Hi,
there seems to be an issue with pulling this egg at least since yesterday.
Some eggs are out of date, attempting to fetch... Fetched http://eggs.g2.bx.psu.edu/pysam/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-... Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/sqlalchemy_migrate/sqlalchemy_migrate-0.5.4-py2.7.... Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/bx_python/bx_python-0.7.1_7b95ff194725-py2.7-linux... Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/numpy/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg Fetched http://eggs.g2.bx.psu.edu/pysqlite/pysqlite-2.5.6_3.6.17_static-py2.7-linux-... Fetched http://eggs.g2.bx.psu.edu/simplejson/simplejson-2.1.1-py2.7-linux-x86_64-ucs... Fetched http://eggs.g2.bx.psu.edu/python_lzo/python_lzo-1.08_2.03_static-py2.7-linux... Fetched http://eggs.g2.bx.psu.edu/wchartype/wchartype-0.1-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/twill/twill-0.9-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/elementtree/elementtree-1.2.6_20050316-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/decorator/decorator-3.1.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/pycrypto/pycrypto-2.0.1-py2.7-linux-x86_64-ucs4.eg... Fetched http://eggs.g2.bx.psu.edu/boto/boto-2.2.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/python_daemon/python_daemon-1.5.5-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/mercurial/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.... Fetched http://eggs.g2.bx.psu.edu/wsgiref/wsgiref-0.1.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/nose/nose-0.11.1-py2.7.egg svgfig 1.1.6 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e svgfig Fetch failed.
I'm getting a linker error while compiling HYPHY with the MPI make target:
Linking CXX executable HYPHYMPI /opt/mvapich2_18a1/lib/libmpich.a(ibv_param.o):(.bss+0x70): multiple definition of `alpha' CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o:(.bss+0xa0): first defined here /usr/bin/ld: Warning: size of symbol `alpha' changed from 256 in CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o to 4 in /opt/mvapich2_18a1/lib/libmpich.a(ibv_param.o) collect2: ld returned 1 exit status make[3]: *** [HYPHYMPI] Error 1 make[2]: *** [CMakeFiles/HYPHYMPI.dir/all] Error 2 make[1]: *** [CMakeFiles/MPI.dir/rule] Error 2 make: *** [MPI] Error 2
Is there a specific version of MPI that this requires?
The 'alpha' symbol is defined on this line in HYPHY source code file src/core/parser1.cpp:
alpha ("ABCDEFGHIJKLMNOPQRSTUVWXYZ_abcdefghijklmnopqrstuvwxyz"), numeric (".0123456789eE");
which looks reasonable. I'm not sure what is going on in the MPI library.
On Sun, July 15, 2012 3:09 pm, Di Pe wrote:
Hi,
there seems to be an issue with pulling this egg at least since yesterday.
Some eggs are out of date, attempting to fetch... Fetched http://eggs.g2.bx.psu.edu/pysam/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-... Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/sqlalchemy_migrate/sqlalchemy_migrate-0.5.4-py2.7.... Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/bx_python/bx_python-0.7.1_7b95ff194725-py2.7-linux... Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/numpy/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg Fetched http://eggs.g2.bx.psu.edu/pysqlite/pysqlite-2.5.6_3.6.17_static-py2.7-linux-... Fetched http://eggs.g2.bx.psu.edu/simplejson/simplejson-2.1.1-py2.7-linux-x86_64-ucs... Fetched http://eggs.g2.bx.psu.edu/python_lzo/python_lzo-1.08_2.03_static-py2.7-linux... Fetched http://eggs.g2.bx.psu.edu/wchartype/wchartype-0.1-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/twill/twill-0.9-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/elementtree/elementtree-1.2.6_20050316-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/decorator/decorator-3.1.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/pycrypto/pycrypto-2.0.1-py2.7-linux-x86_64-ucs4.eg... Fetched http://eggs.g2.bx.psu.edu/boto/boto-2.2.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/python_daemon/python_daemon-1.5.5-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/mercurial/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.... Fetched http://eggs.g2.bx.psu.edu/wsgiref/wsgiref-0.1.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/nose/nose-0.11.1-py2.7.egg svgfig 1.1.6 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e svgfig Fetch failed. ___________________________________________________________ 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:
This is still not working.
is it just me ?
galaxdev@galaxy1:~$ hg clone https://bitbucket.org/galaxy/galaxy-dist galaxy-dist3 requesting all changes adding changesets adding manifests adding file changes added 7149 changesets with 28071 changes to 5807 files updating to branch default 3772 files updated, 0 files merged, 0 files removed, 0 files unresolved galaxdev@galaxy1:~$ cd galaxy-dist3 galaxdev@galaxy1:~/galaxy-dist3$ galaxy-slurm-setup slurm config written to universe_wsgi.ini drmaa config written to eggs.ini This is a new install. Do you also want to configure this instance for production? [Y/N]: n galaxdev@galaxy1:~/galaxy-dist3$ galaxdev@galaxy1:~/galaxy-dist3$ sh ./run.sh Initializing community_wsgi.ini from community_wsgi.ini.sample Initializing datatypes_conf.xml from datatypes_conf.xml.sample Initializing external_service_types_conf.xml from external_service_types_conf.xml.sample Initializing migrated_tools_conf.xml from migrated_tools_conf.xml.sample Initializing reports_wsgi.ini from reports_wsgi.ini.sample Initializing shed_tool_conf.xml from shed_tool_conf.xml.sample Initializing tool_conf.xml from tool_conf.xml.sample Initializing tool_data_table_conf.xml from tool_data_table_conf.xml.sample Initializing tool_sheds_conf.xml from tool_sheds_conf.xml.sample Initializing openid_conf.xml from openid_conf.xml.sample Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample Initializing tool-data/add_scores.loc from add_scores.loc.sample Initializing tool-data/alignseq.loc from alignseq.loc.sample Initializing tool-data/all_fasta.loc from all_fasta.loc.sample Initializing tool-data/annotation_profiler_options.xml from annotation_profiler_options.xml.sample Initializing tool-data/annotation_profiler_valid_builds.txt from annotation_profiler_valid_builds.txt.sample Initializing tool-data/bfast_indexes.loc from bfast_indexes.loc.sample Initializing tool-data/binned_scores.loc from binned_scores.loc.sample Initializing tool-data/blastdb.loc from blastdb.loc.sample Initializing tool-data/blastdb_p.loc from blastdb_p.loc.sample Initializing tool-data/bowtie2_indices.loc from bowtie2_indices.loc.sample Initializing tool-data/bowtie_indices.loc from bowtie_indices.loc.sample Initializing tool-data/bowtie_indices_color.loc from bowtie_indices_color.loc.sample Initializing tool-data/bwa_index.loc from bwa_index.loc.sample Initializing tool-data/bwa_index_color.loc from bwa_index_color.loc.sample Initializing tool-data/ccat_configurations.loc from ccat_configurations.loc.sample Initializing tool-data/codingSnps.loc from codingSnps.loc.sample Initializing tool-data/encode_datasets.loc from encode_datasets.loc.sample Initializing tool-data/faseq.loc from faseq.loc.sample Initializing tool-data/funDo.loc from funDo.loc.sample Initializing tool-data/gatk_annotations.txt from gatk_annotations.txt.sample Initializing tool-data/gatk_sorted_picard_index.loc from gatk_sorted_picard_index.loc.sample Initializing tool-data/lastz_seqs.loc from lastz_seqs.loc.sample Initializing tool-data/liftOver.loc from liftOver.loc.sample Initializing tool-data/maf_index.loc from maf_index.loc.sample Initializing tool-data/maf_pairwise.loc from maf_pairwise.loc.sample Initializing tool-data/microbial_data.loc from microbial_data.loc.sample Initializing tool-data/mosaik_index.loc from mosaik_index.loc.sample Initializing tool-data/ngs_sim_fasta.loc from ngs_sim_fasta.loc.sample Initializing tool-data/perm_base_index.loc from perm_base_index.loc.sample Initializing tool-data/perm_color_index.loc from perm_color_index.loc.sample Initializing tool-data/phastOdds.loc from phastOdds.loc.sample Initializing tool-data/picard_index.loc from picard_index.loc.sample Initializing tool-data/quality_scores.loc from quality_scores.loc.sample Initializing tool-data/regions.loc from regions.loc.sample Initializing tool-data/sam_fa_indices.loc from sam_fa_indices.loc.sample Initializing tool-data/sequence_index_base.loc from sequence_index_base.loc.sample Initializing tool-data/sequence_index_color.loc from sequence_index_color.loc.sample Initializing tool-data/sift_db.loc from sift_db.loc.sample Initializing tool-data/srma_index.loc from srma_index.loc.sample Initializing tool-data/twobit.loc from twobit.loc.sample Initializing static/welcome.html from welcome.html.sample Some eggs are out of date, attempting to fetch... Fetched http://eggs.g2.bx.psu.edu/pysam/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-... Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/sqlalchemy_migrate/sqlalchemy_migrate-0.5.4-py2.7.... Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/bx_python/bx_python-0.7.1_7b95ff194725-py2.7-linux... Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/numpy/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg Fetched http://eggs.g2.bx.psu.edu/pysqlite/pysqlite-2.5.6_3.6.17_static-py2.7-linux-... Fetched http://eggs.g2.bx.psu.edu/simplejson/simplejson-2.1.1-py2.7-linux-x86_64-ucs... Fetched http://eggs.g2.bx.psu.edu/python_lzo/python_lzo-1.08_2.03_static-py2.7-linux... Fetched http://eggs.g2.bx.psu.edu/wchartype/wchartype-0.1-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/twill/twill-0.9-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/elementtree/elementtree-1.2.6_20050316-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/decorator/decorator-3.1.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/pycrypto/pycrypto-2.0.1-py2.7-linux-x86_64-ucs4.eg... Fetched http://eggs.g2.bx.psu.edu/boto/boto-2.2.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/python_daemon/python_daemon-1.5.5-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/mercurial/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.... Fetched http://eggs.g2.bx.psu.edu/wsgiref/wsgiref-0.1.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/nose/nose-0.11.1-py2.7.egg svgfig 1.1.6 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e svgfig Fetch failed.
On Sun, Jul 15, 2012 at 1:09 PM, Di Pe dipeit@gmail.com wrote:
Hi,
there seems to be an issue with pulling this egg at least since yesterday.
Some eggs are out of date, attempting to fetch... Fetched http://eggs.g2.bx.psu.edu/pysam/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-... Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/sqlalchemy_migrate/sqlalchemy_migrate-0.5.4-py2.7.... Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/bx_python/bx_python-0.7.1_7b95ff194725-py2.7-linux... Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/numpy/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg Fetched http://eggs.g2.bx.psu.edu/pysqlite/pysqlite-2.5.6_3.6.17_static-py2.7-linux-... Fetched http://eggs.g2.bx.psu.edu/simplejson/simplejson-2.1.1-py2.7-linux-x86_64-ucs... Fetched http://eggs.g2.bx.psu.edu/python_lzo/python_lzo-1.08_2.03_static-py2.7-linux... Fetched http://eggs.g2.bx.psu.edu/wchartype/wchartype-0.1-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/twill/twill-0.9-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/elementtree/elementtree-1.2.6_20050316-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/decorator/decorator-3.1.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/pycrypto/pycrypto-2.0.1-py2.7-linux-x86_64-ucs4.eg... Fetched http://eggs.g2.bx.psu.edu/boto/boto-2.2.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/python_daemon/python_daemon-1.5.5-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/mercurial/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.... Fetched http://eggs.g2.bx.psu.edu/wsgiref/wsgiref-0.1.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/nose/nose-0.11.1-py2.7.egg svgfig 1.1.6 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e svgfig Fetch failed.
On Jul 15, 2012, at 4:09 PM, Di Pe wrote:
Hi,
there seems to be an issue with pulling this egg at least since yesterday.
Some eggs are out of date, attempting to fetch... Fetched http://eggs.g2.bx.psu.edu/pysam/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-... Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/sqlalchemy_migrate/sqlalchemy_migrate-0.5.4-py2.7.... Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/bx_python/bx_python-0.7.1_7b95ff194725-py2.7-linux... Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/numpy/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg Fetched http://eggs.g2.bx.psu.edu/pysqlite/pysqlite-2.5.6_3.6.17_static-py2.7-linux-... Fetched http://eggs.g2.bx.psu.edu/simplejson/simplejson-2.1.1-py2.7-linux-x86_64-ucs... Fetched http://eggs.g2.bx.psu.edu/python_lzo/python_lzo-1.08_2.03_static-py2.7-linux... Fetched http://eggs.g2.bx.psu.edu/wchartype/wchartype-0.1-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/twill/twill-0.9-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/elementtree/elementtree-1.2.6_20050316-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/decorator/decorator-3.1.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/pycrypto/pycrypto-2.0.1-py2.7-linux-x86_64-ucs4.eg... Fetched http://eggs.g2.bx.psu.edu/boto/boto-2.2.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/python_daemon/python_daemon-1.5.5-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/mercurial/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.... Fetched http://eggs.g2.bx.psu.edu/wsgiref/wsgiref-0.1.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/nose/nose-0.11.1-py2.7.egg svgfig 1.1.6 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e svgfig Fetch failed.
Hi Di,
There seems to be some sort of case sensitivity problem going on here. The egg names in eggs.ini should be case sensitive, and the SVGFig egg should not be all lower case. Has your eggs.ini been modified?
--nate
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Chukhman, Morris -
Di Pe -
Nate Coraor