Re: [galaxy-dev] JBrowse on dev branch: progress
Thanks Peter I managed, on the second attempt, to get past the gnu coreutils problem. Zipho noticed a weird lockup though: conftest that seemed to be from the gnu coreutils install wanted to listen on port 4001, which is the same port our uwsgi server listens on. The install has now completed but I'll try and find time to go back and verify this. On the second attempt perl seems to be installing, so I'll see if it completes or hits the error you're mentioning. Peter On 22 February 2016 at 11:34, Peter Briggs <peter.briggs@manchester.ac.uk> wrote:
Hi Peter
I think that package_perl_5_18 in the tool shed is broken, I came across the same error last week on both our production instance and a local 'test' instance (both v15.10).
My suspicion is that the following lines are to blame:
... <action sha256sum="5c69adb47ab828aa3e8b5be89b88cd49c6a0d0dae2e8b3bca17a9ce699190e7b" type="download_file"> http://www.cpan.org/authors/id/A/AP/APEIRON/local-lib-1.008009.tar.gz </action> <action type="shell_command">tar xfvz local-lib-1.008009.tar.gz</action> ...
Looking at the Galaxy internals I believe that the 'download_file' action automatically unpacks the archive and cd's into the resulting directory, hence the failure for the subsequent 'tar xfvz ...' command. But I haven't had the time yet to verify this or create a patch to see if the removal of this line addresses the problem.
I don't think I've seen the problem with 'package_gnu_coreutils_8_22' that you describe however so it may be that my hypothesis is not correct.
HTH
Best wishes
Peter
On 22/02/16 05:10, Peter van Heusden wrote:
Hi there Eric and others
I tried to install the JBrowse tool on a dev branch server running on an Ubuntu 14.04 VM.
It got stuck at the package_gnu_coreutils_8_22 dependency (revision ac64dfe4b1fb) - this ended up in "Installing tool dependencies" state.
If I go look at the tool details it highlights errors in package_perl_5_18 which in turn refers to errors in gnu_coreutils (just "Error" state) and then this more informative failure for perl:
"tar (child): local-lib-1.008009.tar.gz: Cannot open: No such file or directory tar (child): Error is not recoverable: exiting now tar: Child returned status 2 tar: Error is not recoverable: exiting now"
I wonder if this is a sign of a download error?
Digging a bit more I find the error "Shutting down process id 21094 because it generated no output for the defined timeout period of 3600.0 seconds." for gnu_coreutils.
I'm trying to do a reinstall of the gnu_coreutils and perl packages to see if I can get further.
Peter
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
Ok, second attempt, perl install died with the same error, so I suspect you're right about the cause. Eric? Peter On 22 February 2016 at 11:41, Peter van Heusden <pvh@sanbi.ac.za> wrote:
Thanks Peter
I managed, on the second attempt, to get past the gnu coreutils problem. Zipho noticed a weird lockup though: conftest that seemed to be from the gnu coreutils install wanted to listen on port 4001, which is the same port our uwsgi server listens on. The install has now completed but I'll try and find time to go back and verify this.
On the second attempt perl seems to be installing, so I'll see if it completes or hits the error you're mentioning.
Peter
On 22 February 2016 at 11:34, Peter Briggs <peter.briggs@manchester.ac.uk> wrote:
Hi Peter
I think that package_perl_5_18 in the tool shed is broken, I came across the same error last week on both our production instance and a local 'test' instance (both v15.10).
My suspicion is that the following lines are to blame:
... <action sha256sum="5c69adb47ab828aa3e8b5be89b88cd49c6a0d0dae2e8b3bca17a9ce699190e7b" type="download_file"> http://www.cpan.org/authors/id/A/AP/APEIRON/local-lib-1.008009.tar.gz </action> <action type="shell_command">tar xfvz local-lib-1.008009.tar.gz</action> ...
Looking at the Galaxy internals I believe that the 'download_file' action automatically unpacks the archive and cd's into the resulting directory, hence the failure for the subsequent 'tar xfvz ...' command. But I haven't had the time yet to verify this or create a patch to see if the removal of this line addresses the problem.
I don't think I've seen the problem with 'package_gnu_coreutils_8_22' that you describe however so it may be that my hypothesis is not correct.
HTH
Best wishes
Peter
On 22/02/16 05:10, Peter van Heusden wrote:
Hi there Eric and others
I tried to install the JBrowse tool on a dev branch server running on an Ubuntu 14.04 VM.
It got stuck at the package_gnu_coreutils_8_22 dependency (revision ac64dfe4b1fb) - this ended up in "Installing tool dependencies" state.
If I go look at the tool details it highlights errors in package_perl_5_18 which in turn refers to errors in gnu_coreutils (just "Error" state) and then this more informative failure for perl:
"tar (child): local-lib-1.008009.tar.gz: Cannot open: No such file or directory tar (child): Error is not recoverable: exiting now tar: Child returned status 2 tar: Error is not recoverable: exiting now"
I wonder if this is a sign of a download error?
Digging a bit more I find the error "Shutting down process id 21094 because it generated no output for the defined timeout period of 3600.0 seconds." for gnu_coreutils.
I'm trying to do a reinstall of the gnu_coreutils and perl packages to see if I can get further.
Peter
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
I have occasionally seen this. GNU-coreutils hangs while compiling on ubuntu 14.04 ... there is a `nanosleep` in the configure step, which is never returning. "checking for working nanosleep..." https://bugs.launchpad.net/ubuntu/+source/coreutils/+bug/1079889 Just kill the process (this will happen twice), and it will work. I will have a look if this is still happening with newer versions of coreutils. On 22 February 2016 at 10:43, Peter van Heusden <pvh@sanbi.ac.za> wrote:
Ok, second attempt, perl install died with the same error, so I suspect you're right about the cause. Eric?
Peter
On 22 February 2016 at 11:41, Peter van Heusden <pvh@sanbi.ac.za> wrote:
Thanks Peter
I managed, on the second attempt, to get past the gnu coreutils problem. Zipho noticed a weird lockup though: conftest that seemed to be from the gnu coreutils install wanted to listen on port 4001, which is the same port our uwsgi server listens on. The install has now completed but I'll try and find time to go back and verify this.
On the second attempt perl seems to be installing, so I'll see if it completes or hits the error you're mentioning.
Peter
On 22 February 2016 at 11:34, Peter Briggs <peter.briggs@manchester.ac.uk
wrote:
Hi Peter
I think that package_perl_5_18 in the tool shed is broken, I came across the same error last week on both our production instance and a local 'test' instance (both v15.10).
My suspicion is that the following lines are to blame:
... <action sha256sum="5c69adb47ab828aa3e8b5be89b88cd49c6a0d0dae2e8b3bca17a9ce699190e7b" type="download_file"> http://www.cpan.org/authors/id/A/AP/APEIRON/local-lib-1.008009.tar.gz </action> <action type="shell_command">tar xfvz local-lib-1.008009.tar.gz</action> ...
Looking at the Galaxy internals I believe that the 'download_file' action automatically unpacks the archive and cd's into the resulting directory, hence the failure for the subsequent 'tar xfvz ...' command. But I haven't had the time yet to verify this or create a patch to see if the removal of this line addresses the problem.
I don't think I've seen the problem with 'package_gnu_coreutils_8_22' that you describe however so it may be that my hypothesis is not correct.
HTH
Best wishes
Peter
On 22/02/16 05:10, Peter van Heusden wrote:
Hi there Eric and others
I tried to install the JBrowse tool on a dev branch server running on an Ubuntu 14.04 VM.
It got stuck at the package_gnu_coreutils_8_22 dependency (revision ac64dfe4b1fb) - this ended up in "Installing tool dependencies" state.
If I go look at the tool details it highlights errors in package_perl_5_18 which in turn refers to errors in gnu_coreutils (just "Error" state) and then this more informative failure for perl:
"tar (child): local-lib-1.008009.tar.gz: Cannot open: No such file or directory tar (child): Error is not recoverable: exiting now tar: Child returned status 2 tar: Error is not recoverable: exiting now"
I wonder if this is a sign of a download error?
Digging a bit more I find the error "Shutting down process id 21094 because it generated no output for the defined timeout period of 3600.0 seconds." for gnu_coreutils.
I'm trying to do a reinstall of the gnu_coreutils and perl packages to see if I can get further.
Peter
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hello Peter Re the failing install of 'package_perl_5_18', I've investigated further now and have submitted a patch which seems to fix the problem: https://github.com/galaxyproject/tools-iuc/pull/616 Not sure if this is of any immediate help, Best wishes Peter On 22/02/16 09:43, Peter van Heusden wrote:
Ok, second attempt, perl install died with the same error, so I suspect you're right about the cause. Eric?
Peter
On 22 February 2016 at 11:41, Peter van Heusden <pvh@sanbi.ac.za <mailto:pvh@sanbi.ac.za>> wrote:
Thanks Peter
I managed, on the second attempt, to get past the gnu coreutils problem. Zipho noticed a weird lockup though: conftest that seemed to be from the gnu coreutils install wanted to listen on port 4001, which is the same port our uwsgi server listens on. The install has now completed but I'll try and find time to go back and verify this.
On the second attempt perl seems to be installing, so I'll see if it completes or hits the error you're mentioning.
Peter
On 22 February 2016 at 11:34, Peter Briggs <peter.briggs@manchester.ac.uk <mailto:peter.briggs@manchester.ac.uk>> wrote:
Hi Peter
I think that package_perl_5_18 in the tool shed is broken, I came across the same error last week on both our production instance and a local 'test' instance (both v15.10).
My suspicion is that the following lines are to blame:
... <action sha256sum="5c69adb47ab828aa3e8b5be89b88cd49c6a0d0dae2e8b3bca17a9ce699190e7b" type="download_file"> http://www.cpan.org/authors/id/A/AP/APEIRON/local-lib-1.008009.tar.gz </action> <action type="shell_command">tar xfvz local-lib-1.008009.tar.gz</action> ...
Looking at the Galaxy internals I believe that the 'download_file' action automatically unpacks the archive and cd's into the resulting directory, hence the failure for the subsequent 'tar xfvz ...' command. But I haven't had the time yet to verify this or create a patch to see if the removal of this line addresses the problem.
I don't think I've seen the problem with 'package_gnu_coreutils_8_22' that you describe however so it may be that my hypothesis is not correct.
HTH
Best wishes
Peter
On 22/02/16 05:10, Peter van Heusden wrote:
Hi there Eric and others
I tried to install the JBrowse tool on a dev branch server running on an Ubuntu 14.04 VM.
It got stuck at the package_gnu_coreutils_8_22 dependency (revision ac64dfe4b1fb) - this ended up in "Installing tool dependencies" state.
If I go look at the tool details it highlights errors in package_perl_5_18 which in turn refers to errors in gnu_coreutils (just "Error" state) and then this more informative failure for perl:
"tar (child): local-lib-1.008009.tar.gz: Cannot open: No such file or directory tar (child): Error is not recoverable: exiting now tar: Child returned status 2 tar: Error is not recoverable: exiting now"
I wonder if this is a sign of a download error?
Digging a bit more I find the error "Shutting down process id 21094 because it generated no output for the defined timeout period of 3600.0 seconds." for gnu_coreutils.
I'm trying to do a reinstall of the gnu_coreutils and perl packages to see if I can get further.
Peter
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Peter Briggs peter.briggs@manchester.ac.uk <mailto:peter.briggs@manchester.ac.uk> Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
I knew there was an email that I forgot to send! Nicola Soranzo fixed this with galaxy PR https://github.com/galaxyproject/galaxy/pull/1775 - sometime in November last year Eric added whitespace to the perl package (and a bunch of other things) that broke the download_file action, so Nicola's patch strips whitespace. (The conversation about this happened on IRC and the PR) I tested the PR and it makes the perl install work (which makes the JBrowse installl work, yay!). Peter On 25 Feb 2016 6:10 PM, "Peter Briggs" <peter.briggs@manchester.ac.uk> wrote:
Hello Peter
Re the failing install of 'package_perl_5_18', I've investigated further now and have submitted a patch which seems to fix the problem:
https://github.com/galaxyproject/tools-iuc/pull/616
Not sure if this is of any immediate help,
Best wishes
Peter
On 22/02/16 09:43, Peter van Heusden wrote:
Ok, second attempt, perl install died with the same error, so I suspect you're right about the cause. Eric?
Peter
On 22 February 2016 at 11:41, Peter van Heusden <pvh@sanbi.ac.za <mailto:pvh@sanbi.ac.za>> wrote:
Thanks Peter
I managed, on the second attempt, to get past the gnu coreutils problem. Zipho noticed a weird lockup though: conftest that seemed to be from the gnu coreutils install wanted to listen on port 4001, which is the same port our uwsgi server listens on. The install has now completed but I'll try and find time to go back and verify this.
On the second attempt perl seems to be installing, so I'll see if it completes or hits the error you're mentioning.
Peter
On 22 February 2016 at 11:34, Peter Briggs <peter.briggs@manchester.ac.uk <mailto:peter.briggs@manchester.ac.uk>> wrote:
Hi Peter
I think that package_perl_5_18 in the tool shed is broken, I came across the same error last week on both our production instance and a local 'test' instance (both v15.10).
My suspicion is that the following lines are to blame:
... <action
sha256sum="5c69adb47ab828aa3e8b5be89b88cd49c6a0d0dae2e8b3bca17a9ce699190e7b" type="download_file">
http://www.cpan.org/authors/id/A/AP/APEIRON/local-lib-1.008009.tar.gz </action> <action type="shell_command">tar xfvz local-lib-1.008009.tar.gz</action> ...
Looking at the Galaxy internals I believe that the 'download_file' action automatically unpacks the archive and cd's into the resulting directory, hence the failure for the subsequent 'tar xfvz ...' command. But I haven't had the time yet to verify this or create a patch to see if the removal of this line addresses the problem.
I don't think I've seen the problem with 'package_gnu_coreutils_8_22' that you describe however so it may be that my hypothesis is not correct.
HTH
Best wishes
Peter
On 22/02/16 05:10, Peter van Heusden wrote:
Hi there Eric and others
I tried to install the JBrowse tool on a dev branch server running on an Ubuntu 14.04 VM.
It got stuck at the package_gnu_coreutils_8_22 dependency (revision ac64dfe4b1fb) - this ended up in "Installing tool dependencies" state.
If I go look at the tool details it highlights errors in package_perl_5_18 which in turn refers to errors in gnu_coreutils (just "Error" state) and then this more informative failure for perl:
"tar (child): local-lib-1.008009.tar.gz: Cannot open: No such file or directory tar (child): Error is not recoverable: exiting now tar: Child returned status 2 tar: Error is not recoverable: exiting now"
I wonder if this is a sign of a download error?
Digging a bit more I find the error "Shutting down process id 21094 because it generated no output for the defined timeout period of 3600.0 seconds." for gnu_coreutils.
I'm trying to do a reinstall of the gnu_coreutils and perl packages to see if I can get further.
Peter
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Peter Briggs peter.briggs@manchester.ac.uk <mailto:peter.briggs@manchester.ac.uk> Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
Thanks Peter - this specific package has now been fixed in the toolsheds and should work without patching the Galaxy code. I understand that more generally Nicola is working on applying the same fix (removing whitespace around the target URL when using the "download_file" action) in other packages that might be similarly affected. Big thanks to Bjoern, Marius and Nicola for their efforts in sorting this out. Peter -- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ________________________________ From: Peter van Heusden [pvh@sanbi.ac.za] Sent: Thursday, February 25, 2016 4:17 PM To: Peter Briggs Cc: galaxy-dev@lists.galaxyproject.org Subject: Re: Broken package_perl_5_18, was Re: [galaxy-dev] JBrowse on dev branch: progress I knew there was an email that I forgot to send! Nicola Soranzo fixed this with galaxy PR https://github.com/galaxyproject/galaxy/pull/1775 - sometime in November last year Eric added whitespace to the perl package (and a bunch of other things) that broke the download_file action, so Nicola's patch strips whitespace. (The conversation about this happened on IRC and the PR) I tested the PR and it makes the perl install work (which makes the JBrowse installl work, yay!). Peter On 25 Feb 2016 6:10 PM, "Peter Briggs" <peter.briggs@manchester.ac.uk<mailto:peter.briggs@manchester.ac.uk>> wrote: Hello Peter Re the failing install of 'package_perl_5_18', I've investigated further now and have submitted a patch which seems to fix the problem: https://github.com/galaxyproject/tools-iuc/pull/616 Not sure if this is of any immediate help, Best wishes Peter On 22/02/16 09:43, Peter van Heusden wrote: Ok, second attempt, perl install died with the same error, so I suspect you're right about the cause. Eric? Peter On 22 February 2016 at 11:41, Peter van Heusden <pvh@sanbi.ac.za<mailto:pvh@sanbi.ac.za> <mailto:pvh@sanbi.ac.za<mailto:pvh@sanbi.ac.za>>> wrote: Thanks Peter I managed, on the second attempt, to get past the gnu coreutils problem. Zipho noticed a weird lockup though: conftest that seemed to be from the gnu coreutils install wanted to listen on port 4001, which is the same port our uwsgi server listens on. The install has now completed but I'll try and find time to go back and verify this. On the second attempt perl seems to be installing, so I'll see if it completes or hits the error you're mentioning. Peter On 22 February 2016 at 11:34, Peter Briggs <peter.briggs@manchester.ac.uk<mailto:peter.briggs@manchester.ac.uk> <mailto:peter.briggs@manchester.ac.uk<mailto:peter.briggs@manchester.ac.uk>>> wrote: Hi Peter I think that package_perl_5_18 in the tool shed is broken, I came across the same error last week on both our production instance and a local 'test' instance (both v15.10). My suspicion is that the following lines are to blame: ... <action sha256sum="5c69adb47ab828aa3e8b5be89b88cd49c6a0d0dae2e8b3bca17a9ce699190e7b" type="download_file"> http://www.cpan.org/authors/id/A/AP/APEIRON/local-lib-1.008009.tar.gz </action> <action type="shell_command">tar xfvz local-lib-1.008009.tar.gz</action> ... Looking at the Galaxy internals I believe that the 'download_file' action automatically unpacks the archive and cd's into the resulting directory, hence the failure for the subsequent 'tar xfvz ...' command. But I haven't had the time yet to verify this or create a patch to see if the removal of this line addresses the problem. I don't think I've seen the problem with 'package_gnu_coreutils_8_22' that you describe however so it may be that my hypothesis is not correct. HTH Best wishes Peter On 22/02/16 05:10, Peter van Heusden wrote: Hi there Eric and others I tried to install the JBrowse tool on a dev branch server running on an Ubuntu 14.04 VM. It got stuck at the package_gnu_coreutils_8_22 dependency (revision ac64dfe4b1fb) - this ended up in "Installing tool dependencies" state. If I go look at the tool details it highlights errors in package_perl_5_18 which in turn refers to errors in gnu_coreutils (just "Error" state) and then this more informative failure for perl: "tar (child): local-lib-1.008009.tar.gz: Cannot open: No such file or directory tar (child): Error is not recoverable: exiting now tar: Child returned status 2 tar: Error is not recoverable: exiting now" I wonder if this is a sign of a download error? Digging a bit more I find the error "Shutting down process id 21094 because it generated no output for the defined timeout period of 3600.0 seconds." for gnu_coreutils. I'm trying to do a reinstall of the gnu_coreutils and perl packages to see if I can get further. Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Peter Briggs peter.briggs@manchester.ac.uk<mailto:peter.briggs@manchester.ac.uk> <mailto:peter.briggs@manchester.ac.uk<mailto:peter.briggs@manchester.ac.uk>> Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Peter Briggs peter.briggs@manchester.ac.uk<mailto:peter.briggs@manchester.ac.uk> Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
participants (3)
-
Marius van den Beek -
Peter Briggs -
Peter van Heusden