Hi all,
I'm installing the latest revision of Picard tools (efc56ee1ade4). Picard installs successfully, and the tools are appearing in the appropriate menu, but several packages that install with Picard are reporting dependency issues, and I'm concerned that not all the tools will work appropriately. The tools reporting issues are:
- package_cairo_1_12_14 (last lines of long warning/error sequence) - /vectorbase/web/Galaxy/galaxy-dist/dependency_dir/libpng/1.6.7/devteam/package_libpng_1_6_7/f48b920cae1f/lib: file not recognized: Is a directory collect2: ld returned 1 exit status make[3]: *** [libcairo.la] Error 1 make[2]: *** [all] Error 2 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2 - package_pixman_0_32_4 - /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In function `_start': (.text+0x20): undefined reference to `main' collect2: ld returned 1 exit status make[2]: *** [clip-test] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2 - package_readline_6_2 - Error downloading from URL ftp://ftp.gnu.org/gnu/readline/readline-6.2.tar.gz: <urlopen error ftp error: [Errno 110] Connection timed out>
Is anyone else having issues with these packages? Any suggestions for resolving these problems?
Thanks!
Hello Scott,
thanks to Marius van den Beek the first two issues should be fixed with this PR: https://github.com/galaxyproject/tools-devteam/pull/299
These changes were already propagated to the Main Tool Shed. Note for tool developers: for future endeavours please use packages from the IUC repository ( https://github.com/galaxyproject/tools-iuc/tree/master/packages)
As of the timeout for the readline package it seems the problem was on the ftp.gnu side and it is now resolved. In the future Galaxy plans to use a smart caching proxy to handle&mirror all source codes required by the Tool Shed installations. This effort is lead by Eric Rasche and you can see it here https://github.com/galaxyproject/cargo-port
Thank you for the report (and for using Galaxy :)).
Martin
On Mon, Nov 30, 2015 at 11:29 AM Scott Szakonyi Scott.B.Szakonyi.1@nd.edu wrote:
Hi all,
I'm installing the latest revision of Picard tools (efc56ee1ade4). Picard installs successfully, and the tools are appearing in the appropriate menu, but several packages that install with Picard are reporting dependency issues, and I'm concerned that not all the tools will work appropriately. The tools reporting issues are:
- package_cairo_1_12_14 (last lines of long warning/error sequence)
- /vectorbase/web/Galaxy/galaxy-dist/dependency_dir/libpng/1.6.7/devteam/package_libpng_1_6_7/f48b920cae1f/lib: file not recognized: Is a directory collect2: ld returned 1 exit status make[3]: *** [libcairo.la] Error 1 make[2]: *** [all] Error 2 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2
- package_pixman_0_32_4
- /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In function `_start': (.text+0x20): undefined reference to `main' collect2: ld returned 1 exit status make[2]: *** [clip-test] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2
- package_readline_6_2
- Error downloading from URL ftp://ftp.gnu.org/gnu/readline/readline-6.2.tar.gz: <urlopen error ftp error: [Errno 110] Connection timed out>
Is anyone else having issues with these packages? Any suggestions for resolving these problems?
Thanks!
-- Scott B. Szakonyi Research Programmer
*Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___________________________________________________________ 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/
Hi Martin,
Thanks very much for your reply, and also to Marius.
After some investigation, it appears that there is a firewall issue on my Galaxy server which is preventing the download of the file via FTP. I'm looking into options for that now.
Best,
Scott
On Tue, Dec 1, 2015 at 9:56 AM, Martin Čech marten@bx.psu.edu wrote:
Hello Scott,
thanks to Marius van den Beek the first two issues should be fixed with this PR: https://github.com/galaxyproject/tools-devteam/pull/299
These changes were already propagated to the Main Tool Shed. Note for tool developers: for future endeavours please use packages from the IUC repository ( https://github.com/galaxyproject/tools-iuc/tree/master/packages)
As of the timeout for the readline package it seems the problem was on the ftp.gnu side and it is now resolved. In the future Galaxy plans to use a smart caching proxy to handle&mirror all source codes required by the Tool Shed installations. This effort is lead by Eric Rasche and you can see it here https://github.com/galaxyproject/cargo-port
Thank you for the report (and for using Galaxy :)).
Martin
On Mon, Nov 30, 2015 at 11:29 AM Scott Szakonyi Scott.B.Szakonyi.1@nd.edu wrote:
Hi all,
I'm installing the latest revision of Picard tools (efc56ee1ade4). Picard installs successfully, and the tools are appearing in the appropriate menu, but several packages that install with Picard are reporting dependency issues, and I'm concerned that not all the tools will work appropriately. The tools reporting issues are:
- package_cairo_1_12_14 (last lines of long warning/error sequence)
- /vectorbase/web/Galaxy/galaxy-dist/dependency_dir/libpng/1.6.7/devteam/package_libpng_1_6_7/f48b920cae1f/lib: file not recognized: Is a directory collect2: ld returned 1 exit status make[3]: *** [libcairo.la] Error 1 make[2]: *** [all] Error 2 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2
- package_pixman_0_32_4
- /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In function `_start': (.text+0x20): undefined reference to `main' collect2: ld returned 1 exit status make[2]: *** [clip-test] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2
- package_readline_6_2
- Error downloading from URL ftp://ftp.gnu.org/gnu/readline/readline-6.2.tar.gz: <urlopen error ftp error: [Errno 110] Connection timed out>
Is anyone else having issues with these packages? Any suggestions for resolving these problems?
Thanks!
-- Scott B. Szakonyi Research Programmer
*Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___________________________________________________________ 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/
Hi Martin,
I've been able to resolve all of the issues with Picard dependencies except for Cairo. It's still failing with this error:
Tool shed repository:package_cairo_1_12_14 Tool shed repository changeset revision:f5ab0fdf3716 Tool dependency status:Error Tool dependency installation error:/bin/sh: -c: line 14: syntax error: unexpected end of file
If you have any suggestions about this error, I'd be pleased to attempt to resolve it.
Best,
Scott
On Tue, Dec 1, 2015 at 10:01 AM, Scott Szakonyi Scott.B.Szakonyi.1@nd.edu wrote:
Hi Martin,
Thanks very much for your reply, and also to Marius.
After some investigation, it appears that there is a firewall issue on my Galaxy server which is preventing the download of the file via FTP. I'm looking into options for that now.
Best,
Scott
On Tue, Dec 1, 2015 at 9:56 AM, Martin Čech marten@bx.psu.edu wrote:
Hello Scott,
thanks to Marius van den Beek the first two issues should be fixed with this PR: https://github.com/galaxyproject/tools-devteam/pull/299
These changes were already propagated to the Main Tool Shed. Note for tool developers: for future endeavours please use packages from the IUC repository ( https://github.com/galaxyproject/tools-iuc/tree/master/packages)
As of the timeout for the readline package it seems the problem was on the ftp.gnu side and it is now resolved. In the future Galaxy plans to use a smart caching proxy to handle&mirror all source codes required by the Tool Shed installations. This effort is lead by Eric Rasche and you can see it here https://github.com/galaxyproject/cargo-port
Thank you for the report (and for using Galaxy :)).
Martin
On Mon, Nov 30, 2015 at 11:29 AM Scott Szakonyi < Scott.B.Szakonyi.1@nd.edu> wrote:
Hi all,
I'm installing the latest revision of Picard tools (efc56ee1ade4). Picard installs successfully, and the tools are appearing in the appropriate menu, but several packages that install with Picard are reporting dependency issues, and I'm concerned that not all the tools will work appropriately. The tools reporting issues are:
- package_cairo_1_12_14 (last lines of long warning/error sequence)
- /vectorbase/web/Galaxy/galaxy-dist/dependency_dir/libpng/1.6.7/devteam/package_libpng_1_6_7/f48b920cae1f/lib: file not recognized: Is a directory collect2: ld returned 1 exit status make[3]: *** [libcairo.la] Error 1 make[2]: *** [all] Error 2 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2
- package_pixman_0_32_4
- /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In function `_start': (.text+0x20): undefined reference to `main' collect2: ld returned 1 exit status make[2]: *** [clip-test] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2
- package_readline_6_2
- Error downloading from URL ftp://ftp.gnu.org/gnu/readline/readline-6.2.tar.gz: <urlopen error ftp error: [Errno 110] Connection timed out>
Is anyone else having issues with these packages? Any suggestions for resolving these problems?
Thanks!
-- Scott B. Szakonyi Research Programmer
*Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___________________________________________________________ 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/
-- Scott B. Szakonyi Research Programmer
*Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu
Hi Scott, Martin,
there was still a small problem in cairo. I made a PR to fix this ( https://github.com/galaxyproject/tools-devteam/pull/300) I should have paid a bit more attention ...
Cheers, Marius
On 1 December 2015 at 22:46, Scott Szakonyi Scott.B.Szakonyi.1@nd.edu wrote:
Hi Martin,
I've been able to resolve all of the issues with Picard dependencies except for Cairo. It's still failing with this error:
Tool shed repository:package_cairo_1_12_14 Tool shed repository changeset revision:f5ab0fdf3716 Tool dependency status:Error Tool dependency installation error:/bin/sh: -c: line 14: syntax error: unexpected end of file
If you have any suggestions about this error, I'd be pleased to attempt to resolve it.
Best,
Scott
On Tue, Dec 1, 2015 at 10:01 AM, Scott Szakonyi <Scott.B.Szakonyi.1@nd.edu
wrote:
Hi Martin,
Thanks very much for your reply, and also to Marius.
After some investigation, it appears that there is a firewall issue on my Galaxy server which is preventing the download of the file via FTP. I'm looking into options for that now.
Best,
Scott
On Tue, Dec 1, 2015 at 9:56 AM, Martin Čech marten@bx.psu.edu wrote:
Hello Scott,
thanks to Marius van den Beek the first two issues should be fixed with this PR: https://github.com/galaxyproject/tools-devteam/pull/299
These changes were already propagated to the Main Tool Shed. Note for tool developers: for future endeavours please use packages from the IUC repository ( https://github.com/galaxyproject/tools-iuc/tree/master/packages)
As of the timeout for the readline package it seems the problem was on the ftp.gnu side and it is now resolved. In the future Galaxy plans to use a smart caching proxy to handle&mirror all source codes required by the Tool Shed installations. This effort is lead by Eric Rasche and you can see it here https://github.com/galaxyproject/cargo-port
Thank you for the report (and for using Galaxy :)).
Martin
On Mon, Nov 30, 2015 at 11:29 AM Scott Szakonyi < Scott.B.Szakonyi.1@nd.edu> wrote:
Hi all,
I'm installing the latest revision of Picard tools (efc56ee1ade4). Picard installs successfully, and the tools are appearing in the appropriate menu, but several packages that install with Picard are reporting dependency issues, and I'm concerned that not all the tools will work appropriately. The tools reporting issues are:
- package_cairo_1_12_14 (last lines of long warning/error sequence)
- /vectorbase/web/Galaxy/galaxy-dist/dependency_dir/libpng/1.6.7/devteam/package_libpng_1_6_7/f48b920cae1f/lib: file not recognized: Is a directory collect2: ld returned 1 exit status make[3]: *** [libcairo.la] Error 1 make[2]: *** [all] Error 2 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2
- package_pixman_0_32_4
- /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In function `_start': (.text+0x20): undefined reference to `main' collect2: ld returned 1 exit status make[2]: *** [clip-test] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2
- package_readline_6_2
- Error downloading from URL ftp://ftp.gnu.org/gnu/readline/readline-6.2.tar.gz: <urlopen error ftp error: [Errno 110] Connection timed out>
Is anyone else having issues with these packages? Any suggestions for resolving these problems?
Thanks!
-- Scott B. Szakonyi Research Programmer
*Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___________________________________________________________ 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/
-- Scott B. Szakonyi Research Programmer
*Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu
-- Scott B. Szakonyi Research Programmer
*Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu
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/
This is now updated in MTS. Thanks guys.
M.
On Tue, Dec 1, 2015 at 4:55 PM Marius van den Beek m.vandenbeek@gmail.com wrote:
Hi Scott, Martin,
there was still a small problem in cairo. I made a PR to fix this ( https://github.com/galaxyproject/tools-devteam/pull/300) I should have paid a bit more attention ...
Cheers, Marius
On 1 December 2015 at 22:46, Scott Szakonyi Scott.B.Szakonyi.1@nd.edu wrote:
Hi Martin,
I've been able to resolve all of the issues with Picard dependencies except for Cairo. It's still failing with this error:
Tool shed repository:package_cairo_1_12_14 Tool shed repository changeset revision:f5ab0fdf3716 Tool dependency status:Error Tool dependency installation error:/bin/sh: -c: line 14: syntax error: unexpected end of file
If you have any suggestions about this error, I'd be pleased to attempt to resolve it.
Best,
Scott
On Tue, Dec 1, 2015 at 10:01 AM, Scott Szakonyi < Scott.B.Szakonyi.1@nd.edu> wrote:
Hi Martin,
Thanks very much for your reply, and also to Marius.
After some investigation, it appears that there is a firewall issue on my Galaxy server which is preventing the download of the file via FTP. I'm looking into options for that now.
Best,
Scott
On Tue, Dec 1, 2015 at 9:56 AM, Martin Čech marten@bx.psu.edu wrote:
Hello Scott,
thanks to Marius van den Beek the first two issues should be fixed with this PR: https://github.com/galaxyproject/tools-devteam/pull/299
These changes were already propagated to the Main Tool Shed. Note for tool developers: for future endeavours please use packages from the IUC repository ( https://github.com/galaxyproject/tools-iuc/tree/master/packages)
As of the timeout for the readline package it seems the problem was on the ftp.gnu side and it is now resolved. In the future Galaxy plans to use a smart caching proxy to handle&mirror all source codes required by the Tool Shed installations. This effort is lead by Eric Rasche and you can see it here https://github.com/galaxyproject/cargo-port
Thank you for the report (and for using Galaxy :)).
Martin
On Mon, Nov 30, 2015 at 11:29 AM Scott Szakonyi < Scott.B.Szakonyi.1@nd.edu> wrote:
Hi all,
I'm installing the latest revision of Picard tools (efc56ee1ade4). Picard installs successfully, and the tools are appearing in the appropriate menu, but several packages that install with Picard are reporting dependency issues, and I'm concerned that not all the tools will work appropriately. The tools reporting issues are:
- package_cairo_1_12_14 (last lines of long warning/error sequence)
- /vectorbase/web/Galaxy/galaxy-dist/dependency_dir/libpng/1.6.7/devteam/package_libpng_1_6_7/f48b920cae1f/lib: file not recognized: Is a directory collect2: ld returned 1 exit status make[3]: *** [libcairo.la] Error 1 make[2]: *** [all] Error 2 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2
- package_pixman_0_32_4
- /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In function `_start': (.text+0x20): undefined reference to `main' collect2: ld returned 1 exit status make[2]: *** [clip-test] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2
- package_readline_6_2
- Error downloading from URL ftp://ftp.gnu.org/gnu/readline/readline-6.2.tar.gz: <urlopen error ftp error: [Errno 110] Connection timed out>
Is anyone else having issues with these packages? Any suggestions for resolving these problems?
Thanks!
-- Scott B. Szakonyi Research Programmer
*Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___________________________________________________________ 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/
-- Scott B. Szakonyi Research Programmer
*Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu
-- Scott B. Szakonyi Research Programmer
*Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu
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/
Excellent! Install completed! Thanks very much.
On Tue, Dec 1, 2015 at 3:57 PM, Martin Čech marten@bx.psu.edu wrote:
This is now updated in MTS. Thanks guys.
M.
On Tue, Dec 1, 2015 at 4:55 PM Marius van den Beek m.vandenbeek@gmail.com wrote:
Hi Scott, Martin,
there was still a small problem in cairo. I made a PR to fix this ( https://github.com/galaxyproject/tools-devteam/pull/300) I should have paid a bit more attention ...
Cheers, Marius
On 1 December 2015 at 22:46, Scott Szakonyi Scott.B.Szakonyi.1@nd.edu wrote:
Hi Martin,
I've been able to resolve all of the issues with Picard dependencies except for Cairo. It's still failing with this error:
Tool shed repository:package_cairo_1_12_14 Tool shed repository changeset revision:f5ab0fdf3716 Tool dependency status:Error Tool dependency installation error:/bin/sh: -c: line 14: syntax error: unexpected end of file
If you have any suggestions about this error, I'd be pleased to attempt to resolve it.
Best,
Scott
On Tue, Dec 1, 2015 at 10:01 AM, Scott Szakonyi < Scott.B.Szakonyi.1@nd.edu> wrote:
Hi Martin,
Thanks very much for your reply, and also to Marius.
After some investigation, it appears that there is a firewall issue on my Galaxy server which is preventing the download of the file via FTP. I'm looking into options for that now.
Best,
Scott
On Tue, Dec 1, 2015 at 9:56 AM, Martin Čech marten@bx.psu.edu wrote:
Hello Scott,
thanks to Marius van den Beek the first two issues should be fixed with this PR: https://github.com/galaxyproject/tools-devteam/pull/299
These changes were already propagated to the Main Tool Shed. Note for tool developers: for future endeavours please use packages from the IUC repository ( https://github.com/galaxyproject/tools-iuc/tree/master/packages)
As of the timeout for the readline package it seems the problem was on the ftp.gnu side and it is now resolved. In the future Galaxy plans to use a smart caching proxy to handle&mirror all source codes required by the Tool Shed installations. This effort is lead by Eric Rasche and you can see it here https://github.com/galaxyproject/cargo-port
Thank you for the report (and for using Galaxy :)).
Martin
On Mon, Nov 30, 2015 at 11:29 AM Scott Szakonyi < Scott.B.Szakonyi.1@nd.edu> wrote:
Hi all,
I'm installing the latest revision of Picard tools (efc56ee1ade4). Picard installs successfully, and the tools are appearing in the appropriate menu, but several packages that install with Picard are reporting dependency issues, and I'm concerned that not all the tools will work appropriately. The tools reporting issues are:
- package_cairo_1_12_14 (last lines of long warning/error
sequence)
- /vectorbase/web/Galaxy/galaxy-dist/dependency_dir/libpng/1.6.7/devteam/package_libpng_1_6_7/f48b920cae1f/lib: file not recognized: Is a directory collect2: ld returned 1 exit status make[3]: *** [libcairo.la] Error 1 make[2]: *** [all] Error 2 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2
- package_pixman_0_32_4
- /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In function `_start': (.text+0x20): undefined reference to `main' collect2: ld returned 1 exit status make[2]: *** [clip-test] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2
- package_readline_6_2
- Error downloading from URL ftp://ftp.gnu.org/gnu/readline/readline-6.2.tar.gz: <urlopen error ftp error: [Errno 110] Connection timed out>
Is anyone else having issues with these packages? Any suggestions for resolving these problems?
Thanks!
-- Scott B. Szakonyi Research Programmer
*Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___________________________________________________________ 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/
-- Scott B. Szakonyi Research Programmer
*Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu
-- Scott B. Szakonyi Research Programmer
*Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu
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/
galaxy-dev@lists.galaxyproject.org
-
Marius van den Beek -
Martin Čech -
Scott Szakonyi