then your python would in fact not
>>> have httplib.HTTPSConnection() defined. This would be very likely if
>>> hand-built.
>>>
>>> You may wish to simply try running /usr/bin/python rather than
>>> /usr/local/bin/python, so that you get the system version and not the local
>>> version. The system version should not throw the same error - it certainly
>>> was built with SSL enabled.
>>>
>>> Thanks,
>>> Matt
>>>
>>>
>>> On Wed, Jan 22, 2014 at 4:39 PM, Pedamallu Chandra Sekhar <
>>> pcs...@gm...> wrote:
>>>
>>>> Hi Matt,
>>>>
>>>> Here is the command i used to install it
>>>>
>>>> yum -y install rsync lynx screen ganglia-gmetad ganglia-gmond
>>>> ganglia-web httpd php
>>>>
>>>> Thanks
>>>> Chandra
>>>>
>>>>
>>>> On Wed, Jan 22, 2014 at 5:36 PM, Pedamallu Chandra Sekhar <
>>>> pcs...@gm...> wrote:
>>>>
>>>>> Hi Matt,
>>>>>
>>>>> Here is the installation
>>>>>
>>>>> httpd-devel.x86_64 0:2.2.9-1.fc8 httpd-devel.i386
>>>>> 0:2.2.9-1.fc8 httpd-manual.x86_64 0:2.2.9-1.fc8
>>>>>
>>>>> Thanks
>>>>> Chandra
>>>>>
>>>>>
>>>>> On Tue, Jan 21, 2014 at 5:07 PM, Matt Domsch <ma...@do...> wrote:
>>>>>
>>>>>> I would have expected that to be new enough. I don't have a Fedora 8
>>>>>> system hanging around to go look though. Perhaps httplib got built without
>>>>>> https support? Where did you get httplib from?
>>>>>>
>>>>>>
>>>>>> On Tue, Jan 21, 2014 at 3:49 PM, Pedamallu Chandra Sekhar <
>>>>>> pcs...@gm...> wrote:
>>>>>>
>>>>>>> [root@ip-10-139-11-31 ~]# python --version
>>>>>>> Python 2.6.9
>>>>>>>
>>>>>>> I am running on Fedora 8
>>>>>>>
>>>>>>>
>>>>>>> On Tue, Jan 21, 2014 at 4:48 PM, Matt Domsch <ma...@do...>wrote:
>>>>>>>
>>>>>>>> What version of Python are you using? Probably something pretty
>>>>>>>> old to not have HTTPSConnection() available.
>>>>>>>>
>>>>>>>>
>>>>>>>> On Tue, Jan 21, 2014 at 3:31 PM, Pedamallu Chandra Sekhar <
>>>>>>>> pcs...@gm...> wrote:
>>>>>>>>
>>>>>>>>> Hi Matt,
>>>>>>>>>
>>>>>>>>> I am getting the following error.
>>>>>>>>>
>>>>>>>>> WARNING: Retrying failed request: /?delimiter=/ ('module' object
>>>>>>>>> has no attribute 'HTTPSConnection')
>>>>>>>>> WARNING: Waiting 3 sec...
>>>>>>>>> WARNING: Retrying failed request: /?delimiter=/ ('module' object
>>>>>>>>> has no attribute 'HTTPSConnection')
>>>>>>>>> WARNING: Waiting 6 sec...
>>>>>>>>> WARNING: Retrying failed request: /?delimiter=/ ('module' object
>>>>>>>>> has no attribute 'HTTPSConnection')
>>>>>>>>> WARNING: Waiting 9 sec...
>>>>>>>>> WARNING: Retrying failed request: /?delimiter=/ ('module' object
>>>>>>>>> has no attribute 'HTTPSConnection')
>>>>>>>>> WARNING: Waiting 12 sec...
>>>>>>>>> WARNING: Retrying failed request: /?delimiter=/ ('module' object
>>>>>>>>> has no attribute 'HTTPSConnection')
>>>>>>>>> WARNING: Waiting 15 sec...
>>>>>>>>>
>>>>>>>>> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>>>>>>>>>
>>>>>>>>> An unexpected error has occurred.
>>>>>>>>> Please try reproducing the error using
>>>>>>>>> the latest s3cmd code from the git master
>>>>>>>>> branch found at:
>>>>>>>>> https://github.com/s3tools/s3cmd
>>>>>>>>> If the error persists, please report the
>>>>>>>>> following lines (removing any private
>>>>>>>>> info as necessary) to:
>>>>>>>>> s3t...@li...
>>>>>>>>> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>>>>>>>>>
>>>>>>>>> Invoked as: /usr/bin/s3cmd -f -c /root/.s3cfg ls
>>>>>>>>> s3://ami-ref-GRCh371234/Problem: S3RequestError: Request failed for:
>>>>>>>>> /?delimiter=/
>>>>>>>>> S3cmd: 1.5.0-beta1
>>>>>>>>>
>>>>>>>>> Please help me to fix this error.
>>>>>>>>>
>>>>>>>>> Thanks
>>>>>>>>> chandra
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Mon, Jan 20, 2014 at 2:06 PM, Matt Domsch <ma...@do...>wrote:
>>>>>>>>>
>>>>>>>>>> Fixed in 1.5.0-beta1 and upstream github.com/s3tools/s3cmdmaster branch.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Mon, Jan 20, 2014 at 8:34 AM, Pedamallu Chandra Sekhar <
>>>>>>>>>> pcs...@gm...> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi,
>>>>>>>>>>>
>>>>>>>>>>> I am trying to use the s3cmd to upload multiple files and
>>>>>>>>>>> getting the following error. Could you please help me in this regard?
>>>>>>>>>>>
>>>>>>>>>>> Command line used:
>>>>>>>>>>> /usr/bin/s3cmd -f -c /root/.s3cfg sync
>>>>>>>>>>> /mnt/mfiles/ami-LP60123-repeato/*.fq1 s3://ami-LP60123-psub/
>>>>>>>>>>>
>>>>>>>>>>> Error:
>>>>>>>>>>> (256, 'WARNING: Module python-magic is not available. Guessing
>>>>>>>>>>> MIME types based on file
>>>>>>>>>>> extensions.\n\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n An unexpected
>>>>>>>>>>> error has occurred.\n Please report the following lines to:\n
>>>>>>>>>>> s3t...@li...\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n\nProblem:
>>>>>>>>>>> KeyError: \'elapsed\'\nS3cmd: 1.1.0-beta3\n\nTraceback (most recent call
>>>>>>>>>>> last):\n File "/usr/bin/s3cmd", line 1800, in <module>\n main()\n File
>>>>>>>>>>> "/usr/bin/s3cmd", line 1741, in main\n cmd_func(args)\n File
>>>>>>>>>>> "/usr/bin/s3cmd", line 965, in cmd_sync\n return
>>>>>>>>>>> cmd_sync_local2remote(args)\n File "/usr/bin/s3cmd", line 932, in
>>>>>>>>>>> cmd_sync_local2remote\n (item[\'full_name_unicode\'], uri,
>>>>>>>>>>> response["size"], response["elapsed"],\nKeyError:
>>>>>>>>>>> \'elapsed\'\n\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n An unexpected
>>>>>>>>>>> error has occurred.\n Please report the above lines to:\n
>>>>>>>>>>> s3t...@li...
>>>>>>>>>>> \n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!')
>>>>>>>>>>>
>>>>>>>>>>> Thanks
>>>>>>>>>>> Sincerely
>>>>>>>>>>> Chandra
>>>>>>>>>>>
>>>>>>>>>>>
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>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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