New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Still Loading... #1160

Closed
tiramisutes opened this Issue Aug 6, 2018 · 15 comments

Comments

Projects
None yet
2 participants
@tiramisutes

tiramisutes commented Aug 6, 2018

Dear,
I want to install the jbrowse software with no root privilege.
I clone it and install in my home as follows

cd /public/home/zpxu/Jbrowse
git clone https://github.com/GMOD/jbrowse
cd jbrowse
./setup.sh

and run with ./utils/jb_run.js -p 3000, But when I open the http://localhost:3000/ using firefox, it just rests on Loading... page.

@cmdcolin

This comment has been minimized.

Show comment
Hide comment
@cmdcolin

cmdcolin Aug 6, 2018

Contributor

Can you check out the setup.log file and paste it here? I am going to suspect that somehow it did not complete properly

Contributor

cmdcolin commented Aug 6, 2018

Can you check out the setup.log file and paste it here? I am going to suspect that somehow it did not complete properly

@tiramisutes

This comment has been minimized.

Show comment
Hide comment
@tiramisutes

tiramisutes Aug 6, 2018

```

Gathering system information ...
============== System information ====

  • lsb_release -a
    LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
    Distributor ID: CentOS
    Description: CentOS release 6.5 (Final)
    Release: 6.5
    Codename: Final

  • uname -a
    Linux node102 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

  • sw_vers
    ./setup.sh: line 74: sw_vers: command not found

  • grep MemTotal /proc/meminfo
    MemTotal: 65939372 kB

  • echo

  • echo

done.

NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, please use JBrowse 1.12.3 or earlier.

Minimal release, skipping node and Webpack build

Installing Perl prerequisites ...

  • bin/cpanm -v --notest -l extlib/ --installdeps .
    cpanm (App::cpanminus) 1.7043 on perl 5.010001 built for x86_64-linux-thread-multi
    Work directory is /public/home/zpxu/.cpanm/work/1533462225.27547
    You have make /usr/bin/make
    You have LWP 5.833
    You have /bin/tar: tar (GNU tar) 1.23
    Copyright (C) 2010 Free Software Foundation, Inc.
    License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html.
    This is free software: you are free to change and redistribute it.
    There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
You have /usr/bin/unzip
Entering /public/home/zpxu/JBrowse-1.15.1
Running Makefile.PL
--> Working on .
Configuring /public/home/zpxu/JBrowse-1.15.1 ... Can't parse version 'dev'
Can't parse version 'dev'
Generating a Unix-style Makefile
Writing Makefile for JBrowse
Writing MYMETA.yml and MYMETA.json
Checking dependencies from MYMETA.json ...
Checking if you have Capture::Tiny 0 ... Yes (0.30)
Checking if you have Pod::Usage 0 ... Yes (1.36)
Checking if you have Storable 0 ... Yes (2.20)
Checking if you have JSON::XS 0 ... Yes (3.04)
Checking if you have List::Util 0 ... Yes (1.21)
Checking if you have PerlIO::gzip 0 ... Yes (0.20)
Checking if you have Digest::Crc32 0 ... Yes (0.01)
Checking if you have File::Path 2 ... Yes (2.08)
Checking if you have local::lib 0 ... Yes (2.000024)
Checking if you have List::MoreUtils 0.28 ... Yes (0.428)
Checking if you have Bio::FeatureIO 0 ... Yes (1.6.905)
Checking if you have DBI 0 ... Yes (1.609)
Checking if you have Getopt::Long 0 ... Yes (2.42)
Checking if you have warnings 0 ... Yes (1.06)
Checking if you have base 0 ... Yes (2.14)
Checking if you have IO::File 0 ... Yes (1.14)
Checking if you have Data::Dumper 0 ... Yes (2.154)
Checking if you have Bio::GFF3::LowLevel 1.8 ... Yes (2.0)
Checking if you have Bio::Index::Fasta 0 ... Yes (undef)
Checking if you have DB_File 0 ... Yes (1.820)
Checking if you have Bio::Root::Version 1.006000 ... Yes (1.007002)
Checking if you have Bio::Annotation::SimpleValue 0 ... Yes (undef)
Checking if you have vars 0 ... Yes (1.01)
Checking if you have Parse::RecDescent 0 ... Yes (1.967015)
Checking if you have Test::More 0 ... Yes (1.001011)
Checking if you have strict 0 ... Yes (1.04)
Checking if you have File::Temp 0 ... Yes (0.22)
Checking if you have File::Copy::Recursive 0 ... Yes (0.44)
Checking if you have Scalar::Util 0 ... Yes (1.21)
Checking if you have FindBin 0 ... Yes (1.50)
Checking if you have DBD::SQLite 0 ... Yes (1.27)
Checking if you have URI::Escape 0 ... Yes (3.31)
Checking if you have File::Spec 0 ... Yes (3.30)
Checking if you have Heap::Simple 0 ... Yes (0.13)
Checking if you have Heap::Simple::XS 0 ... Yes (0.10)
Checking if you have Fcntl 0 ... Yes (1.06)
Checking if you have POSIX 0 ... Yes (1.17)
Checking if you have Devel::Size 0 ... Yes (0.82)
Checking if you have File::Spec::Functions 0 ... Yes (3.30)
Checking if you have Bio::SeqFeature::Lite 0 ... Yes (undef)
Checking if you have Bio::GFF3::LowLevel::Parser 1.8 ... Yes (2.0)
Checking if you have IO::Uncompress::Gunzip 0 ... Yes (2.021)
Checking if you have Hash::Merge 0 ... Yes (0.300)
Checking if you have constant 0 ... Yes (1.17)
Checking if you have Exporter 0 ... Yes (5.63)
Checking if you have Bio::OntologyIO 0 ... Yes (undef)
Checking if you have Bio::SeqFeature::Annotated 0 ... Yes (1.6.905)
Checking if you have Carp 0 ... Yes (1.38)
Checking if you have Test::Warn 0 ... Yes (0.30)
Checking if you have File::Next 0 ... Yes (1.16)
Checking if you have File::Basename 0 ... Yes (2.77)
Checking if you have JSON 2 ... Yes (2.97001)
Checking if you have Cwd 0 ... Yes (3.30)
OK
<== Installed dependencies for .. Finishing.

  • bin/cpanm -v --notest -l extlib/ --installdeps .
    cpanm (App::cpanminus) 1.7043 on perl 5.010001 built for x86_64-linux-thread-multi
    Work directory is /public/home/zpxu/.cpanm/work/1533462230.27658
    You have make /usr/bin/make
    You have LWP 5.833
    You have /bin/tar: tar (GNU tar) 1.23
    Copyright (C) 2010 Free Software Foundation, Inc.
    License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html.
    This is free software: you are free to change and redistribute it.
    There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
You have /usr/bin/unzip
Entering /public/home/zpxu/JBrowse-1.15.1
Running Makefile.PL
--> Working on .
Configuring /public/home/zpxu/JBrowse-1.15.1 ... Can't parse version 'dev'
Can't parse version 'dev'
Generating a Unix-style Makefile
Writing Makefile for JBrowse
Writing MYMETA.yml and MYMETA.json
Checking dependencies from MYMETA.json ...
Checking if you have Capture::Tiny 0 ... Yes (0.30)
Checking if you have Pod::Usage 0 ... Yes (1.36)
Checking if you have Storable 0 ... Yes (2.20)
Checking if you have JSON::XS 0 ... Yes (3.04)
Checking if you have List::Util 0 ... Yes (1.21)
Checking if you have PerlIO::gzip 0 ... Yes (0.20)
Checking if you have Digest::Crc32 0 ... Yes (0.01)
Checking if you have File::Path 2 ... Yes (2.08)
Checking if you have local::lib 0 ... Yes (2.000024)
Checking if you have List::MoreUtils 0.28 ... Yes (0.428)
Checking if you have Bio::FeatureIO 0 ... Yes (1.6.905)
Checking if you have DBI 0 ... Yes (1.609)
Checking if you have Getopt::Long 0 ... Yes (2.42)
Checking if you have warnings 0 ... Yes (1.06)
Checking if you have base 0 ... Yes (2.14)
Checking if you have IO::File 0 ... Yes (1.14)
Checking if you have Data::Dumper 0 ... Yes (2.154)
Checking if you have Bio::GFF3::LowLevel 1.8 ... Yes (2.0)
Checking if you have Bio::Index::Fasta 0 ... Yes (undef)
Checking if you have DB_File 0 ... Yes (1.820)
Checking if you have Bio::Root::Version 1.006000 ... Yes (1.007002)
Checking if you have Bio::Annotation::SimpleValue 0 ... Yes (undef)
Checking if you have vars 0 ... Yes (1.01)
Checking if you have Parse::RecDescent 0 ... Yes (1.967015)
Checking if you have Test::More 0 ... Yes (1.001011)
Checking if you have strict 0 ... Yes (1.04)
Checking if you have File::Temp 0 ... Yes (0.22)
Checking if you have File::Copy::Recursive 0 ... Yes (0.44)
Checking if you have Scalar::Util 0 ... Yes (1.21)
Checking if you have FindBin 0 ... Yes (1.50)
Checking if you have DBD::SQLite 0 ... Yes (1.27)
Checking if you have URI::Escape 0 ... Yes (3.31)
Checking if you have File::Spec 0 ... Yes (3.30)
Checking if you have Heap::Simple 0 ... Yes (0.13)
Checking if you have Heap::Simple::XS 0 ... Yes (0.10)
Checking if you have Fcntl 0 ... Yes (1.06)
Checking if you have POSIX 0 ... Yes (1.17)
Checking if you have Devel::Size 0 ... Yes (0.82)
Checking if you have File::Spec::Functions 0 ... Yes (3.30)
Checking if you have Bio::SeqFeature::Lite 0 ... Yes (undef)
Checking if you have Bio::GFF3::LowLevel::Parser 1.8 ... Yes (2.0)
Checking if you have IO::Uncompress::Gunzip 0 ... Yes (2.021)
Checking if you have Hash::Merge 0 ... Yes (0.300)
Checking if you have constant 0 ... Yes (1.17)
Checking if you have Exporter 0 ... Yes (5.63)
Checking if you have Bio::OntologyIO 0 ... Yes (undef)
Checking if you have Bio::SeqFeature::Annotated 0 ... Yes (1.6.905)
Checking if you have Carp 0 ... Yes (1.38)
Checking if you have Test::Warn 0 ... Yes (0.30)
Checking if you have File::Next 0 ... Yes (1.16)
Checking if you have File::Basename 0 ... Yes (2.77)
Checking if you have JSON 2 ... Yes (2.97001)
Checking if you have Cwd 0 ... Yes (3.30)
OK
<== Installed dependencies for .. Finishing.

  • set -e
  • bin/cpanm -v --notest -l extlib/ --installdeps .
    cpanm (App::cpanminus) 1.7043 on perl 5.010001 built for x86_64-linux-thread-multi
    Work directory is /public/home/zpxu/.cpanm/work/1533462231.27667
    You have make /usr/bin/make
    You have LWP 5.833
    You have /bin/tar: tar (GNU tar) 1.23
    Copyright (C) 2010 Free Software Foundation, Inc.
    License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html.
    This is free software: you are free to change and redistribute it.
    There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
You have /usr/bin/unzip
Entering /public/home/zpxu/JBrowse-1.15.1
Running Makefile.PL
--> Working on .
Configuring /public/home/zpxu/JBrowse-1.15.1 ... Can't parse version 'dev'
Can't parse version 'dev'
Generating a Unix-style Makefile
Writing Makefile for JBrowse
Writing MYMETA.yml and MYMETA.json
Checking dependencies from MYMETA.json ...
Checking if you have Capture::Tiny 0 ... Yes (0.30)
Checking if you have Pod::Usage 0 ... Yes (1.36)
Checking if you have Storable 0 ... Yes (2.20)
Checking if you have JSON::XS 0 ... Yes (3.04)
Checking if you have List::Util 0 ... Yes (1.21)
Checking if you have PerlIO::gzip 0 ... Yes (0.20)
Checking if you have Digest::Crc32 0 ... Yes (0.01)
Checking if you have File::Path 2 ... Yes (2.08)
Checking if you have local::lib 0 ... Yes (2.000024)
Checking if you have List::MoreUtils 0.28 ... Yes (0.428)
Checking if you have Bio::FeatureIO 0 ... Yes (1.6.905)
Checking if you have DBI 0 ... Yes (1.609)
Checking if you have Getopt::Long 0 ... Yes (2.42)
Checking if you have warnings 0 ... Yes (1.06)
Checking if you have base 0 ... Yes (2.14)
Checking if you have IO::File 0 ... Yes (1.14)
Checking if you have Data::Dumper 0 ... Yes (2.154)
Checking if you have Bio::GFF3::LowLevel 1.8 ... Yes (2.0)
Checking if you have Bio::Index::Fasta 0 ... Yes (undef)
Checking if you have DB_File 0 ... Yes (1.820)
Checking if you have Bio::Root::Version 1.006000 ... Yes (1.007002)
Checking if you have Bio::Annotation::SimpleValue 0 ... Yes (undef)
Checking if you have vars 0 ... Yes (1.01)
Checking if you have Parse::RecDescent 0 ... Yes (1.967015)
Checking if you have Test::More 0 ... Yes (1.001011)
Checking if you have strict 0 ... Yes (1.04)
Checking if you have File::Temp 0 ... Yes (0.22)
Checking if you have File::Copy::Recursive 0 ... Yes (0.44)
Checking if you have Scalar::Util 0 ... Yes (1.21)
Checking if you have FindBin 0 ... Yes (1.50)
Checking if you have DBD::SQLite 0 ... Yes (1.27)
Checking if you have URI::Escape 0 ... Yes (3.31)
Checking if you have File::Spec 0 ... Yes (3.30)
Checking if you have Heap::Simple 0 ... Yes (0.13)
Checking if you have Heap::Simple::XS 0 ... Yes (0.10)
Checking if you have Fcntl 0 ... Yes (1.06)
Checking if you have POSIX 0 ... Yes (1.17)
Checking if you have Devel::Size 0 ... Yes (0.82)
Checking if you have File::Spec::Functions 0 ... Yes (3.30)
Checking if you have Bio::SeqFeature::Lite 0 ... Yes (undef)
Checking if you have Bio::GFF3::LowLevel::Parser 1.8 ... Yes (2.0)
Checking if you have IO::Uncompress::Gunzip 0 ... Yes (2.021)
Checking if you have Hash::Merge 0 ... Yes (0.300)
Checking if you have constant 0 ... Yes (1.17)
Checking if you have Exporter 0 ... Yes (5.63)
Checking if you have Bio::OntologyIO 0 ... Yes (undef)
Checking if you have Bio::SeqFeature::Annotated 0 ... Yes (1.6.905)
Checking if you have Carp 0 ... Yes (1.38)
Checking if you have Test::Warn 0 ... Yes (0.30)
Checking if you have File::Next 0 ... Yes (1.16)
Checking if you have File::Basename 0 ... Yes (2.77)
Checking if you have JSON 2 ... Yes (2.97001)
Checking if you have Cwd 0 ... Yes (3.30)
OK
<== Installed dependencies for .. Finishing.

done.

Formatting Volvox example data ...

  • rm -rf sample_data/json/volvox
  • bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa --out sample_data/json/volvox
  • '[' 0 -eq 1 ']'
  • bin/biodb-to-json.pl -v --conf docs/tutorial/conf_files/volvox.json --out sample_data/json/volvox

working on refseq ctgA
working on track ExampleFeatures
mergedTrackCfg: $VAR1 = {
'feature' => [
'remark'
],
'autocomplete' => 'all',
'track' => 'ExampleFeatures',
'style' => {
'className' => 'feature2'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - Example Features'
};
searching for features of type: remark
working on track NameTest
mergedTrackCfg: $VAR1 = {
'feature' => [
'protein_coding_primary_transcript',
'polypeptide'
],
'autocomplete' => 'all',
'track' => 'NameTest',
'style' => {
'className' => 'feature2'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - Name test track has a really long track label'
};
searching for features of type: protein_coding_primary_transcript, polypeptide
working on track snps
mergedTrackCfg: $VAR1 = {
'feature' => [
'SNP'
],
'autocomplete' => 'all',
'track' => 'snps',
'style' => {
'className' => 'triangle hgred'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - SNPs'
};
searching for features of type: SNP
working on track Motifs
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Motifs',
'style' => {
'className' => 'feature3',
'label' => 'function(feature) { return feature.get('Name')+' (via JS callback)' }',
'description' => 'function(feature) { return feature.get('Name')+': '+feature.get('Note'); }'
},
'description' => 1,
'key' => 'HTMLFeatures - Example motifs',
'feature' => [
'polypeptide_domain'
],
'compress' => 0,
'category' => 'Miscellaneous'
};
searching for features of type: polypeptide_domain
working on track malformed_alignments
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'malformed_alignments',
'style' => {
'className' => 'feature4'
},
'menuTemplate' => [
{
'children' => [
{
'children' => [
{
'iconClass' => 'dijitIconBookmark',
'url' => 'http://wiki.trin.org.au/{name}-{start}-{end}',
'action' => 'newWindow',
'label' => 'Query trin for {name}'
},
{
'iconClass' => 'dijitIconSearch',
'url' => 'http://example.com/{name}-{start}-{end}',
'label' => 'Query example.com for {name}'
}
],
'label' => 'Check gene on databases'
},
{
'label' => '2nd child of demo'
},
{
'label' => '3rd child: this is a track'
}
],
'label' => 'Item with submenu'
},
{
'iconClass' => 'dijitIconDatabase',
'url' => 'http://www.example.com?featurename={name}',
'action' => 'iframeDialog',
'title' => 'The magnificent example.com (feature {name})',
'label' => 'Open example.com in an iframe popup'
},
{
'iconClass' => 'dijitIconDatabase',
'url' => 'sample_data/test_snippet.html?featurename={name}:{start}-{end}',
'action' => 'xhrDialog',
'title' => 'function(track,feature,div) { return 'Random XHR HTML '+Math.random()+' title!'; }',
'label' => 'Open popup with XHR HTML snippet (btw this is feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => 'function(track,feature,div) { return '

'+feature.get('name')+'

This is some test content!

This message brought to you by the number '+Math.round(Math.random()*100)+'.

';} ',
'action' => 'contentDialog',
'title' => 'function(track,feature,div) { return 'Random content snippet '+Math.random()+' title!'; }',
'label' => 'Popup with content snippet from a function (feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => '

{name}

This is some test content about {name}, which goes from {start} to {end} on the {strand} strand.

',
'action' => 'contentDialog',
'title' => '{randomNumberTitle}',
'label' => 'Popup with content snippet from string (feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'action' => '{exampleFeatureClick}',
'label' => '{randomNumberLabel}'
}
],
'hooks' => {
'modify' => 'function( track, feature, div ) { div.style.backgroundColor = ['green','blue','red','orange','purple'][Math.round(Math.random()5)];}'
},
'key' => 'HTMLFeatures - Features with right-click menus',
'feature' => [
'match'
],
'shortDescription' => 'Features with customized right-click menus',
'compress' => 0,
'metadata' => {
'category' => 'Miscellaneous',
'Description' => 'Features with extensively customized right-click menus, and with their colors set at random by a JavaScript callback.'
}
};
searching for features of type: match
working on track Genes
mergedTrackCfg: $VAR1 = {
'fmtDetailValue_Name' => 'function(name,feature) { if(feature.get('type')=='gene') { return name + ' <a href=http://www.ncbi.nlm.nih.gov/gquery/?term=\'+name+\'>[NCBI custom link]'; } else { return name; } }',
'fmtMetaDescription_Name' => 'function(name) { return '[Custom description]'; }',
'fmtMetaValue_Name' => 'function(name) { return name+' [Track with custom callbacks for About track popup]'; }',
'key' => 'CanvasFeatures - Protein-coding genes',
'onClick' => {
'action' => 'defaultDialog',
'title' => '{type} {name}',
'label' => '<div style='font:normal 12px Univers,Helvetica,Arial,sans-serif'><div style='font-weight:bold'>Custom tooltip<div style='color:blue;'>Feature name: {name}
Feature start: {start}
Feature end: {end}'
},
'feature' => [
'gene'
],
'fmtDetailField_Name' => 'function(name,feature) { if(feature.get('type')=='gene') { return 'Gene Name'; } else { return name; } }',
'fmtMetaField_Name' => 'function(name) { return 'Track Name'; }',
'fmtDetailField_Load_id' => 'function(name,feature) { /
remove field from dialog box */ return null; }',
'category' => 'Transcripts',
'metadata' => {
'ncbi_submission_model' => 'Generic',
'insdc_first_public' => '2018-05-15T00:00:00Z',
'Link: ENA study page' => 'http://www.ebi.ac.uk/ena/',
'library_total_amount_of_reads' => '3349981',
'insdc_secondary_accession' => 'SRS12345678',
'insdc_center_name' => 'INSDC Sample',
'ncbi_submission_package' => 'Generic.1.0',
'sample_name' => 'GSM12345678',
'ENA first public' => '2018-05-16',
'study' => 'SRP12345678 a study of volvox',
'organism' => 'Volvox',
'library_size_approx' => '1-5mln',
'Link: RNASeq-er analysis results' => 'ftp://ftp.ebi.ac.uk/pub/databases/arrayexpress/',
'insdc_last_update' => '2018-05-15T01:18:23.110Z',
'insdc_status' => 'live',
'developmental_stage' => 'stage 6- 330 min',
'mapping_quality_approx' => 'under 50%',
'tissue' => 'embryo',
'source_name' => 'Volvox 6- 330 min',
'mapping_fraction_of_uniquely_mapped_reads' => '0.429',
'ENA last update' => '2018-05-16',
'description_title' => 'Volvox_mRNA_rep_2_6'
},
'autocomplete' => 'all',
'track' => 'Genes',
'style' => {
'className' => 'feature5'
},
'menuTemplate' => [
{
'label' => 'View details'
},
{
'label' => 'Zoom this gene'
},
{
'label' => 'Highlight this gene'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => '

{name}

This is some test content about {type} {name}, which goes from {start} to {end} on the {strand} strand.',
'action' => 'contentDialog',
'title' => '{randomNumberTitle}',
'label' => 'Popup with content snippet from string (feature {name})'
}
],
'trackType' => 'NeatCanvasFeatures/View/Track/NeatFeatures',
'compress' => 0
};
searching for features of type: gene
working on track ReadingFrame
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'ReadingFrame',
'style' => {
'className' => 'cds'
},
'key' => 'HTMLFeatures - mRNAs',
'onClick' => {
'url' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}',
'title' => 'NCBI search box',
'label' => 'Search for {name} at NCBI
Feature start {start}
Feature end {end}'
},
'feature' => [
'mRNA'
],
'trackType' => 'NeatHTMLFeatures/View/Track/NeatFeatures',
'phase' => 1,
'compress' => 0,
'category' => 'Transcripts'
};
searching for features of type: mRNA
working on track CDS
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'CDS',
'style' => {
'className' => 'cds',
'linkTemplate' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}-{start}-{end}'
},
'key' => 'CanvasFeatures - mixed mRNAs and CDSs',
'feature' => [
'CDS:bare_predicted',
'mRNA:exonerate',
'mRNA:predicted'
],
'trackType' => 'CanvasFeatures',
'compress' => 0,
'category' => 'Transcripts'
};
searching for features of type: CDS:bare_predicted, mRNA:exonerate, mRNA:predicted
working on track Transcript
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Transcript',
'style' => {
'className' => 'feature',
'color' => '#E32A3A',
'description' => 'customdescription'
},
'description' => 1,
'key' => 'CanvasFeatures - transcripts',
'onClick' => '{exampleFeatureClick}',
'feature' => [
'mRNA:exonerate'
],
'trackType' => 'JBrowse/View/Track/CanvasFeatures',
'compress' => 0,
'category' => 'Transcripts',
'showNoteInAttributes' => bless( do{(my $o = 1)}, 'JSON::PP::Boolean' ),
'subfeatures' => $VAR1->{'showNoteInAttributes'}
};
searching for features of type: mRNA:exonerate
working on track Clones
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Clones',
'style' => {
'className' => 'exon'
},
'description' => 1,
'key' => 'HTMLFeatures - Fingerprinted BACs',
'feature' => [
'BAC'
],
'compress' => 0,
'category' => 'Miscellaneous'
};
searching for features of type: BAC
working on track EST
mergedTrackCfg: $VAR1 = {
'feature' => [
'EST_match:est'
],
'autocomplete' => 'all',
'track' => 'EST',
'style' => {
'className' => 'est'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - ESTs'
};
searching for features of type: EST_match:est

working on refseq ctgB
working on track ExampleFeatures
mergedTrackCfg: $VAR1 = {
'feature' => [
'remark'
],
'autocomplete' => 'all',
'track' => 'ExampleFeatures',
'style' => {
'className' => 'feature2'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - Example Features'
};
searching for features of type: remark
working on track NameTest
mergedTrackCfg: $VAR1 = {
'feature' => [
'protein_coding_primary_transcript',
'polypeptide'
],
'autocomplete' => 'all',
'track' => 'NameTest',
'style' => {
'className' => 'feature2'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - Name test track has a really long track label'
};
searching for features of type: protein_coding_primary_transcript, polypeptide
working on track snps
mergedTrackCfg: $VAR1 = {
'feature' => [
'SNP'
],
'autocomplete' => 'all',
'track' => 'snps',
'style' => {
'className' => 'triangle hgred'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - SNPs'
};
searching for features of type: SNP
working on track Motifs
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Motifs',
'style' => {
'className' => 'feature3',
'label' => 'function(feature) { return feature.get('Name')+' (via JS callback)' }',
'description' => 'function(feature) { return feature.get('Name')+': '+feature.get('Note'); }'
},
'description' => 1,
'key' => 'HTMLFeatures - Example motifs',
'feature' => [
'polypeptide_domain'
],
'compress' => 0,
'category' => 'Miscellaneous'
};
searching for features of type: polypeptide_domain
working on track malformed_alignments
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'malformed_alignments',
'style' => {
'className' => 'feature4'
},
'menuTemplate' => [
{
'children' => [
{
'children' => [
{
'iconClass' => 'dijitIconBookmark',
'url' => 'http://wiki.trin.org.au/{name}-{start}-{end}',
'action' => 'newWindow',
'label' => 'Query trin for {name}'
},
{
'iconClass' => 'dijitIconSearch',
'url' => 'http://example.com/{name}-{start}-{end}',
'label' => 'Query example.com for {name}'
}
],
'label' => 'Check gene on databases'
},
{
'label' => '2nd child of demo'
},
{
'label' => '3rd child: this is a track'
}
],
'label' => 'Item with submenu'
},
{
'iconClass' => 'dijitIconDatabase',
'url' => 'http://www.example.com?featurename={name}',
'action' => 'iframeDialog',
'title' => 'The magnificent example.com (feature {name})',
'label' => 'Open example.com in an iframe popup'
},
{
'iconClass' => 'dijitIconDatabase',
'url' => 'sample_data/test_snippet.html?featurename={name}:{start}-{end}',
'action' => 'xhrDialog',
'title' => 'function(track,feature,div) { return 'Random XHR HTML '+Math.random()+' title!'; }',
'label' => 'Open popup with XHR HTML snippet (btw this is feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => 'function(track,feature,div) { return '

'+feature.get('name')+'

This is some test content!

This message brought to you by the number '+Math.round(Math.random()*100)+'.

';} ',
'action' => 'contentDialog',
'title' => 'function(track,feature,div) { return 'Random content snippet '+Math.random()+' title!'; }',
'label' => 'Popup with content snippet from a function (feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => '

{name}

This is some test content about {name}, which goes from {start} to {end} on the {strand} strand.

',
'action' => 'contentDialog',
'title' => '{randomNumberTitle}',
'label' => 'Popup with content snippet from string (feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'action' => '{exampleFeatureClick}',
'label' => '{randomNumberLabel}'
}
],
'hooks' => {
'modify' => 'function( track, feature, div ) { div.style.backgroundColor = ['green','blue','red','orange','purple'][Math.round(Math.random()5)];}'
},
'key' => 'HTMLFeatures - Features with right-click menus',
'feature' => [
'match'
],
'shortDescription' => 'Features with customized right-click menus',
'compress' => 0,
'metadata' => {
'category' => 'Miscellaneous',
'Description' => 'Features with extensively customized right-click menus, and with their colors set at random by a JavaScript callback.'
}
};
searching for features of type: match
working on track Genes
mergedTrackCfg: $VAR1 = {
'fmtDetailValue_Name' => 'function(name,feature) { if(feature.get('type')=='gene') { return name + ' <a href=http://www.ncbi.nlm.nih.gov/gquery/?term=\'+name+\'>[NCBI custom link]'; } else { return name; } }',
'fmtMetaDescription_Name' => 'function(name) { return '[Custom description]'; }',
'fmtMetaValue_Name' => 'function(name) { return name+' [Track with custom callbacks for About track popup]'; }',
'key' => 'CanvasFeatures - Protein-coding genes',
'onClick' => {
'action' => 'defaultDialog',
'title' => '{type} {name}',
'label' => '<div style='font:normal 12px Univers,Helvetica,Arial,sans-serif'><div style='font-weight:bold'>Custom tooltip<div style='color:blue;'>Feature name: {name}
Feature start: {start}
Feature end: {end}'
},
'feature' => [
'gene'
],
'fmtDetailField_Name' => 'function(name,feature) { if(feature.get('type')=='gene') { return 'Gene Name'; } else { return name; } }',
'fmtMetaField_Name' => 'function(name) { return 'Track Name'; }',
'fmtDetailField_Load_id' => 'function(name,feature) { /
remove field from dialog box */ return null; }',
'category' => 'Transcripts',
'metadata' => {
'ncbi_submission_model' => 'Generic',
'insdc_first_public' => '2018-05-15T00:00:00Z',
'Link: ENA study page' => 'http://www.ebi.ac.uk/ena/',
'library_total_amount_of_reads' => '3349981',
'insdc_secondary_accession' => 'SRS12345678',
'insdc_center_name' => 'INSDC Sample',
'ncbi_submission_package' => 'Generic.1.0',
'sample_name' => 'GSM12345678',
'ENA first public' => '2018-05-16',
'study' => 'SRP12345678 a study of volvox',
'organism' => 'Volvox',
'library_size_approx' => '1-5mln',
'Link: RNASeq-er analysis results' => 'ftp://ftp.ebi.ac.uk/pub/databases/arrayexpress/',
'insdc_last_update' => '2018-05-15T01:18:23.110Z',
'insdc_status' => 'live',
'developmental_stage' => 'stage 6- 330 min',
'mapping_quality_approx' => 'under 50%',
'tissue' => 'embryo',
'source_name' => 'Volvox 6- 330 min',
'mapping_fraction_of_uniquely_mapped_reads' => '0.429',
'ENA last update' => '2018-05-16',
'description_title' => 'Volvox_mRNA_rep_2_6'
},
'autocomplete' => 'all',
'track' => 'Genes',
'style' => {
'className' => 'feature5'
},
'menuTemplate' => [
{
'label' => 'View details'
},
{
'label' => 'Zoom this gene'
},
{
'label' => 'Highlight this gene'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => '

{name}

This is some test content about {type} {name}, which goes from {start} to {end} on the {strand} strand.',
'action' => 'contentDialog',
'title' => '{randomNumberTitle}',
'label' => 'Popup with content snippet from string (feature {name})'
}
],
'trackType' => 'NeatCanvasFeatures/View/Track/NeatFeatures',
'compress' => 0
};
searching for features of type: gene
working on track ReadingFrame
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'ReadingFrame',
'style' => {
'className' => 'cds'
},
'key' => 'HTMLFeatures - mRNAs',
'onClick' => {
'url' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}',
'title' => 'NCBI search box',
'label' => 'Search for {name} at NCBI
Feature start {start}
Feature end {end}'
},
'feature' => [
'mRNA'
],
'trackType' => 'NeatHTMLFeatures/View/Track/NeatFeatures',
'phase' => 1,
'compress' => 0,
'category' => 'Transcripts'
};
searching for features of type: mRNA
working on track CDS
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'CDS',
'style' => {
'className' => 'cds',
'linkTemplate' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}-{start}-{end}'
},
'key' => 'CanvasFeatures - mixed mRNAs and CDSs',
'feature' => [
'CDS:bare_predicted',
'mRNA:exonerate',
'mRNA:predicted'
],
'trackType' => 'CanvasFeatures',
'compress' => 0,
'category' => 'Transcripts'
};
searching for features of type: CDS:bare_predicted, mRNA:exonerate, mRNA:predicted
working on track Transcript
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Transcript',
'style' => {
'className' => 'feature',
'color' => '#E32A3A',
'description' => 'customdescription'
},
'description' => 1,
'key' => 'CanvasFeatures - transcripts',
'onClick' => '{exampleFeatureClick}',
'feature' => [
'mRNA:exonerate'
],
'trackType' => 'JBrowse/View/Track/CanvasFeatures',
'compress' => 0,
'category' => 'Transcripts',
'showNoteInAttributes' => bless( do{(my $o = 1)}, 'JSON::PP::Boolean' ),
'subfeatures' => $VAR1->{'showNoteInAttributes'}
};
searching for features of type: mRNA:exonerate
working on track Clones
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Clones',
'style' => {
'className' => 'exon'
},
'description' => 1,
'key' => 'HTMLFeatures - Fingerprinted BACs',
'feature' => [
'BAC'
],
'compress' => 0,
'category' => 'Miscellaneous'
};
searching for features of type: BAC
working on track EST
mergedTrackCfg: $VAR1 = {
'feature' => [
'EST_match:est'
],
'autocomplete' => 'all',
'track' => 'EST',
'style' => {
'className' => 'est'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - ESTs'
};
searching for features of type: EST_match:est

  • cat docs/tutorial/data_files/volvox_microarray.bw.conf docs/tutorial/data_files/volvox_sine.bw.conf docs/tutorial/data_files/volvox-sorted.bam.conf docs/tutorial/data_files/volvox-sorted.bam.coverage.conf docs/tutorial/data_files/volvox-paired.bam.conf docs/tutorial/data_files/volvox.vcf.conf docs/tutorial/data_files/volvox_fromconfig.conf docs/tutorial/data_files/volvox.gff3.conf docs/tutorial/data_files/volvox.gtf.conf docs/tutorial/data_files/volvox.sort.gff3.gz.conf docs/tutorial/data_files/volvox.sort.gff3.gz.htmlfeatures.conf docs/tutorial/data_files/volvox.sort.bed.gz.conf docs/tutorial/data_files/gvcf.vcf.gz.conf docs/tutorial/data_files/bookmarks.conf docs/tutorial/data_files/volvox.subsubparts.gff3.conf docs/tutorial/data_files/volvox-long-reads.fastq.sorted.bam.conf docs/tutorial/data_files/volvox-long-reads.fastq.sorted.cram.conf docs/tutorial/data_files/volvox.bb.conf docs/tutorial/data_files/volvox-sorted.cram.conf
  • bin/add-json.pl '{ "dataset_id": "volvox", "include": [ "../../raw/volvox/functions.conf" ] }' sample_data/json/volvox/trackList.json
  • bin/add-json.pl '{ "dataset_id": "volvox", "plugins": [ "HideTrackLabels", "NeatCanvasFeatures", "NeatHTMLFeatures" ] }' sample_data/json/volvox/trackList.json
  • bin/flatfile-to-json.pl --bed docs/tutorial/data_files/volvox_segment.bed --out sample_data/json/volvox --trackLabel ChromHMM --trackType CanvasFeatures --clientConfig '{"color": "{chromHMM}", "strandArrow": false}' --config '{"displayMode": "collapsed", "enableCollapsedMouseover": true, "category": "Miscellaneous" }'
  • bin/generate-names.pl --safeMode -v --out sample_data/json/volvox
    Tracks:
    CDS
    ChromHMM
    Clones
    DNA
    EST
    ExampleFeatures
    Genes
    Motifs
    NameTest
    ReadingFrame
    Transcript
    fromconfig
    malformed_alignments
    snps
    volvox-long_reads
    volvox-long_reads-cram
    volvox-paired_bam
    volvox-sorted-vcf
    volvox-sorted_bam
    volvox-sorted_bam_coverage
    volvox-sorted_cram
    volvox_bb
    volvox_bed_tabix
    volvox_gff3
    volvox_gff3_subsubparts
    volvox_gff3_tabix
    volvox_gff3_tabix_html
    volvox_gtf
    volvox_gvcf_test
    volvox_microarray_bw_density
    volvox_microarray_bw_xyplot
    volvox_sine_density
    volvox_sine_xyplot
    volvox_vcf_test
    Sampled input stats:
    avg record text bytes 2201.79498861048
    name input records 847
    operation stream estimated count 736
    record stream estimated count 184
    total namerec bytes 1933176
    total input bytes 407148
    operations made 4325
    namerecs buffered 878
    namerecs converted to operations 878
    Removing existing contents of target dir sample_data/json/volvox/names
    Hash store cache size: 2684 buckets
    Using 1 chars for sort log names (16 sort logs)
  • mkdir -p sample_data/raw
  • '[' '!' -e sample_data/raw/volvox ']'
  • ln -sf ../../docs/tutorial/conf_files/volvox.json sample_data/raw/
  • touch sample_data/json/volvox/successfully_run

done.

Formatting Yeast example data ...

  • rm -rf sample_data/json/yeast/
  • bin/prepare-refseqs.pl --fasta sample_data/raw/yeast_scaffolds/chr1.fa.gz --fasta sample_data/raw/yeast_scaffolds/chr2.fa.gzip --out sample_data/json/yeast/
  • gunzip -c sample_data/raw/yeast_scaffolds/chr1.fa.gz sample_data/raw/yeast_scaffolds/chr2.fa.gzip
  • '[' 0 -eq 1 ']'
  • bin/biodb-to-json.pl --conf sample_data/raw/yeast.json --out sample_data/json/yeast/

working on refseq chrI
working on track Genes
working on track transcript_with_no_features

working on refseq chrII
working on track Genes
working on track transcript_with_no_features

  • bin/add-json.pl '{ "dataset_id": "yeast" }' sample_data/json/yeast/trackList.json
  • bin/add-json.pl '{ "dataset_id": "yeast", "plugins": [ "NeatHTMLFeatures","NeatCanvasFeatures","HideTrackLabels" ] }' sample_data/json/yeast/trackList.json
  • bin/generate-names.pl --dir sample_data/json/yeast/

done.

</details>

tiramisutes commented Aug 6, 2018

```

Gathering system information ...
============== System information ====

  • lsb_release -a
    LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
    Distributor ID: CentOS
    Description: CentOS release 6.5 (Final)
    Release: 6.5
    Codename: Final

  • uname -a
    Linux node102 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

  • sw_vers
    ./setup.sh: line 74: sw_vers: command not found

  • grep MemTotal /proc/meminfo
    MemTotal: 65939372 kB

  • echo

  • echo

done.

NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, please use JBrowse 1.12.3 or earlier.

Minimal release, skipping node and Webpack build

Installing Perl prerequisites ...

  • bin/cpanm -v --notest -l extlib/ --installdeps .
    cpanm (App::cpanminus) 1.7043 on perl 5.010001 built for x86_64-linux-thread-multi
    Work directory is /public/home/zpxu/.cpanm/work/1533462225.27547
    You have make /usr/bin/make
    You have LWP 5.833
    You have /bin/tar: tar (GNU tar) 1.23
    Copyright (C) 2010 Free Software Foundation, Inc.
    License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html.
    This is free software: you are free to change and redistribute it.
    There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
You have /usr/bin/unzip
Entering /public/home/zpxu/JBrowse-1.15.1
Running Makefile.PL
--> Working on .
Configuring /public/home/zpxu/JBrowse-1.15.1 ... Can't parse version 'dev'
Can't parse version 'dev'
Generating a Unix-style Makefile
Writing Makefile for JBrowse
Writing MYMETA.yml and MYMETA.json
Checking dependencies from MYMETA.json ...
Checking if you have Capture::Tiny 0 ... Yes (0.30)
Checking if you have Pod::Usage 0 ... Yes (1.36)
Checking if you have Storable 0 ... Yes (2.20)
Checking if you have JSON::XS 0 ... Yes (3.04)
Checking if you have List::Util 0 ... Yes (1.21)
Checking if you have PerlIO::gzip 0 ... Yes (0.20)
Checking if you have Digest::Crc32 0 ... Yes (0.01)
Checking if you have File::Path 2 ... Yes (2.08)
Checking if you have local::lib 0 ... Yes (2.000024)
Checking if you have List::MoreUtils 0.28 ... Yes (0.428)
Checking if you have Bio::FeatureIO 0 ... Yes (1.6.905)
Checking if you have DBI 0 ... Yes (1.609)
Checking if you have Getopt::Long 0 ... Yes (2.42)
Checking if you have warnings 0 ... Yes (1.06)
Checking if you have base 0 ... Yes (2.14)
Checking if you have IO::File 0 ... Yes (1.14)
Checking if you have Data::Dumper 0 ... Yes (2.154)
Checking if you have Bio::GFF3::LowLevel 1.8 ... Yes (2.0)
Checking if you have Bio::Index::Fasta 0 ... Yes (undef)
Checking if you have DB_File 0 ... Yes (1.820)
Checking if you have Bio::Root::Version 1.006000 ... Yes (1.007002)
Checking if you have Bio::Annotation::SimpleValue 0 ... Yes (undef)
Checking if you have vars 0 ... Yes (1.01)
Checking if you have Parse::RecDescent 0 ... Yes (1.967015)
Checking if you have Test::More 0 ... Yes (1.001011)
Checking if you have strict 0 ... Yes (1.04)
Checking if you have File::Temp 0 ... Yes (0.22)
Checking if you have File::Copy::Recursive 0 ... Yes (0.44)
Checking if you have Scalar::Util 0 ... Yes (1.21)
Checking if you have FindBin 0 ... Yes (1.50)
Checking if you have DBD::SQLite 0 ... Yes (1.27)
Checking if you have URI::Escape 0 ... Yes (3.31)
Checking if you have File::Spec 0 ... Yes (3.30)
Checking if you have Heap::Simple 0 ... Yes (0.13)
Checking if you have Heap::Simple::XS 0 ... Yes (0.10)
Checking if you have Fcntl 0 ... Yes (1.06)
Checking if you have POSIX 0 ... Yes (1.17)
Checking if you have Devel::Size 0 ... Yes (0.82)
Checking if you have File::Spec::Functions 0 ... Yes (3.30)
Checking if you have Bio::SeqFeature::Lite 0 ... Yes (undef)
Checking if you have Bio::GFF3::LowLevel::Parser 1.8 ... Yes (2.0)
Checking if you have IO::Uncompress::Gunzip 0 ... Yes (2.021)
Checking if you have Hash::Merge 0 ... Yes (0.300)
Checking if you have constant 0 ... Yes (1.17)
Checking if you have Exporter 0 ... Yes (5.63)
Checking if you have Bio::OntologyIO 0 ... Yes (undef)
Checking if you have Bio::SeqFeature::Annotated 0 ... Yes (1.6.905)
Checking if you have Carp 0 ... Yes (1.38)
Checking if you have Test::Warn 0 ... Yes (0.30)
Checking if you have File::Next 0 ... Yes (1.16)
Checking if you have File::Basename 0 ... Yes (2.77)
Checking if you have JSON 2 ... Yes (2.97001)
Checking if you have Cwd 0 ... Yes (3.30)
OK
<== Installed dependencies for .. Finishing.

  • bin/cpanm -v --notest -l extlib/ --installdeps .
    cpanm (App::cpanminus) 1.7043 on perl 5.010001 built for x86_64-linux-thread-multi
    Work directory is /public/home/zpxu/.cpanm/work/1533462230.27658
    You have make /usr/bin/make
    You have LWP 5.833
    You have /bin/tar: tar (GNU tar) 1.23
    Copyright (C) 2010 Free Software Foundation, Inc.
    License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html.
    This is free software: you are free to change and redistribute it.
    There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
You have /usr/bin/unzip
Entering /public/home/zpxu/JBrowse-1.15.1
Running Makefile.PL
--> Working on .
Configuring /public/home/zpxu/JBrowse-1.15.1 ... Can't parse version 'dev'
Can't parse version 'dev'
Generating a Unix-style Makefile
Writing Makefile for JBrowse
Writing MYMETA.yml and MYMETA.json
Checking dependencies from MYMETA.json ...
Checking if you have Capture::Tiny 0 ... Yes (0.30)
Checking if you have Pod::Usage 0 ... Yes (1.36)
Checking if you have Storable 0 ... Yes (2.20)
Checking if you have JSON::XS 0 ... Yes (3.04)
Checking if you have List::Util 0 ... Yes (1.21)
Checking if you have PerlIO::gzip 0 ... Yes (0.20)
Checking if you have Digest::Crc32 0 ... Yes (0.01)
Checking if you have File::Path 2 ... Yes (2.08)
Checking if you have local::lib 0 ... Yes (2.000024)
Checking if you have List::MoreUtils 0.28 ... Yes (0.428)
Checking if you have Bio::FeatureIO 0 ... Yes (1.6.905)
Checking if you have DBI 0 ... Yes (1.609)
Checking if you have Getopt::Long 0 ... Yes (2.42)
Checking if you have warnings 0 ... Yes (1.06)
Checking if you have base 0 ... Yes (2.14)
Checking if you have IO::File 0 ... Yes (1.14)
Checking if you have Data::Dumper 0 ... Yes (2.154)
Checking if you have Bio::GFF3::LowLevel 1.8 ... Yes (2.0)
Checking if you have Bio::Index::Fasta 0 ... Yes (undef)
Checking if you have DB_File 0 ... Yes (1.820)
Checking if you have Bio::Root::Version 1.006000 ... Yes (1.007002)
Checking if you have Bio::Annotation::SimpleValue 0 ... Yes (undef)
Checking if you have vars 0 ... Yes (1.01)
Checking if you have Parse::RecDescent 0 ... Yes (1.967015)
Checking if you have Test::More 0 ... Yes (1.001011)
Checking if you have strict 0 ... Yes (1.04)
Checking if you have File::Temp 0 ... Yes (0.22)
Checking if you have File::Copy::Recursive 0 ... Yes (0.44)
Checking if you have Scalar::Util 0 ... Yes (1.21)
Checking if you have FindBin 0 ... Yes (1.50)
Checking if you have DBD::SQLite 0 ... Yes (1.27)
Checking if you have URI::Escape 0 ... Yes (3.31)
Checking if you have File::Spec 0 ... Yes (3.30)
Checking if you have Heap::Simple 0 ... Yes (0.13)
Checking if you have Heap::Simple::XS 0 ... Yes (0.10)
Checking if you have Fcntl 0 ... Yes (1.06)
Checking if you have POSIX 0 ... Yes (1.17)
Checking if you have Devel::Size 0 ... Yes (0.82)
Checking if you have File::Spec::Functions 0 ... Yes (3.30)
Checking if you have Bio::SeqFeature::Lite 0 ... Yes (undef)
Checking if you have Bio::GFF3::LowLevel::Parser 1.8 ... Yes (2.0)
Checking if you have IO::Uncompress::Gunzip 0 ... Yes (2.021)
Checking if you have Hash::Merge 0 ... Yes (0.300)
Checking if you have constant 0 ... Yes (1.17)
Checking if you have Exporter 0 ... Yes (5.63)
Checking if you have Bio::OntologyIO 0 ... Yes (undef)
Checking if you have Bio::SeqFeature::Annotated 0 ... Yes (1.6.905)
Checking if you have Carp 0 ... Yes (1.38)
Checking if you have Test::Warn 0 ... Yes (0.30)
Checking if you have File::Next 0 ... Yes (1.16)
Checking if you have File::Basename 0 ... Yes (2.77)
Checking if you have JSON 2 ... Yes (2.97001)
Checking if you have Cwd 0 ... Yes (3.30)
OK
<== Installed dependencies for .. Finishing.

  • set -e
  • bin/cpanm -v --notest -l extlib/ --installdeps .
    cpanm (App::cpanminus) 1.7043 on perl 5.010001 built for x86_64-linux-thread-multi
    Work directory is /public/home/zpxu/.cpanm/work/1533462231.27667
    You have make /usr/bin/make
    You have LWP 5.833
    You have /bin/tar: tar (GNU tar) 1.23
    Copyright (C) 2010 Free Software Foundation, Inc.
    License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html.
    This is free software: you are free to change and redistribute it.
    There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
You have /usr/bin/unzip
Entering /public/home/zpxu/JBrowse-1.15.1
Running Makefile.PL
--> Working on .
Configuring /public/home/zpxu/JBrowse-1.15.1 ... Can't parse version 'dev'
Can't parse version 'dev'
Generating a Unix-style Makefile
Writing Makefile for JBrowse
Writing MYMETA.yml and MYMETA.json
Checking dependencies from MYMETA.json ...
Checking if you have Capture::Tiny 0 ... Yes (0.30)
Checking if you have Pod::Usage 0 ... Yes (1.36)
Checking if you have Storable 0 ... Yes (2.20)
Checking if you have JSON::XS 0 ... Yes (3.04)
Checking if you have List::Util 0 ... Yes (1.21)
Checking if you have PerlIO::gzip 0 ... Yes (0.20)
Checking if you have Digest::Crc32 0 ... Yes (0.01)
Checking if you have File::Path 2 ... Yes (2.08)
Checking if you have local::lib 0 ... Yes (2.000024)
Checking if you have List::MoreUtils 0.28 ... Yes (0.428)
Checking if you have Bio::FeatureIO 0 ... Yes (1.6.905)
Checking if you have DBI 0 ... Yes (1.609)
Checking if you have Getopt::Long 0 ... Yes (2.42)
Checking if you have warnings 0 ... Yes (1.06)
Checking if you have base 0 ... Yes (2.14)
Checking if you have IO::File 0 ... Yes (1.14)
Checking if you have Data::Dumper 0 ... Yes (2.154)
Checking if you have Bio::GFF3::LowLevel 1.8 ... Yes (2.0)
Checking if you have Bio::Index::Fasta 0 ... Yes (undef)
Checking if you have DB_File 0 ... Yes (1.820)
Checking if you have Bio::Root::Version 1.006000 ... Yes (1.007002)
Checking if you have Bio::Annotation::SimpleValue 0 ... Yes (undef)
Checking if you have vars 0 ... Yes (1.01)
Checking if you have Parse::RecDescent 0 ... Yes (1.967015)
Checking if you have Test::More 0 ... Yes (1.001011)
Checking if you have strict 0 ... Yes (1.04)
Checking if you have File::Temp 0 ... Yes (0.22)
Checking if you have File::Copy::Recursive 0 ... Yes (0.44)
Checking if you have Scalar::Util 0 ... Yes (1.21)
Checking if you have FindBin 0 ... Yes (1.50)
Checking if you have DBD::SQLite 0 ... Yes (1.27)
Checking if you have URI::Escape 0 ... Yes (3.31)
Checking if you have File::Spec 0 ... Yes (3.30)
Checking if you have Heap::Simple 0 ... Yes (0.13)
Checking if you have Heap::Simple::XS 0 ... Yes (0.10)
Checking if you have Fcntl 0 ... Yes (1.06)
Checking if you have POSIX 0 ... Yes (1.17)
Checking if you have Devel::Size 0 ... Yes (0.82)
Checking if you have File::Spec::Functions 0 ... Yes (3.30)
Checking if you have Bio::SeqFeature::Lite 0 ... Yes (undef)
Checking if you have Bio::GFF3::LowLevel::Parser 1.8 ... Yes (2.0)
Checking if you have IO::Uncompress::Gunzip 0 ... Yes (2.021)
Checking if you have Hash::Merge 0 ... Yes (0.300)
Checking if you have constant 0 ... Yes (1.17)
Checking if you have Exporter 0 ... Yes (5.63)
Checking if you have Bio::OntologyIO 0 ... Yes (undef)
Checking if you have Bio::SeqFeature::Annotated 0 ... Yes (1.6.905)
Checking if you have Carp 0 ... Yes (1.38)
Checking if you have Test::Warn 0 ... Yes (0.30)
Checking if you have File::Next 0 ... Yes (1.16)
Checking if you have File::Basename 0 ... Yes (2.77)
Checking if you have JSON 2 ... Yes (2.97001)
Checking if you have Cwd 0 ... Yes (3.30)
OK
<== Installed dependencies for .. Finishing.

done.

Formatting Volvox example data ...

  • rm -rf sample_data/json/volvox
  • bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa --out sample_data/json/volvox
  • '[' 0 -eq 1 ']'
  • bin/biodb-to-json.pl -v --conf docs/tutorial/conf_files/volvox.json --out sample_data/json/volvox

working on refseq ctgA
working on track ExampleFeatures
mergedTrackCfg: $VAR1 = {
'feature' => [
'remark'
],
'autocomplete' => 'all',
'track' => 'ExampleFeatures',
'style' => {
'className' => 'feature2'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - Example Features'
};
searching for features of type: remark
working on track NameTest
mergedTrackCfg: $VAR1 = {
'feature' => [
'protein_coding_primary_transcript',
'polypeptide'
],
'autocomplete' => 'all',
'track' => 'NameTest',
'style' => {
'className' => 'feature2'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - Name test track has a really long track label'
};
searching for features of type: protein_coding_primary_transcript, polypeptide
working on track snps
mergedTrackCfg: $VAR1 = {
'feature' => [
'SNP'
],
'autocomplete' => 'all',
'track' => 'snps',
'style' => {
'className' => 'triangle hgred'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - SNPs'
};
searching for features of type: SNP
working on track Motifs
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Motifs',
'style' => {
'className' => 'feature3',
'label' => 'function(feature) { return feature.get('Name')+' (via JS callback)' }',
'description' => 'function(feature) { return feature.get('Name')+': '+feature.get('Note'); }'
},
'description' => 1,
'key' => 'HTMLFeatures - Example motifs',
'feature' => [
'polypeptide_domain'
],
'compress' => 0,
'category' => 'Miscellaneous'
};
searching for features of type: polypeptide_domain
working on track malformed_alignments
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'malformed_alignments',
'style' => {
'className' => 'feature4'
},
'menuTemplate' => [
{
'children' => [
{
'children' => [
{
'iconClass' => 'dijitIconBookmark',
'url' => 'http://wiki.trin.org.au/{name}-{start}-{end}',
'action' => 'newWindow',
'label' => 'Query trin for {name}'
},
{
'iconClass' => 'dijitIconSearch',
'url' => 'http://example.com/{name}-{start}-{end}',
'label' => 'Query example.com for {name}'
}
],
'label' => 'Check gene on databases'
},
{
'label' => '2nd child of demo'
},
{
'label' => '3rd child: this is a track'
}
],
'label' => 'Item with submenu'
},
{
'iconClass' => 'dijitIconDatabase',
'url' => 'http://www.example.com?featurename={name}',
'action' => 'iframeDialog',
'title' => 'The magnificent example.com (feature {name})',
'label' => 'Open example.com in an iframe popup'
},
{
'iconClass' => 'dijitIconDatabase',
'url' => 'sample_data/test_snippet.html?featurename={name}:{start}-{end}',
'action' => 'xhrDialog',
'title' => 'function(track,feature,div) { return 'Random XHR HTML '+Math.random()+' title!'; }',
'label' => 'Open popup with XHR HTML snippet (btw this is feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => 'function(track,feature,div) { return '

'+feature.get('name')+'

This is some test content!

This message brought to you by the number '+Math.round(Math.random()*100)+'.

';} ',
'action' => 'contentDialog',
'title' => 'function(track,feature,div) { return 'Random content snippet '+Math.random()+' title!'; }',
'label' => 'Popup with content snippet from a function (feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => '

{name}

This is some test content about {name}, which goes from {start} to {end} on the {strand} strand.

',
'action' => 'contentDialog',
'title' => '{randomNumberTitle}',
'label' => 'Popup with content snippet from string (feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'action' => '{exampleFeatureClick}',
'label' => '{randomNumberLabel}'
}
],
'hooks' => {
'modify' => 'function( track, feature, div ) { div.style.backgroundColor = ['green','blue','red','orange','purple'][Math.round(Math.random()5)];}'
},
'key' => 'HTMLFeatures - Features with right-click menus',
'feature' => [
'match'
],
'shortDescription' => 'Features with customized right-click menus',
'compress' => 0,
'metadata' => {
'category' => 'Miscellaneous',
'Description' => 'Features with extensively customized right-click menus, and with their colors set at random by a JavaScript callback.'
}
};
searching for features of type: match
working on track Genes
mergedTrackCfg: $VAR1 = {
'fmtDetailValue_Name' => 'function(name,feature) { if(feature.get('type')=='gene') { return name + ' <a href=http://www.ncbi.nlm.nih.gov/gquery/?term=\'+name+\'>[NCBI custom link]'; } else { return name; } }',
'fmtMetaDescription_Name' => 'function(name) { return '[Custom description]'; }',
'fmtMetaValue_Name' => 'function(name) { return name+' [Track with custom callbacks for About track popup]'; }',
'key' => 'CanvasFeatures - Protein-coding genes',
'onClick' => {
'action' => 'defaultDialog',
'title' => '{type} {name}',
'label' => '<div style='font:normal 12px Univers,Helvetica,Arial,sans-serif'><div style='font-weight:bold'>Custom tooltip<div style='color:blue;'>Feature name: {name}
Feature start: {start}
Feature end: {end}'
},
'feature' => [
'gene'
],
'fmtDetailField_Name' => 'function(name,feature) { if(feature.get('type')=='gene') { return 'Gene Name'; } else { return name; } }',
'fmtMetaField_Name' => 'function(name) { return 'Track Name'; }',
'fmtDetailField_Load_id' => 'function(name,feature) { /
remove field from dialog box */ return null; }',
'category' => 'Transcripts',
'metadata' => {
'ncbi_submission_model' => 'Generic',
'insdc_first_public' => '2018-05-15T00:00:00Z',
'Link: ENA study page' => 'http://www.ebi.ac.uk/ena/',
'library_total_amount_of_reads' => '3349981',
'insdc_secondary_accession' => 'SRS12345678',
'insdc_center_name' => 'INSDC Sample',
'ncbi_submission_package' => 'Generic.1.0',
'sample_name' => 'GSM12345678',
'ENA first public' => '2018-05-16',
'study' => 'SRP12345678 a study of volvox',
'organism' => 'Volvox',
'library_size_approx' => '1-5mln',
'Link: RNASeq-er analysis results' => 'ftp://ftp.ebi.ac.uk/pub/databases/arrayexpress/',
'insdc_last_update' => '2018-05-15T01:18:23.110Z',
'insdc_status' => 'live',
'developmental_stage' => 'stage 6- 330 min',
'mapping_quality_approx' => 'under 50%',
'tissue' => 'embryo',
'source_name' => 'Volvox 6- 330 min',
'mapping_fraction_of_uniquely_mapped_reads' => '0.429',
'ENA last update' => '2018-05-16',
'description_title' => 'Volvox_mRNA_rep_2_6'
},
'autocomplete' => 'all',
'track' => 'Genes',
'style' => {
'className' => 'feature5'
},
'menuTemplate' => [
{
'label' => 'View details'
},
{
'label' => 'Zoom this gene'
},
{
'label' => 'Highlight this gene'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => '

{name}

This is some test content about {type} {name}, which goes from {start} to {end} on the {strand} strand.',
'action' => 'contentDialog',
'title' => '{randomNumberTitle}',
'label' => 'Popup with content snippet from string (feature {name})'
}
],
'trackType' => 'NeatCanvasFeatures/View/Track/NeatFeatures',
'compress' => 0
};
searching for features of type: gene
working on track ReadingFrame
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'ReadingFrame',
'style' => {
'className' => 'cds'
},
'key' => 'HTMLFeatures - mRNAs',
'onClick' => {
'url' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}',
'title' => 'NCBI search box',
'label' => 'Search for {name} at NCBI
Feature start {start}
Feature end {end}'
},
'feature' => [
'mRNA'
],
'trackType' => 'NeatHTMLFeatures/View/Track/NeatFeatures',
'phase' => 1,
'compress' => 0,
'category' => 'Transcripts'
};
searching for features of type: mRNA
working on track CDS
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'CDS',
'style' => {
'className' => 'cds',
'linkTemplate' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}-{start}-{end}'
},
'key' => 'CanvasFeatures - mixed mRNAs and CDSs',
'feature' => [
'CDS:bare_predicted',
'mRNA:exonerate',
'mRNA:predicted'
],
'trackType' => 'CanvasFeatures',
'compress' => 0,
'category' => 'Transcripts'
};
searching for features of type: CDS:bare_predicted, mRNA:exonerate, mRNA:predicted
working on track Transcript
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Transcript',
'style' => {
'className' => 'feature',
'color' => '#E32A3A',
'description' => 'customdescription'
},
'description' => 1,
'key' => 'CanvasFeatures - transcripts',
'onClick' => '{exampleFeatureClick}',
'feature' => [
'mRNA:exonerate'
],
'trackType' => 'JBrowse/View/Track/CanvasFeatures',
'compress' => 0,
'category' => 'Transcripts',
'showNoteInAttributes' => bless( do{(my $o = 1)}, 'JSON::PP::Boolean' ),
'subfeatures' => $VAR1->{'showNoteInAttributes'}
};
searching for features of type: mRNA:exonerate
working on track Clones
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Clones',
'style' => {
'className' => 'exon'
},
'description' => 1,
'key' => 'HTMLFeatures - Fingerprinted BACs',
'feature' => [
'BAC'
],
'compress' => 0,
'category' => 'Miscellaneous'
};
searching for features of type: BAC
working on track EST
mergedTrackCfg: $VAR1 = {
'feature' => [
'EST_match:est'
],
'autocomplete' => 'all',
'track' => 'EST',
'style' => {
'className' => 'est'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - ESTs'
};
searching for features of type: EST_match:est

working on refseq ctgB
working on track ExampleFeatures
mergedTrackCfg: $VAR1 = {
'feature' => [
'remark'
],
'autocomplete' => 'all',
'track' => 'ExampleFeatures',
'style' => {
'className' => 'feature2'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - Example Features'
};
searching for features of type: remark
working on track NameTest
mergedTrackCfg: $VAR1 = {
'feature' => [
'protein_coding_primary_transcript',
'polypeptide'
],
'autocomplete' => 'all',
'track' => 'NameTest',
'style' => {
'className' => 'feature2'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - Name test track has a really long track label'
};
searching for features of type: protein_coding_primary_transcript, polypeptide
working on track snps
mergedTrackCfg: $VAR1 = {
'feature' => [
'SNP'
],
'autocomplete' => 'all',
'track' => 'snps',
'style' => {
'className' => 'triangle hgred'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - SNPs'
};
searching for features of type: SNP
working on track Motifs
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Motifs',
'style' => {
'className' => 'feature3',
'label' => 'function(feature) { return feature.get('Name')+' (via JS callback)' }',
'description' => 'function(feature) { return feature.get('Name')+': '+feature.get('Note'); }'
},
'description' => 1,
'key' => 'HTMLFeatures - Example motifs',
'feature' => [
'polypeptide_domain'
],
'compress' => 0,
'category' => 'Miscellaneous'
};
searching for features of type: polypeptide_domain
working on track malformed_alignments
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'malformed_alignments',
'style' => {
'className' => 'feature4'
},
'menuTemplate' => [
{
'children' => [
{
'children' => [
{
'iconClass' => 'dijitIconBookmark',
'url' => 'http://wiki.trin.org.au/{name}-{start}-{end}',
'action' => 'newWindow',
'label' => 'Query trin for {name}'
},
{
'iconClass' => 'dijitIconSearch',
'url' => 'http://example.com/{name}-{start}-{end}',
'label' => 'Query example.com for {name}'
}
],
'label' => 'Check gene on databases'
},
{
'label' => '2nd child of demo'
},
{
'label' => '3rd child: this is a track'
}
],
'label' => 'Item with submenu'
},
{
'iconClass' => 'dijitIconDatabase',
'url' => 'http://www.example.com?featurename={name}',
'action' => 'iframeDialog',
'title' => 'The magnificent example.com (feature {name})',
'label' => 'Open example.com in an iframe popup'
},
{
'iconClass' => 'dijitIconDatabase',
'url' => 'sample_data/test_snippet.html?featurename={name}:{start}-{end}',
'action' => 'xhrDialog',
'title' => 'function(track,feature,div) { return 'Random XHR HTML '+Math.random()+' title!'; }',
'label' => 'Open popup with XHR HTML snippet (btw this is feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => 'function(track,feature,div) { return '

'+feature.get('name')+'

This is some test content!

This message brought to you by the number '+Math.round(Math.random()*100)+'.

';} ',
'action' => 'contentDialog',
'title' => 'function(track,feature,div) { return 'Random content snippet '+Math.random()+' title!'; }',
'label' => 'Popup with content snippet from a function (feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => '

{name}

This is some test content about {name}, which goes from {start} to {end} on the {strand} strand.

',
'action' => 'contentDialog',
'title' => '{randomNumberTitle}',
'label' => 'Popup with content snippet from string (feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'action' => '{exampleFeatureClick}',
'label' => '{randomNumberLabel}'
}
],
'hooks' => {
'modify' => 'function( track, feature, div ) { div.style.backgroundColor = ['green','blue','red','orange','purple'][Math.round(Math.random()5)];}'
},
'key' => 'HTMLFeatures - Features with right-click menus',
'feature' => [
'match'
],
'shortDescription' => 'Features with customized right-click menus',
'compress' => 0,
'metadata' => {
'category' => 'Miscellaneous',
'Description' => 'Features with extensively customized right-click menus, and with their colors set at random by a JavaScript callback.'
}
};
searching for features of type: match
working on track Genes
mergedTrackCfg: $VAR1 = {
'fmtDetailValue_Name' => 'function(name,feature) { if(feature.get('type')=='gene') { return name + ' <a href=http://www.ncbi.nlm.nih.gov/gquery/?term=\'+name+\'>[NCBI custom link]'; } else { return name; } }',
'fmtMetaDescription_Name' => 'function(name) { return '[Custom description]'; }',
'fmtMetaValue_Name' => 'function(name) { return name+' [Track with custom callbacks for About track popup]'; }',
'key' => 'CanvasFeatures - Protein-coding genes',
'onClick' => {
'action' => 'defaultDialog',
'title' => '{type} {name}',
'label' => '<div style='font:normal 12px Univers,Helvetica,Arial,sans-serif'><div style='font-weight:bold'>Custom tooltip<div style='color:blue;'>Feature name: {name}
Feature start: {start}
Feature end: {end}'
},
'feature' => [
'gene'
],
'fmtDetailField_Name' => 'function(name,feature) { if(feature.get('type')=='gene') { return 'Gene Name'; } else { return name; } }',
'fmtMetaField_Name' => 'function(name) { return 'Track Name'; }',
'fmtDetailField_Load_id' => 'function(name,feature) { /
remove field from dialog box */ return null; }',
'category' => 'Transcripts',
'metadata' => {
'ncbi_submission_model' => 'Generic',
'insdc_first_public' => '2018-05-15T00:00:00Z',
'Link: ENA study page' => 'http://www.ebi.ac.uk/ena/',
'library_total_amount_of_reads' => '3349981',
'insdc_secondary_accession' => 'SRS12345678',
'insdc_center_name' => 'INSDC Sample',
'ncbi_submission_package' => 'Generic.1.0',
'sample_name' => 'GSM12345678',
'ENA first public' => '2018-05-16',
'study' => 'SRP12345678 a study of volvox',
'organism' => 'Volvox',
'library_size_approx' => '1-5mln',
'Link: RNASeq-er analysis results' => 'ftp://ftp.ebi.ac.uk/pub/databases/arrayexpress/',
'insdc_last_update' => '2018-05-15T01:18:23.110Z',
'insdc_status' => 'live',
'developmental_stage' => 'stage 6- 330 min',
'mapping_quality_approx' => 'under 50%',
'tissue' => 'embryo',
'source_name' => 'Volvox 6- 330 min',
'mapping_fraction_of_uniquely_mapped_reads' => '0.429',
'ENA last update' => '2018-05-16',
'description_title' => 'Volvox_mRNA_rep_2_6'
},
'autocomplete' => 'all',
'track' => 'Genes',
'style' => {
'className' => 'feature5'
},
'menuTemplate' => [
{
'label' => 'View details'
},
{
'label' => 'Zoom this gene'
},
{
'label' => 'Highlight this gene'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => '

{name}

This is some test content about {type} {name}, which goes from {start} to {end} on the {strand} strand.',
'action' => 'contentDialog',
'title' => '{randomNumberTitle}',
'label' => 'Popup with content snippet from string (feature {name})'
}
],
'trackType' => 'NeatCanvasFeatures/View/Track/NeatFeatures',
'compress' => 0
};
searching for features of type: gene
working on track ReadingFrame
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'ReadingFrame',
'style' => {
'className' => 'cds'
},
'key' => 'HTMLFeatures - mRNAs',
'onClick' => {
'url' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}',
'title' => 'NCBI search box',
'label' => 'Search for {name} at NCBI
Feature start {start}
Feature end {end}'
},
'feature' => [
'mRNA'
],
'trackType' => 'NeatHTMLFeatures/View/Track/NeatFeatures',
'phase' => 1,
'compress' => 0,
'category' => 'Transcripts'
};
searching for features of type: mRNA
working on track CDS
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'CDS',
'style' => {
'className' => 'cds',
'linkTemplate' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}-{start}-{end}'
},
'key' => 'CanvasFeatures - mixed mRNAs and CDSs',
'feature' => [
'CDS:bare_predicted',
'mRNA:exonerate',
'mRNA:predicted'
],
'trackType' => 'CanvasFeatures',
'compress' => 0,
'category' => 'Transcripts'
};
searching for features of type: CDS:bare_predicted, mRNA:exonerate, mRNA:predicted
working on track Transcript
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Transcript',
'style' => {
'className' => 'feature',
'color' => '#E32A3A',
'description' => 'customdescription'
},
'description' => 1,
'key' => 'CanvasFeatures - transcripts',
'onClick' => '{exampleFeatureClick}',
'feature' => [
'mRNA:exonerate'
],
'trackType' => 'JBrowse/View/Track/CanvasFeatures',
'compress' => 0,
'category' => 'Transcripts',
'showNoteInAttributes' => bless( do{(my $o = 1)}, 'JSON::PP::Boolean' ),
'subfeatures' => $VAR1->{'showNoteInAttributes'}
};
searching for features of type: mRNA:exonerate
working on track Clones
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Clones',
'style' => {
'className' => 'exon'
},
'description' => 1,
'key' => 'HTMLFeatures - Fingerprinted BACs',
'feature' => [
'BAC'
],
'compress' => 0,
'category' => 'Miscellaneous'
};
searching for features of type: BAC
working on track EST
mergedTrackCfg: $VAR1 = {
'feature' => [
'EST_match:est'
],
'autocomplete' => 'all',
'track' => 'EST',
'style' => {
'className' => 'est'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - ESTs'
};
searching for features of type: EST_match:est

  • cat docs/tutorial/data_files/volvox_microarray.bw.conf docs/tutorial/data_files/volvox_sine.bw.conf docs/tutorial/data_files/volvox-sorted.bam.conf docs/tutorial/data_files/volvox-sorted.bam.coverage.conf docs/tutorial/data_files/volvox-paired.bam.conf docs/tutorial/data_files/volvox.vcf.conf docs/tutorial/data_files/volvox_fromconfig.conf docs/tutorial/data_files/volvox.gff3.conf docs/tutorial/data_files/volvox.gtf.conf docs/tutorial/data_files/volvox.sort.gff3.gz.conf docs/tutorial/data_files/volvox.sort.gff3.gz.htmlfeatures.conf docs/tutorial/data_files/volvox.sort.bed.gz.conf docs/tutorial/data_files/gvcf.vcf.gz.conf docs/tutorial/data_files/bookmarks.conf docs/tutorial/data_files/volvox.subsubparts.gff3.conf docs/tutorial/data_files/volvox-long-reads.fastq.sorted.bam.conf docs/tutorial/data_files/volvox-long-reads.fastq.sorted.cram.conf docs/tutorial/data_files/volvox.bb.conf docs/tutorial/data_files/volvox-sorted.cram.conf
  • bin/add-json.pl '{ "dataset_id": "volvox", "include": [ "../../raw/volvox/functions.conf" ] }' sample_data/json/volvox/trackList.json
  • bin/add-json.pl '{ "dataset_id": "volvox", "plugins": [ "HideTrackLabels", "NeatCanvasFeatures", "NeatHTMLFeatures" ] }' sample_data/json/volvox/trackList.json
  • bin/flatfile-to-json.pl --bed docs/tutorial/data_files/volvox_segment.bed --out sample_data/json/volvox --trackLabel ChromHMM --trackType CanvasFeatures --clientConfig '{"color": "{chromHMM}", "strandArrow": false}' --config '{"displayMode": "collapsed", "enableCollapsedMouseover": true, "category": "Miscellaneous" }'
  • bin/generate-names.pl --safeMode -v --out sample_data/json/volvox
    Tracks:
    CDS
    ChromHMM
    Clones
    DNA
    EST
    ExampleFeatures
    Genes
    Motifs
    NameTest
    ReadingFrame
    Transcript
    fromconfig
    malformed_alignments
    snps
    volvox-long_reads
    volvox-long_reads-cram
    volvox-paired_bam
    volvox-sorted-vcf
    volvox-sorted_bam
    volvox-sorted_bam_coverage
    volvox-sorted_cram
    volvox_bb
    volvox_bed_tabix
    volvox_gff3
    volvox_gff3_subsubparts
    volvox_gff3_tabix
    volvox_gff3_tabix_html
    volvox_gtf
    volvox_gvcf_test
    volvox_microarray_bw_density
    volvox_microarray_bw_xyplot
    volvox_sine_density
    volvox_sine_xyplot
    volvox_vcf_test
    Sampled input stats:
    avg record text bytes 2201.79498861048
    name input records 847
    operation stream estimated count 736
    record stream estimated count 184
    total namerec bytes 1933176
    total input bytes 407148
    operations made 4325
    namerecs buffered 878
    namerecs converted to operations 878
    Removing existing contents of target dir sample_data/json/volvox/names
    Hash store cache size: 2684 buckets
    Using 1 chars for sort log names (16 sort logs)
  • mkdir -p sample_data/raw
  • '[' '!' -e sample_data/raw/volvox ']'
  • ln -sf ../../docs/tutorial/conf_files/volvox.json sample_data/raw/
  • touch sample_data/json/volvox/successfully_run

done.

Formatting Yeast example data ...

  • rm -rf sample_data/json/yeast/
  • bin/prepare-refseqs.pl --fasta sample_data/raw/yeast_scaffolds/chr1.fa.gz --fasta sample_data/raw/yeast_scaffolds/chr2.fa.gzip --out sample_data/json/yeast/
  • gunzip -c sample_data/raw/yeast_scaffolds/chr1.fa.gz sample_data/raw/yeast_scaffolds/chr2.fa.gzip
  • '[' 0 -eq 1 ']'
  • bin/biodb-to-json.pl --conf sample_data/raw/yeast.json --out sample_data/json/yeast/

working on refseq chrI
working on track Genes
working on track transcript_with_no_features

working on refseq chrII
working on track Genes
working on track transcript_with_no_features

  • bin/add-json.pl '{ "dataset_id": "yeast" }' sample_data/json/yeast/trackList.json
  • bin/add-json.pl '{ "dataset_id": "yeast", "plugins": [ "NeatHTMLFeatures","NeatCanvasFeatures","HideTrackLabels" ] }' sample_data/json/yeast/trackList.json
  • bin/generate-names.pl --dir sample_data/json/yeast/

done.

</details>
@cmdcolin

This comment has been minimized.

Show comment
Hide comment
@cmdcolin

cmdcolin Aug 6, 2018

Contributor

I think you are not running from the github clone, I can see in the setup.log that this is from JBrowse-1.15.1.zip or similar.

Are you using the github clone or the downloaded zip release files? I'm just wondering because it depends on what you're using for what instructions you need :)

Contributor

cmdcolin commented Aug 6, 2018

I think you are not running from the github clone, I can see in the setup.log that this is from JBrowse-1.15.1.zip or similar.

Are you using the github clone or the downloaded zip release files? I'm just wondering because it depends on what you're using for what instructions you need :)

@tiramisutes

This comment has been minimized.

Show comment
Hide comment
@tiramisutes

tiramisutes Aug 6, 2018

Yes, from downloading with JBrowse-1.15.1.zip. I don't knower It's different with git clone.

tiramisutes commented Aug 6, 2018

Yes, from downloading with JBrowse-1.15.1.zip. I don't knower It's different with git clone.

@cmdcolin

This comment has been minimized.

Show comment
Hide comment
@cmdcolin

cmdcolin Aug 7, 2018

Contributor

There are actually three cases here

  1. In the min release e.g. JBrowse-1.15.1.zip the utils/jb_run does not work so we actually decided to disable it in further releases. That was a bug and sorry you ran into it
  2. If you get the dv release e.g. JBrowse-1.15.1-dev.zip then the utils/jb_run.js does work. Same with the GitHub clone. So if you want to use jb_run.js then use one of those.

Otherwise just setup with Apache or nginx probably :)

Contributor

cmdcolin commented Aug 7, 2018

There are actually three cases here

  1. In the min release e.g. JBrowse-1.15.1.zip the utils/jb_run does not work so we actually decided to disable it in further releases. That was a bug and sorry you ran into it
  2. If you get the dv release e.g. JBrowse-1.15.1-dev.zip then the utils/jb_run.js does work. Same with the GitHub clone. So if you want to use jb_run.js then use one of those.

Otherwise just setup with Apache or nginx probably :)

@cmdcolin

This comment has been minimized.

Show comment
Hide comment
@cmdcolin

cmdcolin Aug 7, 2018

Contributor

We will be rewriting the so called "quick start guide" and hopefully make this easier

Contributor

cmdcolin commented Aug 7, 2018

We will be rewriting the so called "quick start guide" and hopefully make this easier

@tiramisutes

This comment has been minimized.

Show comment
Hide comment
@tiramisutes

tiramisutes Aug 7, 2018

I try git clone from GitHub, but have same problem as show in picture (
jbrowse).

``` Gathering system information ... ============== System information ==== + lsb_release -a LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch Distributor ID: CentOS Description: CentOS release 6.5 (Final) Release: 6.5 Codename: Final + uname -a Linux node102 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux + sw_vers ./setup.sh: line 74: sw_vers: command not found + grep MemTotal /proc/meminfo MemTotal: 65939372 kB + echo
  • echo

done.

NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, please use JBrowse 1.12.3 or earlier.

Installing node.js dependencies and building with webpack ...
Node v8.9.4 installed at /public/home/zpxu/.nvm/versions/node/v8.9.4/bin/node with npm 5.6.0
yarn install v1.9.4
warning package-lock.json found. Your project contains lock files generated by tools other than Yarn. It is advised not to mix package managers in order to avoid resolution inconsistencies caused by unsynchronized lock files. To clear this warning, remove package-lock.json.
[1/4] Resolving packages...
success Already up-to-date.
Done in 1.92s.
yarn run v1.9.4
$ webpack
clean-webpack-plugin: /public/home/zpxu/jbrowse/dist has been removed.
jbrowse-glob-loader: building 201 JBrowse modules
jbrowse-glob-loader: adding plugin module RegexSequenceSearch/View/SearchSeqDialog
jbrowse-glob-loader: adding plugin module RegexSequenceSearch/Store/SeqFeature/RegexSearch
jbrowse-glob-loader: adding plugin module RegexSequenceSearch/main
jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/View/Track/NeatFeatures
jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/main
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/Track/NeatFeatures
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Segments
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/ProcessedTranscript
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Gene
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Box
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/main
jbrowse-glob-loader: adding plugin module HideTrackLabels/main
jbrowse-glob-loader: adding plugin module DebugEvents/main
jbrowse-glob-loader: adding plugin module CategoryUrl/main
jbrowse-glob-loader: discovered a total of 215 modules
jbrowse-glob-loader: skipping entry point module JBrowse/main
Hash: 7101a07a714193e1b9a5
Version: webpack 3.11.0
Time: 90248ms
Asset Size Chunks Chunk Names
0.bundle.js.map 8.73 MB 0, 1, 2, 3 [emitted]
0.bundle.js 6.39 MB 0, 1, 2, 3 [emitted] [big]
2.bundle.js 145 kB 2 [emitted]
3.bundle.js 398 kB 3 [emitted] [big]
4.bundle.js 1.68 kB 4 [emitted]
5.bundle.js 921 bytes 5 [emitted]
run_jasmine.bundle.js 557 kB 6 [emitted] [big] run_jasmine
browser.bundle.js 363 kB 7 [emitted] [big] browser
main.bundle.js 373 kB 8 [emitted] [big] main
1.bundle.js 494 kB 1 [emitted] [big]
1.bundle.js.map 676 kB 1 [emitted]
2.bundle.js.map 199 kB 2 [emitted]
3.bundle.js.map 503 kB 3 [emitted]
4.bundle.js.map 1.87 kB 4 [emitted]
5.bundle.js.map 1.13 kB 5 [emitted]
run_jasmine.bundle.js.map 836 kB 6 [emitted] run_jasmine
browser.bundle.js.map 517 kB 7 [emitted] browser
main.bundle.js.map 534 kB 8 [emitted] main
dojo/resources/blank.gif 43 bytes [emitted]
[129] ./build/dojo-webpack-plugin-loader/dojo/dojo.js 70.7 kB {6} {7} {8} [built]
[334] ./src/JBrowse/Util.js 22.1 kB {0} {1} [built]
[336] ./src/JBrowse/QueryParamConfigMapper.js 6.13 kB {0} {2} [built]
[337] ./src/JBrowse/standalone.js 140 bytes {0} {7} [built]
[338] ./src/JBrowse/Model/SimpleFeature.js 2.86 kB {0} {1} [built]
[340] ./src/JBrowse/FeatureFiltererMixin.js 3.19 kB {0} [built]
[341] ./src/JBrowse/Store/RemoteBinaryFile.js 18.6 kB {0} {1} [built]
[342] ./src/JBrowse/View/Track/_AlignmentsMixin.js 15.8 kB {0} [built]
[343] ./src/JBrowse/Store/SeqFeature/_MismatchesMixin.js 12.6 kB {0} [built]
[344] ./src/JBrowse/Model/NestedFrequencyTable.js 3.41 kB {0} {1} [built]
[345] ./src/JBrowse/View/GranularRectLayout.js 16.5 kB {0} {2} [built]
[371] ./src/JBrowse/main.js 11.8 kB {8} [built]
[372] ./tests/js_tests/main.js 1.55 kB {6} [built]
[454] ./src/JBrowse/View/Track/_VariantDetailMixin.js 13.3 kB {0} [built]
[469] ./src/JBrowse/View/Track/BlockBased/Block.js 1.03 kB {0} [built]
+ 1413 hidden modules
Done in 162.03s.

done.

Installing Perl prerequisites ...

  • bin/cpanm -v --notest -l extlib/ --installdeps .
    cpanm (App::cpanminus) 1.7043 on perl 5.010001 built for x86_64-linux-thread-multi
    Work directory is /public/home/zpxu/.cpanm/work/1533608547.10840
    You have make /usr/bin/make
    You have LWP 5.833
    You have /bin/tar: tar (GNU tar) 1.23
    Copyright (C) 2010 Free Software Foundation, Inc.
    License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html.
    This is free software: you are free to change and redistribute it.
    There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
You have /usr/bin/unzip
Entering /public/home/zpxu/jbrowse
Running Makefile.PL
--> Working on .
Configuring /public/home/zpxu/jbrowse ... Warning: prerequisite Devel::Size 0 not found.
Warning: prerequisite Heap::Simple::XS 0 not found.
Warning: prerequisite JSON::XS 0 not found.
Can't parse version 'dev'
Can't parse version 'dev'
Generating a Unix-style Makefile
Writing Makefile for JBrowse
Writing MYMETA.yml and MYMETA.json
Checking dependencies from MYMETA.json ...
Checking if you have Capture::Tiny 0 ... Yes (0.30)
Checking if you have Pod::Usage 0 ... Yes (1.36)
Checking if you have Storable 0 ... Yes (2.20)
Checking if you have JSON::XS 0 ... No
Checking if you have List::Util 0 ... Yes (1.46)
Checking if you have PerlIO::gzip 0 ... Yes (0.19)
Checking if you have Digest::Crc32 0 ... Yes (0.01)
Checking if you have File::Path 2 ... Yes (2.08)
Checking if you have local::lib 0 ... Yes (2.000024)
Checking if you have List::MoreUtils 0.28 ... Yes (0.416)
Checking if you have Bio::FeatureIO 0 ... Yes (1.6.905)
Checking if you have DBI 0 ... Yes (1.641)
Checking if you have Getopt::Long 0 ... Yes (2.38)
Checking if you have warnings 0 ... Yes (1.06)
Checking if you have base 0 ... Yes (2.14)
Checking if you have IO::File 0 ... Yes (1.14)
Checking if you have Data::Dumper 0 ... Yes (2.154)
Checking if you have Bio::GFF3::LowLevel 1.8 ... Yes (2.0)
Checking if you have Bio::Index::Fasta 0 ... Yes (undef)
Checking if you have DB_File 0 ... Yes (1.820)
Checking if you have Bio::Root::Version 1.006000 ... Yes (1.007001)
Checking if you have Bio::Annotation::SimpleValue 0 ... Yes (undef)
Checking if you have vars 0 ... Yes (1.01)
Checking if you have Parse::RecDescent 0 ... Yes (1.967015)
Checking if you have Test::More 0 ... Yes (1.001014)
Checking if you have strict 0 ... Yes (1.04)
Checking if you have File::Temp 0 ... Yes (0.22)
Checking if you have File::Copy::Recursive 0 ... Yes (0.44)
Checking if you have Scalar::Util 0 ... Yes (1.46)
Checking if you have FindBin 0 ... Yes (1.50)
Checking if you have DBD::SQLite 0 ... Yes (1.27)
Checking if you have URI::Escape 0 ... Yes (3.31)
Checking if you have File::Spec 0 ... Yes (3.30)
Checking if you have Heap::Simple 0 ... Yes (0.13)
Checking if you have Heap::Simple::XS 0 ... No
Checking if you have Fcntl 0 ... Yes (1.06)
Checking if you have POSIX 0 ... Yes (1.17)
Checking if you have Devel::Size 0 ... No
Checking if you have File::Spec::Functions 0 ... Yes (3.30)
Checking if you have Bio::SeqFeature::Lite 0 ... Yes (undef)
Checking if you have Bio::GFF3::LowLevel::Parser 1.8 ... Yes (2.0)
Checking if you have IO::Uncompress::Gunzip 0 ... Yes (2.021)
Checking if you have Hash::Merge 0 ... Yes (0.300)
Checking if you have constant 0 ... Yes (1.17)
Checking if you have Exporter 0 ... Yes (5.63)
Checking if you have Bio::OntologyIO 0 ... Yes (undef)
Checking if you have Bio::SeqFeature::Annotated 0 ... Yes (1.6.905)
Checking if you have Carp 0 ... Yes (1.38)
Checking if you have Test::Warn 0 ... Yes (0.30)
Checking if you have File::Next 0 ... Yes (1.16)
Checking if you have File::Basename 0 ... Yes (2.77)
Checking if you have JSON 2 ... Yes (2.97001)
Checking if you have Cwd 0 ... Yes (3.30)
Searching JSON::XS (0) on cpanmetadb ...
Unpacking JSON-XS-3.04.tar.gz
OK
==> Found dependencies: JSON::XS, Heap::Simple::XS, Devel::Size
--> Working on JSON::XS
Fetching http://www.cpan.org/authors/id/M/ML/MLEHMANN/JSON-XS-3.04.tar.gz ... OK
JSON-XS-3.04/
JSON-XS-3.04/typemap
JSON-XS-3.04/t/
JSON-XS-3.04/t/14_latin1.t
JSON-XS-3.04/t/02_error.t
JSON-XS-3.04/t/15_prefix.t
JSON-XS-3.04/t/11_pc_expo.t
JSON-XS-3.04/t/99_binary.t
JSON-XS-3.04/t/22_comment_at_eof.t
JSON-XS-3.04/t/03_types.t
JSON-XS-3.04/t/05_dwiw_decode.t
JSON-XS-3.04/t/21_evans.t
JSON-XS-3.04/t/06_pc_pretty.t
JSON-XS-3.04/t/01_utf8.t
JSON-XS-3.04/t/10_pc_keysort.t
JSON-XS-3.04/t/16_tied.t
JSON-XS-3.04/t/09_pc_extra_number.t
JSON-XS-3.04/t/07_pc_esc.t
JSON-XS-3.04/t/52_object.t
JSON-XS-3.04/t/18_json_checker.t
JSON-XS-3.04/t/20_faihu.t
JSON-XS-3.04/t/13_limit.t
JSON-XS-3.04/t/12_blessed.t
JSON-XS-3.04/t/19_incr.t
JSON-XS-3.04/t/04_dwiw_encode.t
JSON-XS-3.04/t/08_pc_base.t
JSON-XS-3.04/t/17_relaxed.t
JSON-XS-3.04/t/00_load.t
JSON-XS-3.04/README
JSON-XS-3.04/Changes
JSON-XS-3.04/COPYING
JSON-XS-3.04/XS.pm
JSON-XS-3.04/XS/
JSON-XS-3.04/XS/Boolean.pm
JSON-XS-3.04/MANIFEST
JSON-XS-3.04/eg/
JSON-XS-3.04/eg/bench
JSON-XS-3.04/bin/
JSON-XS-3.04/bin/json_xs
JSON-XS-3.04/XS.xs
JSON-XS-3.04/Makefile.PL
JSON-XS-3.04/META.yml
JSON-XS-3.04/META.json
Entering JSON-XS-3.04
Checking configure dependencies from META.json
Checking if you have ExtUtils::MakeMaker 6.58 ... Yes (7.10)
Checking if you have Canary::Stability 0 ... Yes (2012)
Running Makefile.PL
Configuring JSON-XS-3.04 ...


*** Canary::Stability COMPATIBILITY AND SUPPORT CHECK
*** =================================================


*** Hi!


*** I do my best to provide predictable and reliable software.


*** However, in recent releases, P5P (who maintain perl) have been
*** introducing regressions that are sometimes subtle and at other times
*** catastrophic, often for personal preferences with little or no concern
*** for existing code, most notably CPAN.


*** For this reason, it has become very hard for me to maintain the level
*** of reliability and support I have committed myself to in the past, at
*** least with some perl versions: I simply can't keep up working around new
*** bugs or gratituous incompatibilities, and in turn you might suffer from
*** unanticipated problems.


*** Therefore I have introduced a support and compatibility check, the results
*** of which follow below, together with a FAQ and some recommendations.


*** This check is just to let you know that there might be a risk, so you can
*** make judgement calls on how to proceed - it will not keep the module from
*** installing or working.


*** The stability canary says: chirp! chirp! (it seems to be quite happy)


*** Your version of perl (5.010001) is quite supported by JSON::XS, nothing
*** else to be said, hope it comes in handy.
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for JSON::XS
Writing MYMETA.yml and MYMETA.json
Checking dependencies from MYMETA.json ...
Checking if you have ExtUtils::MakeMaker 0 ... Yes (7.10)
Checking if you have Types::Serialiser 0 ... Yes (1.0)
Checking if you have common::sense 0 ... Yes (3.74)
OK
Building JSON-XS-3.04 ... cp XS/Boolean.pm blib/lib/JSON/XS/Boolean.pm
cp XS.pm blib/lib/JSON/XS.pm
Running Mkbootstrap for JSON::XS ()
chmod 644 "XS.bs"
"/usr/bin/perl" "/usr/share/perl5/ExtUtils/xsubpp" -typemap "/usr/share/perl5/ExtUtils/typemap" -typemap "typemap" XS.xs > XS.xsc && mv XS.xsc XS.c
gcc -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DVERSION="3.04" -DXS_VERSION="3.04" -fPIC "-I/usr/lib64/perl5/CORE" XS.c
XS.xs: In function ‘ptr_to_index’:
XS.xs:233:10: warning: pointer targets in passing argument 2 of ‘Perl_utf8_distance’ differ in signedness [-Wpointer-sign]
? utf8_distance (offset, SvPVX (sv))
^
In file included from /usr/lib64/perl5/CORE/perl.h:4829:0,
from XS.xs:2:
/usr/lib64/perl5/CORE/proto.h:3558:18: note: expected ‘const U8 *’ but argument is of type ‘char *’
PERL_CALLCONV IV Perl_utf8_distance(pTHX_ const U8 *a, const U8 *b)
^
XS.xs:233:10: warning: pointer targets in passing argument 3 of ‘Perl_utf8_distance’ differ in signedness [-Wpointer-sign]
? utf8_distance (offset, SvPVX (sv))
^
In file included from /usr/lib64/perl5/CORE/perl.h:4829:0,
from XS.xs:2:
/usr/lib64/perl5/CORE/proto.h:3558:18: note: expected ‘const U8 *’ but argument is of type ‘char *’
PERL_CALLCONV IV Perl_utf8_distance(pTHX_ const U8 *a, const U8 *b)
^
XS.xs: In function ‘ref_bool_type’:
XS.xs:344:10: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if (len == 1)
^
XS.xs: In function ‘encode_str’:
XS.xs:455:23: warning: pointer targets in passing argument 1 of ‘decode_utf8’ differ in signedness [-Wpointer-sign]
uch = decode_utf8 (str, end - str, &clen);
^
XS.xs:191:1: note: expected ‘unsigned char *’ but argument is of type ‘char *’
decode_utf8 (unsigned char *s, STRLEN len, STRLEN *clen)
^
XS.xs:508:23: warning: pointer targets in passing argument 1 of ‘encode_utf8’ differ in signedness [-Wpointer-sign]
enc->cur = encode_utf8 (enc->cur, uch);
^
XS.xs:208:1: note: expected ‘unsigned char *’ but argument is of type ‘char *’
encode_utf8 (unsigned char *s, UV ch)
^
XS.xs:508:32: warning: pointer targets in assignment differ in signedness [-Wpointer-sign]
enc->cur = encode_utf8 (enc->cur, uch);
^
XS.xs: In function ‘decode_str’:
XS.xs:1121:26: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if (hi >= 0xd800)
^
XS.xs:1147:27: warning: pointer targets in passing argument 1 of ‘encode_utf8’ differ in signedness [-Wpointer-sign]
cur = encode_utf8 (cur, hi);
^
XS.xs:208:1: note: expected ‘unsigned char *’ but argument is of type ‘char *’
encode_utf8 (unsigned char *s, UV ch)
^
XS.xs:1147:31: warning: pointer targets in assignment differ in signedness [-Wpointer-sign]
cur = encode_utf8 (cur, hi);
^
XS.xs:1167:15: warning: pointer targets in passing argument 1 of ‘decode_utf8’ differ in signedness [-Wpointer-sign]
decode_utf8 (dec_cur, dec->end - dec_cur, &clen);
^
XS.xs:191:1: note: expected ‘unsigned char *’ but argument is of type ‘char *’
decode_utf8 (unsigned char *s, STRLEN len, STRLEN *clen)
^
XS.xs: In function ‘decode_num’:
XS.xs:1320:12: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if (numtype & IS_NUMBER_IN_UV)
^
XS.xs: In function ‘decode_json’:
XS.xs:1807:7: warning: pointer targets in passing argument 3 of ‘Perl_pv_uni_display’ differ in signedness [-Wpointer-sign]
pv_uni_display (uni, dec.cur, dec.end - dec.cur, 20, UNI_DISPLAY_QQ);
^
In file included from /usr/lib64/perl5/CORE/perl.h:4829:0,
from XS.xs:2:
/usr/lib64/perl5/CORE/proto.h:3651:21: note: expected ‘const U8 *’ but argument is of type ‘char
PERL_CALLCONV char
Perl_pv_uni_display(pTHX_ SV *dsv, const U8 *spv, STRLEN len, STRLEN pvlim, UV flags)
^
XS.xs: In function ‘incr_parse’:
XS.xs:1908:26: warning: multi-line comment [-Wcomment]
++p; // "virtually" consumes character after
^
XS.xs:1972:7: warning: label ‘modechange’ defined but not used [-Wunused-label]
modechange:
^
In file included from XS.xs:3:0:
XS.c: In function ‘XS_JSON__XS_CLONE’:
/usr/lib64/perl5/CORE/XSUB.h:136:20: warning: unused variable ‘items’ [-Wunused-variable]
#define dITEMS I32 items = (I32)(SP - MARK)
^
/usr/lib64/perl5/CORE/XSUB.h:144:16: note: in expansion of macro ‘dITEMS’
dSP; dAXMARK; dITEMS
^
XS.c:2052:11: note: in expansion of macro ‘dXSARGS’
dVAR; dXSARGS;
^
XS.xs: In function ‘XS_JSON__XS_incr_parse’:
XS.xs:2155:12: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if (!DECODE_WANTS_OCTETS (self) == !SvUTF8 (self->incr_text))
^
XS.xs:2177:16: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if (SvUTF8 (jsonstr) != SvUTF8 (self->incr_text))
^
In file included from /usr/lib64/perl5/CORE/perl.h:38:0,
from XS.xs:2:
XS.xs: In function ‘encode_sv’:
/usr/lib64/perl5/CORE/config.h:2961:31: warning: ignoring return value of ‘gcvt’, declared with attribute warn_unused_result [-Wunused-result]
#define Gconvert(x,n,t,b) gcvt((x),(n),(b))
^
XS.xs:899:7: note: in expansion of macro ‘Gconvert’
Gconvert (SvNVX (sv), NV_DIG, 0, enc->cur);
^
rm -f blib/arch/auto/JSON/XS/XS.so
gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic XS.o -o blib/arch/auto/JSON/XS/XS.so
\

chmod 755 blib/arch/auto/JSON/XS/XS.so
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- XS.bs blib/arch/auto/JSON/XS/XS.bs 644
cp bin/json_xs blib/script/json_xs
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/json_xs
Manifying 1 pod document
Manifying 2 pod documents
Running Mkbootstrap for JSON::XS ()
chmod 644 "XS.bs"
Manifying 1 pod document
Manifying 2 pod documents
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/auto/JSON/XS/XS.so
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/JSON/XS.pm
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/JSON/XS/Boolean.pm
Installing /public/home/zpxu/jbrowse/extlib/man/man1/json_xs.1
Installing /public/home/zpxu/jbrowse/extlib/man/man3/JSON::XS.3pm
Installing /public/home/zpxu/jbrowse/extlib/man/man3/JSON::XS::Boolean.3pm
Installing /public/home/zpxu/jbrowse/extlib/bin/json_xs
Appending installation info to /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/perllocal.pod
OK
Successfully installed JSON-XS-3.04
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/.meta/JSON-XS-3.04/install.json
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/.meta/JSON-XS-3.04/MYMETA.json
Searching Heap::Simple::XS (0) on cpanmetadb ...
Unpacking Heap-Simple-XS-0.10.tar.gz
--> Working on Heap::Simple::XS
Fetching http://www.cpan.org/authors/id/T/TH/THOSPEL/Heap-Simple-XS-0.10.tar.gz ... OK
Heap-Simple-XS-0.10/
Heap-Simple-XS-0.10/Makefile.PL
Heap-Simple-XS-0.10/ppport.h
Heap-Simple-XS-0.10/Changes
Heap-Simple-XS-0.10/README
Heap-Simple-XS-0.10/t/
Heap-Simple-XS-0.10/t/speed_priority
Heap-Simple-XS-0.10/t/speed_binary
Heap-Simple-XS-0.10/t/speed_array
Heap-Simple-XS-0.10/t/speed_hash
Heap-Simple-XS-0.10/t/speed_binomial
Heap-Simple-XS-0.10/t/Ties.pm
Heap-Simple-XS-0.10/t/speed_scalar
Heap-Simple-XS-0.10/t/04_overload.t
Heap-Simple-XS-0.10/t/02_stress.t
Heap-Simple-XS-0.10/t/99_speed.t
Heap-Simple-XS-0.10/t/FakeHeap.pm
Heap-Simple-XS-0.10/t/03_magic.t
Heap-Simple-XS-0.10/t/00_load.t
Heap-Simple-XS-0.10/t/01_basic.t
Heap-Simple-XS-0.10/t/speed_fibonacci
Heap-Simple-XS-0.10/XS.xs
Heap-Simple-XS-0.10/typemap
Heap-Simple-XS-0.10/MANIFEST.SKIP
Heap-Simple-XS-0.10/MANIFEST
Heap-Simple-XS-0.10/META.yml
Heap-Simple-XS-0.10/lib/
Heap-Simple-XS-0.10/lib/Heap/
Heap-Simple-XS-0.10/lib/Heap/Simple/
Heap-Simple-XS-0.10/lib/Heap/Simple/XS/
Heap-Simple-XS-0.10/lib/Heap/Simple/XS/Package.pm
Heap-Simple-XS-0.10/lib/Heap/Simple/XS.pm
Heap-Simple-XS-0.10/md5-versions
Entering Heap-Simple-XS-0.10
Checking configure dependencies from META.yml
Running Makefile.PL
Configuring Heap-Simple-XS-0.10 ...
Note that you can avoid these questions by passing
the '-n' or '-y' option to 'Makefile.PL'.

Run Heap::Simple benchmarks during 'make test' ? [n] n
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Heap::Simple::XS
Writing MYMETA.yml and MYMETA.json
Checking dependencies from MYMETA.json ...
Checking if you have Test::More 0.11 ... Yes (1.001014)
Checking if you have ExtUtils::MakeMaker 0 ... Yes (7.10)
Checking if you have Heap::Simple 0.09 ... Yes (0.13)
OK
Building Heap-Simple-XS-0.10 ... cp lib/Heap/Simple/XS/Package.pm blib/lib/Heap/Simple/XS/Package.pm
cp lib/Heap/Simple/XS.pm blib/lib/Heap/Simple/XS.pm
Running Mkbootstrap for Heap::Simple::XS ()
chmod 644 "XS.bs"
"/usr/bin/perl" "/usr/share/perl5/ExtUtils/xsubpp" -typemap "/usr/share/perl5/ExtUtils/typemap" -typemap "typemap" XS.xs > XS.xsc && mv XS.xsc XS.c
gcc -c -I. -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION="0.10" -DXS_VERSION="0.10" -fPIC "-I/usr/lib64/perl5/CORE" XS.c
In file included from /usr/include/string.h:637:0,
from /usr/lib64/perl5/CORE/perl.h:1001,
from XS.xs:3:
XS.xs: In function ‘my_isa_lookup’:
/usr/lib64/perl5/CORE/hv.h:278:28: warning: null argument where non-null required (argument 1) [-Wnonnull]
#define HvAUX(hv) ((struct xpvhv_aux*)&(HvARRAY(hv)[HvMAX(hv)+1]))
^
XS.xs:116:9: note: in expansion of macro ‘strEQ’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:298:7: note: in expansion of macro ‘HEK_KEY’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:298:15: note: in expansion of macro ‘HvAUX’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:285:20: note: in expansion of macro ‘HvNAME_get’
#define HvNAME(hv) HvNAME_get(hv)
^
XS.xs:116:15: note: in expansion of macro ‘HvNAME’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:278:28: warning: null argument where non-null required (argument 1) [-Wnonnull]
#define HvAUX(hv) ((struct xpvhv_aux*)&(HvARRAY(hv)[HvMAX(hv)+1]))
^
XS.xs:116:9: note: in expansion of macro ‘strEQ’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:298:7: note: in expansion of macro ‘HEK_KEY’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:298:15: note: in expansion of macro ‘HvAUX’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:285:20: note: in expansion of macro ‘HvNAME_get’
#define HvNAME(hv) HvNAME_get(hv)
^
XS.xs:116:15: note: in expansion of macro ‘HvNAME’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:278:28: warning: null argument where non-null required (argument 1) [-Wnonnull]
#define HvAUX(hv) ((struct xpvhv_aux*)&(HvARRAY(hv)[HvMAX(hv)+1]))
^
XS.xs:116:9: note: in expansion of macro ‘strEQ’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:298:7: note: in expansion of macro ‘HEK_KEY’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:298:15: note: in expansion of macro ‘HvAUX’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:285:20: note: in expansion of macro ‘HvNAME_get’
#define HvNAME(hv) HvNAME_get(hv)
^
XS.xs:116:15: note: in expansion of macro ‘HvNAME’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:278:28: warning: null argument where non-null required (argument 1) [-Wnonnull]
#define HvAUX(hv) ((struct xpvhv_aux*)&(HvARRAY(hv)[HvMAX(hv)+1]))
^
XS.xs:116:9: note: in expansion of macro ‘strEQ’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:298:7: note: in expansion of macro ‘HEK_KEY’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:298:15: note: in expansion of macro ‘HvAUX’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:285:20: note: in expansion of macro ‘HvNAME_get’
#define HvNAME(hv) HvNAME_get(hv)
^
XS.xs:116:15: note: in expansion of macro ‘HvNAME’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:278:28: warning: null argument where non-null required (argument 1) [-Wnonnull]
#define HvAUX(hv) ((struct xpvhv_aux*)&(HvARRAY(hv)[HvMAX(hv)+1]))
^
XS.xs:116:9: note: in expansion of macro ‘strEQ’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:298:7: note: in expansion of macro ‘HEK_KEY’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:298:15: note: in expansion of macro ‘HvAUX’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:285:20: note: in expansion of macro ‘HvNAME_get’
#define HvNAME(hv) HvNAME_get(hv)
^
XS.xs:116:15: note: in expansion of macro ‘HvNAME’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:278:28: warning: null argument where non-null required (argument 1) [-Wnonnull]
#define HvAUX(hv) ((struct xpvhv_aux*)&(HvARRAY(hv)[HvMAX(hv)+1]))
^
XS.xs:116:9: note: in expansion of macro ‘strEQ’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:298:7: note: in expansion of macro ‘HEK_KEY’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:298:15: note: in expansion of macro ‘HvAUX’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:285:20: note: in expansion of macro ‘HvNAME_get’
#define HvNAME(hv) HvNAME_get(hv)
^
XS.xs:116:15: note: in expansion of macro ‘HvNAME’
strEQ(HvNAME(stash), name) ||
^
XS.xs: In function ‘elements_name’:
XS.xs:270:7: warning: case value ‘0’ not in enumerated type ‘enum elements’ [-Wswitch]
case 0: croak("Element type is unspecified");
^
XS.xs: In function ‘order_name’:
XS.xs:284:7: warning: case value ‘0’ not in enumerated type ‘enum order’ [-Wswitch]
case 0: croak("Order type is unspecified");
^
In file included from /usr/lib64/perl5/CORE/perl.h:3413:0,
from XS.xs:3:
XS.xs: In function ‘key_insert’:
/usr/lib64/perl5/CORE/sv.h:214:26: warning: ‘t1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define SvREFCNT(sv) (sv)->sv_refcnt
^
XS.xs:438:15: note: ‘t1’ was declared here
SV *new, *t1, *t2;
^
XS.xs:500:30: warning: ‘new’ may be used uninitialized in this function [-Wmaybe-uninitialized]
h->values[l] = new;
^
In file included from /usr/lib64/perl5/CORE/perl.h:976:0,
from XS.xs:3:
XS.c: In function ‘XS_Heap__Simple__XS__absorb’:
/usr/lib64/perl5/CORE/embed.h:3251:37: warning: ‘value’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define sv_setnv(a,b) Perl_sv_setnv(aTHX_ a,b)
^
XS.xs:1648:21: note: ‘value’ was declared here
SV *heap1_ref, *value;
^
In file included from /usr/lib64/perl5/CORE/perl.h:976:0,
from XS.xs:3:
XS.c: In function ‘XS_Heap__Simple__XS__key_absorb’:
/usr/lib64/perl5/CORE/embed.h:3251:37: warning: ‘key’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define sv_setnv(a,b) Perl_sv_setnv(aTHX_ a,b)
^
XS.xs:1859:21: note: ‘key’ was declared here
SV *heap1_ref, *key, *value;
^
In file included from /usr/lib64/perl5/CORE/perl.h:976:0,
from XS.xs:3:
/usr/lib64/perl5/CORE/embed.h:3251:37: warning: ‘value’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define sv_setnv(a,b) Perl_sv_setnv(aTHX_ a,b)
^
XS.xs:1859:27: note: ‘value’ was declared here
SV *heap1_ref, *key, *value;
^
XS.c: In function ‘XS_Heap__Simple__XS_merge_arrays’:
XS.xs:2309:17: warning: ‘av’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr = av_fetch(av, k0, 0);
^
XS.xs:2275:9: note: ‘av’ was declared here
AV *av, *work_av;
^
rm -f blib/arch/auto/Heap/Simple/XS/XS.so
gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic XS.o -o blib/arch/auto/Heap/Simple/XS/XS.so
\

chmod 755 blib/arch/auto/Heap/Simple/XS/XS.so
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- XS.bs blib/arch/auto/Heap/Simple/XS/XS.bs 644
Manifying 1 pod document
Running Mkbootstrap for Heap::Simple::XS ()
chmod 644 "XS.bs"
Manifying 1 pod document
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/auto/Heap/Simple/XS/XS.so
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/Heap/Simple/XS.pm
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/Heap/Simple/XS/Package.pm
Installing /public/home/zpxu/jbrowse/extlib/man/man3/Heap::Simple::XS.3pm
Appending installation info to /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/perllocal.pod
OK
Successfully installed Heap-Simple-XS-0.10
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/.meta/Heap-Simple-XS-0.10/install.json
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/.meta/Heap-Simple-XS-0.10/MYMETA.json
Searching Devel::Size (0) on cpanmetadb ...
Unpacking Devel-Size-0.82.tar.gz
--> Working on Devel::Size
Fetching http://www.cpan.org/authors/id/N/NW/NWCLARK/Devel-Size-0.82.tar.gz ... OK
Devel-Size-0.82/
Devel-Size-0.82/META.yml
Devel-Size-0.82/META.json
Devel-Size-0.82/Size.xs
Devel-Size-0.82/ppport.h
Devel-Size-0.82/MANIFEST
Devel-Size-0.82/MANIFEST.SKIP
Devel-Size-0.82/lib/
Devel-Size-0.82/lib/Devel/
Devel-Size-0.82/lib/Devel/Size.pm
Devel-Size-0.82/Makefile.PL
Devel-Size-0.82/t/
Devel-Size-0.82/t/pvbm.t
Devel-Size-0.82/t/pod.t
Devel-Size-0.82/t/warnings.t
Devel-Size-0.82/t/code.t
Devel-Size-0.82/t/globs.t
Devel-Size-0.82/t/magic.t
Devel-Size-0.82/t/basic.t
Devel-Size-0.82/t/recurse.t
Devel-Size-0.82/t/pod_cov.t
Devel-Size-0.82/CHANGES
Devel-Size-0.82/typemap
Devel-Size-0.82/README
Entering Devel-Size-0.82
Checking configure dependencies from META.json
Checking if you have ExtUtils::MakeMaker 6.58 ... Yes (7.10)
Running Makefile.PL
Configuring Devel-Size-0.82 ... Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Devel::Size
Writing MYMETA.yml and MYMETA.json
Checking dependencies from MYMETA.json ...
Checking if you have Test::More 0 ... Yes (1.001014)
Checking if you have XSLoader 0 ... Yes (0.22)
Checking if you have ExtUtils::MakeMaker 0 ... Yes (7.10)
OK
Building Devel-Size-0.82 ... cp lib/Devel/Size.pm blib/lib/Devel/Size.pm
Running Mkbootstrap for Devel::Size ()
chmod 644 "Size.bs"
"/usr/bin/perl" "/usr/share/perl5/ExtUtils/xsubpp" -typemap "/usr/share/perl5/ExtUtils/typemap" -typemap "typemap" Size.xs > Size.xsc && mv Size.xsc Size.c
gcc -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DVERSION="0.82" -DXS_VERSION="0.82" -fPIC "-I/usr/lib64/perl5/CORE" -DALIGN_BITS=3 Size.c
Size.xs: In function ‘check_new’:
Size.xs:115:20: warning: unused variable ‘c’ [-Wunused-variable]
const char c = (const char )p;
^
In file included from Size.xs:6:0:
Size.c: In function ‘XS_Devel__Size_size’:
/usr/lib64/perl5/CORE/perl.h:362:39: warning: unused variable ‘Perl___notused’ [-Wunused-variable]
#define dNOOP extern int /
@unused@
/ Perl___notused PERL_UNUSED_DECL
^
/usr/lib64/perl5/CORE/perl.h:180:17: note: in expansion of macro ‘dNOOP’

define dVAR dNOOP

             ^

Size.c:1153:5: note: in expansion of macro ‘dVAR’
dVAR; dXSARGS;
^
Size.c: In function ‘boot_Devel__Size’:
/usr/lib64/perl5/CORE/perl.h:362:39: warning: unused variable ‘Perl___notused’ [-Wunused-variable]
#define dNOOP extern int /@unused@/ Perl___notused PERL_UNUSED_DECL
^
/usr/lib64/perl5/CORE/perl.h:180:17: note: in expansion of macro ‘dNOOP’

define dVAR dNOOP

             ^

Size.c:1192:5: note: in expansion of macro ‘dVAR’
dVAR; dXSARGS;
^
rm -f blib/arch/auto/Devel/Size/Size.so
gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic Size.o -o blib/arch/auto/Devel/Size/Size.so
\

chmod 755 blib/arch/auto/Devel/Size/Size.so
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- Size.bs blib/arch/auto/Devel/Size/Size.bs 644
Manifying 1 pod document
Running Mkbootstrap for Devel::Size ()
chmod 644 "Size.bs"
Manifying 1 pod document
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/auto/Devel/Size/Size.so
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/Devel/Size.pm
Installing /public/home/zpxu/jbrowse/extlib/man/man3/Devel::Size.3pm
Appending installation info to /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/perllocal.pod
OK
Successfully installed Devel-Size-0.82
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/.meta/Devel-Size-0.82/install.json
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/.meta/Devel-Size-0.82/MYMETA.json
<== Installed dependencies for .. Finishing.
3 distributions installed

  • bin/cpanm -v --notest -l extlib/ --installdeps .
    cpanm (App::cpanminus) 1.7043 on perl 5.010001 built for x86_64-linux-thread-multi
    Work directory is /public/home/zpxu/.cpanm/work/1533608572.11696
    You have make /usr/bin/make
    You have LWP 5.833
    You have /bin/tar: tar (GNU tar) 1.23
    Copyright (C) 2010 Free Software Foundation, Inc.
    License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html.
    This is free software: you are free to change and redistribute it.
    There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
You have /usr/bin/unzip
Entering /public/home/zpxu/jbrowse
Running Makefile.PL
--> Working on .
Configuring /public/home/zpxu/jbrowse ... Can't parse version 'dev'
Can't parse version 'dev'
Generating a Unix-style Makefile
Writing Makefile for JBrowse
Writing MYMETA.yml and MYMETA.json
Checking dependencies from MYMETA.json ...
Checking if you have Capture::Tiny 0 ... Yes (0.30)
Checking if you have Pod::Usage 0 ... Yes (1.36)
Checking if you have Storable 0 ... Yes (2.20)
Checking if you have JSON::XS 0 ... Yes (3.04)
Checking if you have List::Util 0 ... Yes (1.46)
Checking if you have PerlIO::gzip 0 ... Yes (0.19)
Checking if you have Digest::Crc32 0 ... Yes (0.01)
Checking if you have File::Path 2 ... Yes (2.08)
Checking if you have local::lib 0 ... Yes (2.000024)
Checking if you have List::MoreUtils 0.28 ... Yes (0.416)
Checking if you have Bio::FeatureIO 0 ... Yes (1.6.905)
Checking if you have DBI 0 ... Yes (1.641)
Checking if you have Getopt::Long 0 ... Yes (2.38)
Checking if you have warnings 0 ... Yes (1.06)
Checking if you have base 0 ... Yes (2.14)
Checking if you have IO::File 0 ... Yes (1.14)
Checking if you have Data::Dumper 0 ... Yes (2.154)
Checking if you have Bio::GFF3::LowLevel 1.8 ... Yes (2.0)
Checking if you have Bio::Index::Fasta 0 ... Yes (undef)
Checking if you have DB_File 0 ... Yes (1.820)
Checking if you have Bio::Root::Version 1.006000 ... Yes (1.007001)
Checking if you have Bio::Annotation::SimpleValue 0 ... Yes (undef)
Checking if you have vars 0 ... Yes (1.01)
Checking if you have Parse::RecDescent 0 ... Yes (1.967015)
Checking if you have Test::More 0 ... Yes (1.001014)
Checking if you have strict 0 ... Yes (1.04)
Checking if you have File::Temp 0 ... Yes (0.22)
Checking if you have File::Copy::Recursive 0 ... Yes (0.44)
Checking if you have Scalar::Util 0 ... Yes (1.46)
Checking if you have FindBin 0 ... Yes (1.50)
Checking if you have DBD::SQLite 0 ... Yes (1.27)
Checking if you have URI::Escape 0 ... Yes (3.31)
Checking if you have File::Spec 0 ... Yes (3.30)
Checking if you have Heap::Simple 0 ... Yes (0.13)
Checking if you have Heap::Simple::XS 0 ... Yes (0.10)
Checking if you have Fcntl 0 ... Yes (1.06)
Checking if you have POSIX 0 ... Yes (1.17)
Checking if you have Devel::Size 0 ... Yes (0.82)
Checking if you have File::Spec::Functions 0 ... Yes (3.30)
Checking if you have Bio::SeqFeature::Lite 0 ... Yes (undef)
Checking if you have Bio::GFF3::LowLevel::Parser 1.8 ... Yes (2.0)
Checking if you have IO::Uncompress::Gunzip 0 ... Yes (2.021)
Checking if you have Hash::Merge 0 ... Yes (0.300)
Checking if you have constant 0 ... Yes (1.17)
Checking if you have Exporter 0 ... Yes (5.63)
Checking if you have Bio::OntologyIO 0 ... Yes (undef)
Checking if you have Bio::SeqFeature::Annotated 0 ... Yes (1.6.905)
Checking if you have Carp 0 ... Yes (1.38)
Checking if you have Test::Warn 0 ... Yes (0.30)
Checking if you have File::Next 0 ... Yes (1.16)
Checking if you have File::Basename 0 ... Yes (2.77)
Checking if you have JSON 2 ... Yes (2.97001)
Checking if you have Cwd 0 ... Yes (3.30)
OK
<== Installed dependencies for .. Finishing.

  • set -e
  • bin/cpanm -v --notest -l extlib/ --installdeps .
    cpanm (App::cpanminus) 1.7043 on perl 5.010001 built for x86_64-linux-thread-multi
    Work directory is /public/home/zpxu/.cpanm/work/1533608573.11731
    You have make /usr/bin/make
    You have LWP 5.833
    You have /bin/tar: tar (GNU tar) 1.23
    Copyright (C) 2010 Free Software Foundation, Inc.
    License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html.
    This is free software: you are free to change and redistribute it.
    There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
You have /usr/bin/unzip
Entering /public/home/zpxu/jbrowse
Running Makefile.PL
--> Working on .
Configuring /public/home/zpxu/jbrowse ... Can't parse version 'dev'
Can't parse version 'dev'
Generating a Unix-style Makefile
Writing Makefile for JBrowse
Writing MYMETA.yml and MYMETA.json
Checking dependencies from MYMETA.json ...
Checking if you have Capture::Tiny 0 ... Yes (0.30)
Checking if you have Pod::Usage 0 ... Yes (1.36)
Checking if you have Storable 0 ... Yes (2.20)
Checking if you have JSON::XS 0 ... Yes (3.04)
Checking if you have List::Util 0 ... Yes (1.46)
Checking if you have PerlIO::gzip 0 ... Yes (0.19)
Checking if you have Digest::Crc32 0 ... Yes (0.01)
Checking if you have File::Path 2 ... Yes (2.08)
Checking if you have local::lib 0 ... Yes (2.000024)
Checking if you have List::MoreUtils 0.28 ... Yes (0.416)
Checking if you have Bio::FeatureIO 0 ... Yes (1.6.905)
Checking if you have DBI 0 ... Yes (1.641)
Checking if you have Getopt::Long 0 ... Yes (2.38)
Checking if you have warnings 0 ... Yes (1.06)
Checking if you have base 0 ... Yes (2.14)
Checking if you have IO::File 0 ... Yes (1.14)
Checking if you have Data::Dumper 0 ... Yes (2.154)
Checking if you have Bio::GFF3::LowLevel 1.8 ... Yes (2.0)
Checking if you have Bio::Index::Fasta 0 ... Yes (undef)
Checking if you have DB_File 0 ... Yes (1.820)
Checking if you have Bio::Root::Version 1.006000 ... Yes (1.007001)
Checking if you have Bio::Annotation::SimpleValue 0 ... Yes (undef)
Checking if you have vars 0 ... Yes (1.01)
Checking if you have Parse::RecDescent 0 ... Yes (1.967015)
Checking if you have Test::More 0 ... Yes (1.001014)
Checking if you have strict 0 ... Yes (1.04)
Checking if you have File::Temp 0 ... Yes (0.22)
Checking if you have File::Copy::Recursive 0 ... Yes (0.44)
Checking if you have Scalar::Util 0 ... Yes (1.46)
Checking if you have FindBin 0 ... Yes (1.50)
Checking if you have DBD::SQLite 0 ... Yes (1.27)
Checking if you have URI::Escape 0 ... Yes (3.31)
Checking if you have File::Spec 0 ... Yes (3.30)
Checking if you have Heap::Simple 0 ... Yes (0.13)
Checking if you have Heap::Simple::XS 0 ... Yes (0.10)
Checking if you have Fcntl 0 ... Yes (1.06)
Checking if you have POSIX 0 ... Yes (1.17)
Checking if you have Devel::Size 0 ... Yes (0.82)
Checking if you have File::Spec::Functions 0 ... Yes (3.30)
Checking if you have Bio::SeqFeature::Lite 0 ... Yes (undef)
Checking if you have Bio::GFF3::LowLevel::Parser 1.8 ... Yes (2.0)
Checking if you have IO::Uncompress::Gunzip 0 ... Yes (2.021)
Checking if you have Hash::Merge 0 ... Yes (0.300)
Checking if you have constant 0 ... Yes (1.17)
Checking if you have Exporter 0 ... Yes (5.63)
Checking if you have Bio::OntologyIO 0 ... Yes (undef)
Checking if you have Bio::SeqFeature::Annotated 0 ... Yes (1.6.905)
Checking if you have Carp 0 ... Yes (1.38)
Checking if you have Test::Warn 0 ... Yes (0.30)
Checking if you have File::Next 0 ... Yes (1.16)
Checking if you have File::Basename 0 ... Yes (2.77)
Checking if you have JSON 2 ... Yes (2.97001)
Checking if you have Cwd 0 ... Yes (3.30)
OK
<== Installed dependencies for .. Finishing.

done.

Formatting Volvox example data ...

  • rm -rf sample_data/json/volvox
  • bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa --out sample_data/json/volvox
  • '[' 0 -eq 1 ']'
  • bin/biodb-to-json.pl -v --conf docs/tutorial/conf_files/volvox.json --out sample_data/json/volvox

working on refseq ctgA
working on track ExampleFeatures
mergedTrackCfg: $VAR1 = {
'feature' => [
'remark'
],
'autocomplete' => 'all',
'track' => 'ExampleFeatures',
'style' => {
'className' => 'feature2'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - Example Features'
};
searching for features of type: remark
working on track NameTest
mergedTrackCfg: $VAR1 = {
'feature' => [
'protein_coding_primary_transcript',
'polypeptide'
],
'autocomplete' => 'all',
'track' => 'NameTest',
'style' => {
'className' => 'feature2'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - Name test track has a really long track label'
};
searching for features of type: protein_coding_primary_transcript, polypeptide
working on track snps
mergedTrackCfg: $VAR1 = {
'feature' => [
'SNP'
],
'autocomplete' => 'all',
'track' => 'snps',
'style' => {
'className' => 'triangle hgred'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - SNPs'
};
searching for features of type: SNP
working on track Motifs
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Motifs',
'style' => {
'className' => 'feature3',
'label' => 'function(feature) { return feature.get('Name')+' (via JS callback)' }',
'description' => 'function(feature) { return feature.get('Name')+': '+feature.get('Note'); }'
},
'description' => 1,
'key' => 'HTMLFeatures - Example motifs',
'feature' => [
'polypeptide_domain'
],
'compress' => 0,
'category' => 'Miscellaneous'
};
searching for features of type: polypeptide_domain
working on track malformed_alignments
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'malformed_alignments',
'style' => {
'className' => 'feature4'
},
'menuTemplate' => [
{
'children' => [
{
'children' => [
{
'iconClass' => 'dijitIconBookmark',
'url' => 'http://wiki.trin.org.au/{name}-{start}-{end}',
'action' => 'newWindow',
'label' => 'Query trin for {name}'
},
{
'iconClass' => 'dijitIconSearch',
'url' => 'http://example.com/{name}-{start}-{end}',
'label' => 'Query example.com for {name}'
}
],
'label' => 'Check gene on databases'
},
{
'label' => '2nd child of demo'
},
{
'label' => '3rd child: this is a track'
}
],
'label' => 'Item with submenu'
},
{
'iconClass' => 'dijitIconDatabase',
'url' => 'http://www.example.com?featurename={name}',
'action' => 'iframeDialog',
'title' => 'The magnificent example.com (feature {name})',
'label' => 'Open example.com in an iframe popup'
},
{
'iconClass' => 'dijitIconDatabase',
'url' => 'sample_data/test_snippet.html?featurename={name}:{start}-{end}',
'action' => 'xhrDialog',
'title' => 'function(track,feature,div) { return 'Random XHR HTML '+Math.random()+' title!'; }',
'label' => 'Open popup with XHR HTML snippet (btw this is feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => 'function(track,feature,div) { return '

'+feature.get('name')+'

This is some test content!

This message brought to you by the number '+Math.round(Math.random()*100)+'.

';} ',
'action' => 'contentDialog',
'title' => 'function(track,feature,div) { return 'Random content snippet '+Math.random()+' title!'; }',
'label' => 'Popup with content snippet from a function (feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => '

{name}

This is some test content about {name}, which goes from {start} to {end} on the {strand} strand.

',
'action' => 'contentDialog',
'title' => '{randomNumberTitle}',
'label' => 'Popup with content snippet from string (feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'action' => '{exampleFeatureClick}',
'label' => '{randomNumberLabel}'
}
],
'hooks' => {
'modify' => 'function( track, feature, div ) { div.style.backgroundColor = ['green','blue','red','orange','purple'][Math.round(Math.random()5)];}'
},
'key' => 'HTMLFeatures - Features with right-click menus',
'feature' => [
'match'
],
'shortDescription' => 'Features with customized right-click menus',
'compress' => 0,
'metadata' => {
'category' => 'Miscellaneous',
'Description' => 'Features with extensively customized right-click menus, and with their colors set at random by a JavaScript callback.'
}
};
searching for features of type: match
working on track Genes
mergedTrackCfg: $VAR1 = {
'fmtDetailValue_Name' => 'function(name,feature) { if(feature.get('type')=='gene') { return name + ' <a href=http://www.ncbi.nlm.nih.gov/gquery/?term=\'+name+\'>[NCBI custom link]'; } else { return name; } }',
'fmtMetaDescription_Name' => 'function(name) { return '[Custom description]'; }',
'fmtMetaValue_Name' => 'function(name) { return name+' [Track with custom callbacks for About track popup]'; }',
'key' => 'CanvasFeatures - Protein-coding genes',
'onClick' => {
'action' => 'defaultDialog',
'title' => '{type} {name}',
'label' => '<div style='font:normal 12px Univers,Helvetica,Arial,sans-serif'><div style='font-weight:bold'>Custom tooltip<div style='color:blue;'>Feature name: {name}
Feature start: {start}
Feature end: {end}'
},
'feature' => [
'gene'
],
'fmtDetailField_Name' => 'function(name,feature) { if(feature.get('type')=='gene') { return 'Gene Name'; } else { return name; } }',
'fmtMetaField_Name' => 'function(name) { return 'Track Name'; }',
'fmtDetailField_Load_id' => 'function(name,feature) { /
remove field from dialog box */ return null; }',
'category' => 'Transcripts',
'metadata' => {
'ncbi_submission_model' => 'Generic',
'insdc_first_public' => '2018-05-15T00:00:00Z',
'Link: ENA study page' => 'http://www.ebi.ac.uk/ena/',
'library_total_amount_of_reads' => '3349981',
'insdc_secondary_accession' => 'SRS12345678',
'insdc_center_name' => 'INSDC Sample',
'ncbi_submission_package' => 'Generic.1.0',
'sample_name' => 'GSM12345678',
'ENA first public' => '2018-05-16',
'study' => 'SRP12345678 a study of volvox',
'organism' => 'Volvox',
'library_size_approx' => '1-5mln',
'Link: RNASeq-er analysis results' => 'ftp://ftp.ebi.ac.uk/pub/databases/arrayexpress/',
'insdc_last_update' => '2018-05-15T01:18:23.110Z',
'insdc_status' => 'live',
'developmental_stage' => 'stage 6- 330 min',
'mapping_quality_approx' => 'under 50%',
'tissue' => 'embryo',
'source_name' => 'Volvox 6- 330 min',
'mapping_fraction_of_uniquely_mapped_reads' => '0.429',
'ENA last update' => '2018-05-16',
'description_title' => 'Volvox_mRNA_rep_2_6'
},
'autocomplete' => 'all',
'track' => 'Genes',
'style' => {
'className' => 'feature5'
},
'menuTemplate' => [
{
'label' => 'View details'
},
{
'label' => 'Zoom this gene'
},
{
'label' => 'Highlight this gene'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => '

{name}

This is some test content about {type} {name}, which goes from {start} to {end} on the {strand} strand.',
'action' => 'contentDialog',
'title' => '{randomNumberTitle}',
'label' => 'Popup with content snippet from string (feature {name})'
}
],
'trackType' => 'NeatCanvasFeatures/View/Track/NeatFeatures',
'compress' => 0
};
searching for features of type: gene
working on track ReadingFrame
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'ReadingFrame',
'style' => {
'className' => 'cds'
},
'key' => 'HTMLFeatures - mRNAs',
'onClick' => {
'url' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}',
'title' => 'NCBI search box',
'label' => 'Search for {name} at NCBI
Feature start {start}
Feature end {end}'
},
'feature' => [
'mRNA'
],
'trackType' => 'NeatHTMLFeatures/View/Track/NeatFeatures',
'phase' => 1,
'compress' => 0,
'category' => 'Transcripts'
};
searching for features of type: mRNA
working on track CDS
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'CDS',
'style' => {
'className' => 'cds',
'linkTemplate' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}-{start}-{end}'
},
'key' => 'CanvasFeatures - mixed mRNAs and CDSs',
'feature' => [
'CDS:bare_predicted',
'mRNA:exonerate',
'mRNA:predicted'
],
'trackType' => 'CanvasFeatures',
'compress' => 0,
'category' => 'Transcripts'
};
searching for features of type: CDS:bare_predicted, mRNA:exonerate, mRNA:predicted
working on track Transcript
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Transcript',
'style' => {
'className' => 'feature',
'color' => '#E32A3A',
'description' => 'customdescription'
},
'description' => 1,
'key' => 'CanvasFeatures - transcripts',
'onClick' => '{exampleFeatureClick}',
'feature' => [
'mRNA:exonerate'
],
'trackType' => 'JBrowse/View/Track/CanvasFeatures',
'compress' => 0,
'category' => 'Transcripts',
'showNoteInAttributes' => bless( do{(my $o = 1)}, 'JSON::PP::Boolean' ),
'subfeatures' => $VAR1->{'showNoteInAttributes'}
};
searching for features of type: mRNA:exonerate
working on track Clones
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Clones',
'style' => {
'className' => 'exon'
},
'description' => 1,
'key' => 'HTMLFeatures - Fingerprinted BACs',
'feature' => [
'BAC'
],
'compress' => 0,
'category' => 'Miscellaneous'
};
searching for features of type: BAC
working on track EST
mergedTrackCfg: $VAR1 = {
'feature' => [
'EST_match:est'
],
'autocomplete' => 'all',
'track' => 'EST',
'style' => {
'className' => 'est'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - ESTs'
};
searching for features of type: EST_match:est

working on refseq ctgB
working on track ExampleFeatures
mergedTrackCfg: $VAR1 = {
'feature' => [
'remark'
],
'autocomplete' => 'all',
'track' => 'ExampleFeatures',
'style' => {
'className' => 'feature2'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - Example Features'
};
searching for features of type: remark
working on track NameTest
mergedTrackCfg: $VAR1 = {
'feature' => [
'protein_coding_primary_transcript',
'polypeptide'
],
'autocomplete' => 'all',
'track' => 'NameTest',
'style' => {
'className' => 'feature2'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - Name test track has a really long track label'
};
searching for features of type: protein_coding_primary_transcript, polypeptide
working on track snps
mergedTrackCfg: $VAR1 = {
'feature' => [
'SNP'
],
'autocomplete' => 'all',
'track' => 'snps',
'style' => {
'className' => 'triangle hgred'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - SNPs'
};
searching for features of type: SNP
working on track Motifs
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Motifs',
'style' => {
'className' => 'feature3',
'label' => 'function(feature) { return feature.get('Name')+' (via JS callback)' }',
'description' => 'function(feature) { return feature.get('Name')+': '+feature.get('Note'); }'
},
'description' => 1,
'key' => 'HTMLFeatures - Example motifs',
'feature' => [
'polypeptide_domain'
],
'compress' => 0,
'category' => 'Miscellaneous'
};
searching for features of type: polypeptide_domain
working on track malformed_alignments
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'malformed_alignments',
'style' => {
'className' => 'feature4'
},
'menuTemplate' => [
{
'children' => [
{
'children' => [
{
'iconClass' => 'dijitIconBookmark',
'url' => 'http://wiki.trin.org.au/{name}-{start}-{end}',
'action' => 'newWindow',
'label' => 'Query trin for {name}'
},
{
'iconClass' => 'dijitIconSearch',
'url' => 'http://example.com/{name}-{start}-{end}',
'label' => 'Query example.com for {name}'
}
],
'label' => 'Check gene on databases'
},
{
'label' => '2nd child of demo'
},
{
'label' => '3rd child: this is a track'
}
],
'label' => 'Item with submenu'
},
{
'iconClass' => 'dijitIconDatabase',
'url' => 'http://www.example.com?featurename={name}',
'action' => 'iframeDialog',
'title' => 'The magnificent example.com (feature {name})',
'label' => 'Open example.com in an iframe popup'
},
{
'iconClass' => 'dijitIconDatabase',
'url' => 'sample_data/test_snippet.html?featurename={name}:{start}-{end}',
'action' => 'xhrDialog',
'title' => 'function(track,feature,div) { return 'Random XHR HTML '+Math.random()+' title!'; }',
'label' => 'Open popup with XHR HTML snippet (btw this is feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => 'function(track,feature,div) { return '

'+feature.get('name')+'

This is some test content!

This message brought to you by the number '+Math.round(Math.random()*100)+'.

';} ',
'action' => 'contentDialog',
'title' => 'function(track,feature,div) { return 'Random content snippet '+Math.random()+' title!'; }',
'label' => 'Popup with content snippet from a function (feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => '

{name}

This is some test content about {name}, which goes from {start} to {end} on the {strand} strand.

',
'action' => 'contentDialog',
'title' => '{randomNumberTitle}',
'label' => 'Popup with content snippet from string (feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'action' => '{exampleFeatureClick}',
'label' => '{randomNumberLabel}'
}
],
'hooks' => {
'modify' => 'function( track, feature, div ) { div.style.backgroundColor = ['green','blue','red','orange','purple'][Math.round(Math.random()5)];}'
},
'key' => 'HTMLFeatures - Features with right-click menus',
'feature' => [
'match'
],
'shortDescription' => 'Features with customized right-click menus',
'compress' => 0,
'metadata' => {
'category' => 'Miscellaneous',
'Description' => 'Features with extensively customized right-click menus, and with their colors set at random by a JavaScript callback.'
}
};
searching for features of type: match
working on track Genes
mergedTrackCfg: $VAR1 = {
'fmtDetailValue_Name' => 'function(name,feature) { if(feature.get('type')=='gene') { return name + ' <a href=http://www.ncbi.nlm.nih.gov/gquery/?term=\'+name+\'>[NCBI custom link]'; } else { return name; } }',
'fmtMetaDescription_Name' => 'function(name) { return '[Custom description]'; }',
'fmtMetaValue_Name' => 'function(name) { return name+' [Track with custom callbacks for About track popup]'; }',
'key' => 'CanvasFeatures - Protein-coding genes',
'onClick' => {
'action' => 'defaultDialog',
'title' => '{type} {name}',
'label' => '<div style='font:normal 12px Univers,Helvetica,Arial,sans-serif'><div style='font-weight:bold'>Custom tooltip<div style='color:blue;'>Feature name: {name}
Feature start: {start}
Feature end: {end}'
},
'feature' => [
'gene'
],
'fmtDetailField_Name' => 'function(name,feature) { if(feature.get('type')=='gene') { return 'Gene Name'; } else { return name; } }',
'fmtMetaField_Name' => 'function(name) { return 'Track Name'; }',
'fmtDetailField_Load_id' => 'function(name,feature) { /
remove field from dialog box */ return null; }',
'category' => 'Transcripts',
'metadata' => {
'ncbi_submission_model' => 'Generic',
'insdc_first_public' => '2018-05-15T00:00:00Z',
'Link: ENA study page' => 'http://www.ebi.ac.uk/ena/',
'library_total_amount_of_reads' => '3349981',
'insdc_secondary_accession' => 'SRS12345678',
'insdc_center_name' => 'INSDC Sample',
'ncbi_submission_package' => 'Generic.1.0',
'sample_name' => 'GSM12345678',
'ENA first public' => '2018-05-16',
'study' => 'SRP12345678 a study of volvox',
'organism' => 'Volvox',
'library_size_approx' => '1-5mln',
'Link: RNASeq-er analysis results' => 'ftp://ftp.ebi.ac.uk/pub/databases/arrayexpress/',
'insdc_last_update' => '2018-05-15T01:18:23.110Z',
'insdc_status' => 'live',
'developmental_stage' => 'stage 6- 330 min',
'mapping_quality_approx' => 'under 50%',
'tissue' => 'embryo',
'source_name' => 'Volvox 6- 330 min',
'mapping_fraction_of_uniquely_mapped_reads' => '0.429',
'ENA last update' => '2018-05-16',
'description_title' => 'Volvox_mRNA_rep_2_6'
},
'autocomplete' => 'all',
'track' => 'Genes',
'style' => {
'className' => 'feature5'
},
'menuTemplate' => [
{
'label' => 'View details'
},
{
'label' => 'Zoom this gene'
},
{
'label' => 'Highlight this gene'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => '

{name}

This is some test content about {type} {name}, which goes from {start} to {end} on the {strand} strand.',
'action' => 'contentDialog',
'title' => '{randomNumberTitle}',
'label' => 'Popup with content snippet from string (feature {name})'
}
],
'trackType' => 'NeatCanvasFeatures/View/Track/NeatFeatures',
'compress' => 0
};
searching for features of type: gene
working on track ReadingFrame
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'ReadingFrame',
'style' => {
'className' => 'cds'
},
'key' => 'HTMLFeatures - mRNAs',
'onClick' => {
'url' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}',
'title' => 'NCBI search box',
'label' => 'Search for {name} at NCBI
Feature start {start}
Feature end {end}'
},
'feature' => [
'mRNA'
],
'trackType' => 'NeatHTMLFeatures/View/Track/NeatFeatures',
'phase' => 1,
'compress' => 0,
'category' => 'Transcripts'
};
searching for features of type: mRNA
working on track CDS
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'CDS',
'style' => {
'className' => 'cds',
'linkTemplate' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}-{start}-{end}'
},
'key' => 'CanvasFeatures - mixed mRNAs and CDSs',
'feature' => [
'CDS:bare_predicted',
'mRNA:exonerate',
'mRNA:predicted'
],
'trackType' => 'CanvasFeatures',
'compress' => 0,
'category' => 'Transcripts'
};
searching for features of type: CDS:bare_predicted, mRNA:exonerate, mRNA:predicted
working on track Transcript
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Transcript',
'style' => {
'className' => 'feature',
'color' => '#E32A3A',
'description' => 'customdescription'
},
'description' => 1,
'key' => 'CanvasFeatures - transcripts',
'onClick' => '{exampleFeatureClick}',
'feature' => [
'mRNA:exonerate'
],
'trackType' => 'JBrowse/View/Track/CanvasFeatures',
'compress' => 0,
'category' => 'Transcripts',
'showNoteInAttributes' => bless( do{(my $o = 1)}, 'JSON::PP::Boolean' ),
'subfeatures' => $VAR1->{'showNoteInAttributes'}
};
searching for features of type: mRNA:exonerate
working on track Clones
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Clones',
'style' => {
'className' => 'exon'
},
'description' => 1,
'key' => 'HTMLFeatures - Fingerprinted BACs',
'feature' => [
'BAC'
],
'compress' => 0,
'category' => 'Miscellaneous'
};
searching for features of type: BAC
working on track EST
mergedTrackCfg: $VAR1 = {
'feature' => [
'EST_match:est'
],
'autocomplete' => 'all',
'track' => 'EST',
'style' => {
'className' => 'est'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - ESTs'
};
searching for features of type: EST_match:est

  • cat docs/tutorial/data_files/volvox_microarray.bw.conf docs/tutorial/data_files/volvox_sine.bw.conf docs/tutorial/data_files/volvox-sorted.bam.conf docs/tutorial/data_files/volvox-sorted.bam.coverage.conf docs/tutorial/data_files/volvox-paired.bam.conf docs/tutorial/data_files/volvox.vcf.conf docs/tutorial/data_files/volvox_fromconfig.conf docs/tutorial/data_files/volvox.gff3.conf docs/tutorial/data_files/volvox.gtf.conf docs/tutorial/data_files/volvox.sort.gff3.gz.conf docs/tutorial/data_files/volvox.sort.gff3.gz.htmlfeatures.conf docs/tutorial/data_files/volvox.sort.bed.gz.conf docs/tutorial/data_files/gvcf.vcf.gz.conf docs/tutorial/data_files/bookmarks.conf docs/tutorial/data_files/volvox.subsubparts.gff3.conf docs/tutorial/data_files/volvox-long-reads.fastq.sorted.bam.conf docs/tutorial/data_files/volvox-long-reads.fastq.sorted.cram.conf docs/tutorial/data_files/volvox.bb.conf docs/tutorial/data_files/volvox-sorted.cram.conf
  • bin/add-json.pl '{ "dataset_id": "volvox", "include": [ "../../raw/volvox/functions.conf" ] }' sample_data/json/volvox/trackList.json
  • bin/add-json.pl '{ "dataset_id": "volvox", "plugins": [ "HideTrackLabels", "NeatCanvasFeatures", "NeatHTMLFeatures" ] }' sample_data/json/volvox/trackList.json
  • bin/flatfile-to-json.pl --bed docs/tutorial/data_files/volvox_segment.bed --out sample_data/json/volvox --trackLabel ChromHMM --trackType CanvasFeatures --clientConfig '{"color": "{chromHMM}", "strandArrow": false}' --config '{"displayMode": "collapsed", "enableCollapsedMouseover": true, "category": "Miscellaneous" }'
  • bin/generate-names.pl --safeMode -v --out sample_data/json/volvox
    Tracks:
    CDS
    ChromHMM
    Clones
    DNA
    EST
    ExampleFeatures
    Genes
    Motifs
    NameTest
    ReadingFrame
    Transcript
    fromconfig
    malformed_alignments
    snps
    volvox-long_reads
    volvox-long_reads-cram
    volvox-paired_bam
    volvox-sorted-vcf
    volvox-sorted_bam
    volvox-sorted_bam_coverage
    volvox-sorted_cram
    volvox_bb
    volvox_bed_tabix
    volvox_gff3
    volvox_gff3_subsubparts
    volvox_gff3_tabix
    volvox_gff3_tabix_html
    volvox_gtf
    volvox_gvcf_test
    volvox_microarray_bw_density
    volvox_microarray_bw_xyplot
    volvox_sine_density
    volvox_sine_xyplot
    volvox_vcf_test
    Sampled input stats:
    avg record text bytes 2201.79498861048
    name input records 847
    operation stream estimated count 736
    record stream estimated count 184
    total namerec bytes 1933176
    total input bytes 407148
    operations made 4325
    namerecs buffered 878
    namerecs converted to operations 878
    Removing existing contents of target dir sample_data/json/volvox/names
    Hash store cache size: 2684 buckets
    Using 1 chars for sort log names (16 sort logs)
  • mkdir -p sample_data/raw
  • '[' '!' -e sample_data/raw/volvox ']'
  • ln -sf ../../docs/tutorial/conf_files/volvox.json sample_data/raw/
  • touch sample_data/json/volvox/successfully_run

done.

Formatting Yeast example data ...

  • rm -rf sample_data/json/yeast/
  • bin/prepare-refseqs.pl --fasta sample_data/raw/yeast_scaffolds/chr1.fa.gz --fasta sample_data/raw/yeast_scaffolds/chr2.fa.gzip --out sample_data/json/yeast/
  • gunzip -c sample_data/raw/yeast_scaffolds/chr1.fa.gz sample_data/raw/yeast_scaffolds/chr2.fa.gzip
  • '[' 0 -eq 1 ']'
  • bin/biodb-to-json.pl --conf sample_data/raw/yeast.json --out sample_data/json/yeast/

working on refseq chrI
working on track Genes
working on track transcript_with_no_features

working on refseq chrII
working on track Genes
working on track transcript_with_no_features

  • bin/add-json.pl '{ "dataset_id": "yeast" }' sample_data/json/yeast/trackList.json
  • bin/add-json.pl '{ "dataset_id": "yeast", "plugins": [ "NeatHTMLFeatures","NeatCanvasFeatures","HideTrackLabels" ] }' sample_data/json/yeast/trackList.json
  • bin/generate-names.pl --dir sample_data/json/yeast/

done.

</details>

tiramisutes commented Aug 7, 2018

I try git clone from GitHub, but have same problem as show in picture (
jbrowse).

``` Gathering system information ... ============== System information ==== + lsb_release -a LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch Distributor ID: CentOS Description: CentOS release 6.5 (Final) Release: 6.5 Codename: Final + uname -a Linux node102 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux + sw_vers ./setup.sh: line 74: sw_vers: command not found + grep MemTotal /proc/meminfo MemTotal: 65939372 kB + echo
  • echo

done.

NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, please use JBrowse 1.12.3 or earlier.

Installing node.js dependencies and building with webpack ...
Node v8.9.4 installed at /public/home/zpxu/.nvm/versions/node/v8.9.4/bin/node with npm 5.6.0
yarn install v1.9.4
warning package-lock.json found. Your project contains lock files generated by tools other than Yarn. It is advised not to mix package managers in order to avoid resolution inconsistencies caused by unsynchronized lock files. To clear this warning, remove package-lock.json.
[1/4] Resolving packages...
success Already up-to-date.
Done in 1.92s.
yarn run v1.9.4
$ webpack
clean-webpack-plugin: /public/home/zpxu/jbrowse/dist has been removed.
jbrowse-glob-loader: building 201 JBrowse modules
jbrowse-glob-loader: adding plugin module RegexSequenceSearch/View/SearchSeqDialog
jbrowse-glob-loader: adding plugin module RegexSequenceSearch/Store/SeqFeature/RegexSearch
jbrowse-glob-loader: adding plugin module RegexSequenceSearch/main
jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/View/Track/NeatFeatures
jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/main
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/Track/NeatFeatures
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Segments
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/ProcessedTranscript
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Gene
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Box
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/main
jbrowse-glob-loader: adding plugin module HideTrackLabels/main
jbrowse-glob-loader: adding plugin module DebugEvents/main
jbrowse-glob-loader: adding plugin module CategoryUrl/main
jbrowse-glob-loader: discovered a total of 215 modules
jbrowse-glob-loader: skipping entry point module JBrowse/main
Hash: 7101a07a714193e1b9a5
Version: webpack 3.11.0
Time: 90248ms
Asset Size Chunks Chunk Names
0.bundle.js.map 8.73 MB 0, 1, 2, 3 [emitted]
0.bundle.js 6.39 MB 0, 1, 2, 3 [emitted] [big]
2.bundle.js 145 kB 2 [emitted]
3.bundle.js 398 kB 3 [emitted] [big]
4.bundle.js 1.68 kB 4 [emitted]
5.bundle.js 921 bytes 5 [emitted]
run_jasmine.bundle.js 557 kB 6 [emitted] [big] run_jasmine
browser.bundle.js 363 kB 7 [emitted] [big] browser
main.bundle.js 373 kB 8 [emitted] [big] main
1.bundle.js 494 kB 1 [emitted] [big]
1.bundle.js.map 676 kB 1 [emitted]
2.bundle.js.map 199 kB 2 [emitted]
3.bundle.js.map 503 kB 3 [emitted]
4.bundle.js.map 1.87 kB 4 [emitted]
5.bundle.js.map 1.13 kB 5 [emitted]
run_jasmine.bundle.js.map 836 kB 6 [emitted] run_jasmine
browser.bundle.js.map 517 kB 7 [emitted] browser
main.bundle.js.map 534 kB 8 [emitted] main
dojo/resources/blank.gif 43 bytes [emitted]
[129] ./build/dojo-webpack-plugin-loader/dojo/dojo.js 70.7 kB {6} {7} {8} [built]
[334] ./src/JBrowse/Util.js 22.1 kB {0} {1} [built]
[336] ./src/JBrowse/QueryParamConfigMapper.js 6.13 kB {0} {2} [built]
[337] ./src/JBrowse/standalone.js 140 bytes {0} {7} [built]
[338] ./src/JBrowse/Model/SimpleFeature.js 2.86 kB {0} {1} [built]
[340] ./src/JBrowse/FeatureFiltererMixin.js 3.19 kB {0} [built]
[341] ./src/JBrowse/Store/RemoteBinaryFile.js 18.6 kB {0} {1} [built]
[342] ./src/JBrowse/View/Track/_AlignmentsMixin.js 15.8 kB {0} [built]
[343] ./src/JBrowse/Store/SeqFeature/_MismatchesMixin.js 12.6 kB {0} [built]
[344] ./src/JBrowse/Model/NestedFrequencyTable.js 3.41 kB {0} {1} [built]
[345] ./src/JBrowse/View/GranularRectLayout.js 16.5 kB {0} {2} [built]
[371] ./src/JBrowse/main.js 11.8 kB {8} [built]
[372] ./tests/js_tests/main.js 1.55 kB {6} [built]
[454] ./src/JBrowse/View/Track/_VariantDetailMixin.js 13.3 kB {0} [built]
[469] ./src/JBrowse/View/Track/BlockBased/Block.js 1.03 kB {0} [built]
+ 1413 hidden modules
Done in 162.03s.

done.

Installing Perl prerequisites ...

  • bin/cpanm -v --notest -l extlib/ --installdeps .
    cpanm (App::cpanminus) 1.7043 on perl 5.010001 built for x86_64-linux-thread-multi
    Work directory is /public/home/zpxu/.cpanm/work/1533608547.10840
    You have make /usr/bin/make
    You have LWP 5.833
    You have /bin/tar: tar (GNU tar) 1.23
    Copyright (C) 2010 Free Software Foundation, Inc.
    License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html.
    This is free software: you are free to change and redistribute it.
    There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
You have /usr/bin/unzip
Entering /public/home/zpxu/jbrowse
Running Makefile.PL
--> Working on .
Configuring /public/home/zpxu/jbrowse ... Warning: prerequisite Devel::Size 0 not found.
Warning: prerequisite Heap::Simple::XS 0 not found.
Warning: prerequisite JSON::XS 0 not found.
Can't parse version 'dev'
Can't parse version 'dev'
Generating a Unix-style Makefile
Writing Makefile for JBrowse
Writing MYMETA.yml and MYMETA.json
Checking dependencies from MYMETA.json ...
Checking if you have Capture::Tiny 0 ... Yes (0.30)
Checking if you have Pod::Usage 0 ... Yes (1.36)
Checking if you have Storable 0 ... Yes (2.20)
Checking if you have JSON::XS 0 ... No
Checking if you have List::Util 0 ... Yes (1.46)
Checking if you have PerlIO::gzip 0 ... Yes (0.19)
Checking if you have Digest::Crc32 0 ... Yes (0.01)
Checking if you have File::Path 2 ... Yes (2.08)
Checking if you have local::lib 0 ... Yes (2.000024)
Checking if you have List::MoreUtils 0.28 ... Yes (0.416)
Checking if you have Bio::FeatureIO 0 ... Yes (1.6.905)
Checking if you have DBI 0 ... Yes (1.641)
Checking if you have Getopt::Long 0 ... Yes (2.38)
Checking if you have warnings 0 ... Yes (1.06)
Checking if you have base 0 ... Yes (2.14)
Checking if you have IO::File 0 ... Yes (1.14)
Checking if you have Data::Dumper 0 ... Yes (2.154)
Checking if you have Bio::GFF3::LowLevel 1.8 ... Yes (2.0)
Checking if you have Bio::Index::Fasta 0 ... Yes (undef)
Checking if you have DB_File 0 ... Yes (1.820)
Checking if you have Bio::Root::Version 1.006000 ... Yes (1.007001)
Checking if you have Bio::Annotation::SimpleValue 0 ... Yes (undef)
Checking if you have vars 0 ... Yes (1.01)
Checking if you have Parse::RecDescent 0 ... Yes (1.967015)
Checking if you have Test::More 0 ... Yes (1.001014)
Checking if you have strict 0 ... Yes (1.04)
Checking if you have File::Temp 0 ... Yes (0.22)
Checking if you have File::Copy::Recursive 0 ... Yes (0.44)
Checking if you have Scalar::Util 0 ... Yes (1.46)
Checking if you have FindBin 0 ... Yes (1.50)
Checking if you have DBD::SQLite 0 ... Yes (1.27)
Checking if you have URI::Escape 0 ... Yes (3.31)
Checking if you have File::Spec 0 ... Yes (3.30)
Checking if you have Heap::Simple 0 ... Yes (0.13)
Checking if you have Heap::Simple::XS 0 ... No
Checking if you have Fcntl 0 ... Yes (1.06)
Checking if you have POSIX 0 ... Yes (1.17)
Checking if you have Devel::Size 0 ... No
Checking if you have File::Spec::Functions 0 ... Yes (3.30)
Checking if you have Bio::SeqFeature::Lite 0 ... Yes (undef)
Checking if you have Bio::GFF3::LowLevel::Parser 1.8 ... Yes (2.0)
Checking if you have IO::Uncompress::Gunzip 0 ... Yes (2.021)
Checking if you have Hash::Merge 0 ... Yes (0.300)
Checking if you have constant 0 ... Yes (1.17)
Checking if you have Exporter 0 ... Yes (5.63)
Checking if you have Bio::OntologyIO 0 ... Yes (undef)
Checking if you have Bio::SeqFeature::Annotated 0 ... Yes (1.6.905)
Checking if you have Carp 0 ... Yes (1.38)
Checking if you have Test::Warn 0 ... Yes (0.30)
Checking if you have File::Next 0 ... Yes (1.16)
Checking if you have File::Basename 0 ... Yes (2.77)
Checking if you have JSON 2 ... Yes (2.97001)
Checking if you have Cwd 0 ... Yes (3.30)
Searching JSON::XS (0) on cpanmetadb ...
Unpacking JSON-XS-3.04.tar.gz
OK
==> Found dependencies: JSON::XS, Heap::Simple::XS, Devel::Size
--> Working on JSON::XS
Fetching http://www.cpan.org/authors/id/M/ML/MLEHMANN/JSON-XS-3.04.tar.gz ... OK
JSON-XS-3.04/
JSON-XS-3.04/typemap
JSON-XS-3.04/t/
JSON-XS-3.04/t/14_latin1.t
JSON-XS-3.04/t/02_error.t
JSON-XS-3.04/t/15_prefix.t
JSON-XS-3.04/t/11_pc_expo.t
JSON-XS-3.04/t/99_binary.t
JSON-XS-3.04/t/22_comment_at_eof.t
JSON-XS-3.04/t/03_types.t
JSON-XS-3.04/t/05_dwiw_decode.t
JSON-XS-3.04/t/21_evans.t
JSON-XS-3.04/t/06_pc_pretty.t
JSON-XS-3.04/t/01_utf8.t
JSON-XS-3.04/t/10_pc_keysort.t
JSON-XS-3.04/t/16_tied.t
JSON-XS-3.04/t/09_pc_extra_number.t
JSON-XS-3.04/t/07_pc_esc.t
JSON-XS-3.04/t/52_object.t
JSON-XS-3.04/t/18_json_checker.t
JSON-XS-3.04/t/20_faihu.t
JSON-XS-3.04/t/13_limit.t
JSON-XS-3.04/t/12_blessed.t
JSON-XS-3.04/t/19_incr.t
JSON-XS-3.04/t/04_dwiw_encode.t
JSON-XS-3.04/t/08_pc_base.t
JSON-XS-3.04/t/17_relaxed.t
JSON-XS-3.04/t/00_load.t
JSON-XS-3.04/README
JSON-XS-3.04/Changes
JSON-XS-3.04/COPYING
JSON-XS-3.04/XS.pm
JSON-XS-3.04/XS/
JSON-XS-3.04/XS/Boolean.pm
JSON-XS-3.04/MANIFEST
JSON-XS-3.04/eg/
JSON-XS-3.04/eg/bench
JSON-XS-3.04/bin/
JSON-XS-3.04/bin/json_xs
JSON-XS-3.04/XS.xs
JSON-XS-3.04/Makefile.PL
JSON-XS-3.04/META.yml
JSON-XS-3.04/META.json
Entering JSON-XS-3.04
Checking configure dependencies from META.json
Checking if you have ExtUtils::MakeMaker 6.58 ... Yes (7.10)
Checking if you have Canary::Stability 0 ... Yes (2012)
Running Makefile.PL
Configuring JSON-XS-3.04 ...


*** Canary::Stability COMPATIBILITY AND SUPPORT CHECK
*** =================================================


*** Hi!


*** I do my best to provide predictable and reliable software.


*** However, in recent releases, P5P (who maintain perl) have been
*** introducing regressions that are sometimes subtle and at other times
*** catastrophic, often for personal preferences with little or no concern
*** for existing code, most notably CPAN.


*** For this reason, it has become very hard for me to maintain the level
*** of reliability and support I have committed myself to in the past, at
*** least with some perl versions: I simply can't keep up working around new
*** bugs or gratituous incompatibilities, and in turn you might suffer from
*** unanticipated problems.


*** Therefore I have introduced a support and compatibility check, the results
*** of which follow below, together with a FAQ and some recommendations.


*** This check is just to let you know that there might be a risk, so you can
*** make judgement calls on how to proceed - it will not keep the module from
*** installing or working.


*** The stability canary says: chirp! chirp! (it seems to be quite happy)


*** Your version of perl (5.010001) is quite supported by JSON::XS, nothing
*** else to be said, hope it comes in handy.
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for JSON::XS
Writing MYMETA.yml and MYMETA.json
Checking dependencies from MYMETA.json ...
Checking if you have ExtUtils::MakeMaker 0 ... Yes (7.10)
Checking if you have Types::Serialiser 0 ... Yes (1.0)
Checking if you have common::sense 0 ... Yes (3.74)
OK
Building JSON-XS-3.04 ... cp XS/Boolean.pm blib/lib/JSON/XS/Boolean.pm
cp XS.pm blib/lib/JSON/XS.pm
Running Mkbootstrap for JSON::XS ()
chmod 644 "XS.bs"
"/usr/bin/perl" "/usr/share/perl5/ExtUtils/xsubpp" -typemap "/usr/share/perl5/ExtUtils/typemap" -typemap "typemap" XS.xs > XS.xsc && mv XS.xsc XS.c
gcc -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DVERSION="3.04" -DXS_VERSION="3.04" -fPIC "-I/usr/lib64/perl5/CORE" XS.c
XS.xs: In function ‘ptr_to_index’:
XS.xs:233:10: warning: pointer targets in passing argument 2 of ‘Perl_utf8_distance’ differ in signedness [-Wpointer-sign]
? utf8_distance (offset, SvPVX (sv))
^
In file included from /usr/lib64/perl5/CORE/perl.h:4829:0,
from XS.xs:2:
/usr/lib64/perl5/CORE/proto.h:3558:18: note: expected ‘const U8 *’ but argument is of type ‘char *’
PERL_CALLCONV IV Perl_utf8_distance(pTHX_ const U8 *a, const U8 *b)
^
XS.xs:233:10: warning: pointer targets in passing argument 3 of ‘Perl_utf8_distance’ differ in signedness [-Wpointer-sign]
? utf8_distance (offset, SvPVX (sv))
^
In file included from /usr/lib64/perl5/CORE/perl.h:4829:0,
from XS.xs:2:
/usr/lib64/perl5/CORE/proto.h:3558:18: note: expected ‘const U8 *’ but argument is of type ‘char *’
PERL_CALLCONV IV Perl_utf8_distance(pTHX_ const U8 *a, const U8 *b)
^
XS.xs: In function ‘ref_bool_type’:
XS.xs:344:10: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if (len == 1)
^
XS.xs: In function ‘encode_str’:
XS.xs:455:23: warning: pointer targets in passing argument 1 of ‘decode_utf8’ differ in signedness [-Wpointer-sign]
uch = decode_utf8 (str, end - str, &clen);
^
XS.xs:191:1: note: expected ‘unsigned char *’ but argument is of type ‘char *’
decode_utf8 (unsigned char *s, STRLEN len, STRLEN *clen)
^
XS.xs:508:23: warning: pointer targets in passing argument 1 of ‘encode_utf8’ differ in signedness [-Wpointer-sign]
enc->cur = encode_utf8 (enc->cur, uch);
^
XS.xs:208:1: note: expected ‘unsigned char *’ but argument is of type ‘char *’
encode_utf8 (unsigned char *s, UV ch)
^
XS.xs:508:32: warning: pointer targets in assignment differ in signedness [-Wpointer-sign]
enc->cur = encode_utf8 (enc->cur, uch);
^
XS.xs: In function ‘decode_str’:
XS.xs:1121:26: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if (hi >= 0xd800)
^
XS.xs:1147:27: warning: pointer targets in passing argument 1 of ‘encode_utf8’ differ in signedness [-Wpointer-sign]
cur = encode_utf8 (cur, hi);
^
XS.xs:208:1: note: expected ‘unsigned char *’ but argument is of type ‘char *’
encode_utf8 (unsigned char *s, UV ch)
^
XS.xs:1147:31: warning: pointer targets in assignment differ in signedness [-Wpointer-sign]
cur = encode_utf8 (cur, hi);
^
XS.xs:1167:15: warning: pointer targets in passing argument 1 of ‘decode_utf8’ differ in signedness [-Wpointer-sign]
decode_utf8 (dec_cur, dec->end - dec_cur, &clen);
^
XS.xs:191:1: note: expected ‘unsigned char *’ but argument is of type ‘char *’
decode_utf8 (unsigned char *s, STRLEN len, STRLEN *clen)
^
XS.xs: In function ‘decode_num’:
XS.xs:1320:12: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if (numtype & IS_NUMBER_IN_UV)
^
XS.xs: In function ‘decode_json’:
XS.xs:1807:7: warning: pointer targets in passing argument 3 of ‘Perl_pv_uni_display’ differ in signedness [-Wpointer-sign]
pv_uni_display (uni, dec.cur, dec.end - dec.cur, 20, UNI_DISPLAY_QQ);
^
In file included from /usr/lib64/perl5/CORE/perl.h:4829:0,
from XS.xs:2:
/usr/lib64/perl5/CORE/proto.h:3651:21: note: expected ‘const U8 *’ but argument is of type ‘char
PERL_CALLCONV char
Perl_pv_uni_display(pTHX_ SV *dsv, const U8 *spv, STRLEN len, STRLEN pvlim, UV flags)
^
XS.xs: In function ‘incr_parse’:
XS.xs:1908:26: warning: multi-line comment [-Wcomment]
++p; // "virtually" consumes character after
^
XS.xs:1972:7: warning: label ‘modechange’ defined but not used [-Wunused-label]
modechange:
^
In file included from XS.xs:3:0:
XS.c: In function ‘XS_JSON__XS_CLONE’:
/usr/lib64/perl5/CORE/XSUB.h:136:20: warning: unused variable ‘items’ [-Wunused-variable]
#define dITEMS I32 items = (I32)(SP - MARK)
^
/usr/lib64/perl5/CORE/XSUB.h:144:16: note: in expansion of macro ‘dITEMS’
dSP; dAXMARK; dITEMS
^
XS.c:2052:11: note: in expansion of macro ‘dXSARGS’
dVAR; dXSARGS;
^
XS.xs: In function ‘XS_JSON__XS_incr_parse’:
XS.xs:2155:12: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if (!DECODE_WANTS_OCTETS (self) == !SvUTF8 (self->incr_text))
^
XS.xs:2177:16: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if (SvUTF8 (jsonstr) != SvUTF8 (self->incr_text))
^
In file included from /usr/lib64/perl5/CORE/perl.h:38:0,
from XS.xs:2:
XS.xs: In function ‘encode_sv’:
/usr/lib64/perl5/CORE/config.h:2961:31: warning: ignoring return value of ‘gcvt’, declared with attribute warn_unused_result [-Wunused-result]
#define Gconvert(x,n,t,b) gcvt((x),(n),(b))
^
XS.xs:899:7: note: in expansion of macro ‘Gconvert’
Gconvert (SvNVX (sv), NV_DIG, 0, enc->cur);
^
rm -f blib/arch/auto/JSON/XS/XS.so
gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic XS.o -o blib/arch/auto/JSON/XS/XS.so
\

chmod 755 blib/arch/auto/JSON/XS/XS.so
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- XS.bs blib/arch/auto/JSON/XS/XS.bs 644
cp bin/json_xs blib/script/json_xs
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/json_xs
Manifying 1 pod document
Manifying 2 pod documents
Running Mkbootstrap for JSON::XS ()
chmod 644 "XS.bs"
Manifying 1 pod document
Manifying 2 pod documents
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/auto/JSON/XS/XS.so
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/JSON/XS.pm
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/JSON/XS/Boolean.pm
Installing /public/home/zpxu/jbrowse/extlib/man/man1/json_xs.1
Installing /public/home/zpxu/jbrowse/extlib/man/man3/JSON::XS.3pm
Installing /public/home/zpxu/jbrowse/extlib/man/man3/JSON::XS::Boolean.3pm
Installing /public/home/zpxu/jbrowse/extlib/bin/json_xs
Appending installation info to /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/perllocal.pod
OK
Successfully installed JSON-XS-3.04
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/.meta/JSON-XS-3.04/install.json
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/.meta/JSON-XS-3.04/MYMETA.json
Searching Heap::Simple::XS (0) on cpanmetadb ...
Unpacking Heap-Simple-XS-0.10.tar.gz
--> Working on Heap::Simple::XS
Fetching http://www.cpan.org/authors/id/T/TH/THOSPEL/Heap-Simple-XS-0.10.tar.gz ... OK
Heap-Simple-XS-0.10/
Heap-Simple-XS-0.10/Makefile.PL
Heap-Simple-XS-0.10/ppport.h
Heap-Simple-XS-0.10/Changes
Heap-Simple-XS-0.10/README
Heap-Simple-XS-0.10/t/
Heap-Simple-XS-0.10/t/speed_priority
Heap-Simple-XS-0.10/t/speed_binary
Heap-Simple-XS-0.10/t/speed_array
Heap-Simple-XS-0.10/t/speed_hash
Heap-Simple-XS-0.10/t/speed_binomial
Heap-Simple-XS-0.10/t/Ties.pm
Heap-Simple-XS-0.10/t/speed_scalar
Heap-Simple-XS-0.10/t/04_overload.t
Heap-Simple-XS-0.10/t/02_stress.t
Heap-Simple-XS-0.10/t/99_speed.t
Heap-Simple-XS-0.10/t/FakeHeap.pm
Heap-Simple-XS-0.10/t/03_magic.t
Heap-Simple-XS-0.10/t/00_load.t
Heap-Simple-XS-0.10/t/01_basic.t
Heap-Simple-XS-0.10/t/speed_fibonacci
Heap-Simple-XS-0.10/XS.xs
Heap-Simple-XS-0.10/typemap
Heap-Simple-XS-0.10/MANIFEST.SKIP
Heap-Simple-XS-0.10/MANIFEST
Heap-Simple-XS-0.10/META.yml
Heap-Simple-XS-0.10/lib/
Heap-Simple-XS-0.10/lib/Heap/
Heap-Simple-XS-0.10/lib/Heap/Simple/
Heap-Simple-XS-0.10/lib/Heap/Simple/XS/
Heap-Simple-XS-0.10/lib/Heap/Simple/XS/Package.pm
Heap-Simple-XS-0.10/lib/Heap/Simple/XS.pm
Heap-Simple-XS-0.10/md5-versions
Entering Heap-Simple-XS-0.10
Checking configure dependencies from META.yml
Running Makefile.PL
Configuring Heap-Simple-XS-0.10 ...
Note that you can avoid these questions by passing
the '-n' or '-y' option to 'Makefile.PL'.

Run Heap::Simple benchmarks during 'make test' ? [n] n
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Heap::Simple::XS
Writing MYMETA.yml and MYMETA.json
Checking dependencies from MYMETA.json ...
Checking if you have Test::More 0.11 ... Yes (1.001014)
Checking if you have ExtUtils::MakeMaker 0 ... Yes (7.10)
Checking if you have Heap::Simple 0.09 ... Yes (0.13)
OK
Building Heap-Simple-XS-0.10 ... cp lib/Heap/Simple/XS/Package.pm blib/lib/Heap/Simple/XS/Package.pm
cp lib/Heap/Simple/XS.pm blib/lib/Heap/Simple/XS.pm
Running Mkbootstrap for Heap::Simple::XS ()
chmod 644 "XS.bs"
"/usr/bin/perl" "/usr/share/perl5/ExtUtils/xsubpp" -typemap "/usr/share/perl5/ExtUtils/typemap" -typemap "typemap" XS.xs > XS.xsc && mv XS.xsc XS.c
gcc -c -I. -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION="0.10" -DXS_VERSION="0.10" -fPIC "-I/usr/lib64/perl5/CORE" XS.c
In file included from /usr/include/string.h:637:0,
from /usr/lib64/perl5/CORE/perl.h:1001,
from XS.xs:3:
XS.xs: In function ‘my_isa_lookup’:
/usr/lib64/perl5/CORE/hv.h:278:28: warning: null argument where non-null required (argument 1) [-Wnonnull]
#define HvAUX(hv) ((struct xpvhv_aux*)&(HvARRAY(hv)[HvMAX(hv)+1]))
^
XS.xs:116:9: note: in expansion of macro ‘strEQ’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:298:7: note: in expansion of macro ‘HEK_KEY’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:298:15: note: in expansion of macro ‘HvAUX’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:285:20: note: in expansion of macro ‘HvNAME_get’
#define HvNAME(hv) HvNAME_get(hv)
^
XS.xs:116:15: note: in expansion of macro ‘HvNAME’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:278:28: warning: null argument where non-null required (argument 1) [-Wnonnull]
#define HvAUX(hv) ((struct xpvhv_aux*)&(HvARRAY(hv)[HvMAX(hv)+1]))
^
XS.xs:116:9: note: in expansion of macro ‘strEQ’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:298:7: note: in expansion of macro ‘HEK_KEY’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:298:15: note: in expansion of macro ‘HvAUX’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:285:20: note: in expansion of macro ‘HvNAME_get’
#define HvNAME(hv) HvNAME_get(hv)
^
XS.xs:116:15: note: in expansion of macro ‘HvNAME’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:278:28: warning: null argument where non-null required (argument 1) [-Wnonnull]
#define HvAUX(hv) ((struct xpvhv_aux*)&(HvARRAY(hv)[HvMAX(hv)+1]))
^
XS.xs:116:9: note: in expansion of macro ‘strEQ’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:298:7: note: in expansion of macro ‘HEK_KEY’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:298:15: note: in expansion of macro ‘HvAUX’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:285:20: note: in expansion of macro ‘HvNAME_get’
#define HvNAME(hv) HvNAME_get(hv)
^
XS.xs:116:15: note: in expansion of macro ‘HvNAME’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:278:28: warning: null argument where non-null required (argument 1) [-Wnonnull]
#define HvAUX(hv) ((struct xpvhv_aux*)&(HvARRAY(hv)[HvMAX(hv)+1]))
^
XS.xs:116:9: note: in expansion of macro ‘strEQ’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:298:7: note: in expansion of macro ‘HEK_KEY’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:298:15: note: in expansion of macro ‘HvAUX’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:285:20: note: in expansion of macro ‘HvNAME_get’
#define HvNAME(hv) HvNAME_get(hv)
^
XS.xs:116:15: note: in expansion of macro ‘HvNAME’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:278:28: warning: null argument where non-null required (argument 1) [-Wnonnull]
#define HvAUX(hv) ((struct xpvhv_aux*)&(HvARRAY(hv)[HvMAX(hv)+1]))
^
XS.xs:116:9: note: in expansion of macro ‘strEQ’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:298:7: note: in expansion of macro ‘HEK_KEY’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:298:15: note: in expansion of macro ‘HvAUX’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:285:20: note: in expansion of macro ‘HvNAME_get’
#define HvNAME(hv) HvNAME_get(hv)
^
XS.xs:116:15: note: in expansion of macro ‘HvNAME’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:278:28: warning: null argument where non-null required (argument 1) [-Wnonnull]
#define HvAUX(hv) ((struct xpvhv_aux*)&(HvARRAY(hv)[HvMAX(hv)+1]))
^
XS.xs:116:9: note: in expansion of macro ‘strEQ’
strEQ(HvNAME(stash), name) ||
^
/usr/lib64/perl5/CORE/hv.h:298:7: note: in expansion of macro ‘HEK_KEY’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:298:15: note: in expansion of macro ‘HvAUX’
? HEK_KEY(HvAUX(hv)->xhv_name) : NULL)
^
/usr/lib64/perl5/CORE/hv.h:285:20: note: in expansion of macro ‘HvNAME_get’
#define HvNAME(hv) HvNAME_get(hv)
^
XS.xs:116:15: note: in expansion of macro ‘HvNAME’
strEQ(HvNAME(stash), name) ||
^
XS.xs: In function ‘elements_name’:
XS.xs:270:7: warning: case value ‘0’ not in enumerated type ‘enum elements’ [-Wswitch]
case 0: croak("Element type is unspecified");
^
XS.xs: In function ‘order_name’:
XS.xs:284:7: warning: case value ‘0’ not in enumerated type ‘enum order’ [-Wswitch]
case 0: croak("Order type is unspecified");
^
In file included from /usr/lib64/perl5/CORE/perl.h:3413:0,
from XS.xs:3:
XS.xs: In function ‘key_insert’:
/usr/lib64/perl5/CORE/sv.h:214:26: warning: ‘t1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define SvREFCNT(sv) (sv)->sv_refcnt
^
XS.xs:438:15: note: ‘t1’ was declared here
SV *new, *t1, *t2;
^
XS.xs:500:30: warning: ‘new’ may be used uninitialized in this function [-Wmaybe-uninitialized]
h->values[l] = new;
^
In file included from /usr/lib64/perl5/CORE/perl.h:976:0,
from XS.xs:3:
XS.c: In function ‘XS_Heap__Simple__XS__absorb’:
/usr/lib64/perl5/CORE/embed.h:3251:37: warning: ‘value’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define sv_setnv(a,b) Perl_sv_setnv(aTHX_ a,b)
^
XS.xs:1648:21: note: ‘value’ was declared here
SV *heap1_ref, *value;
^
In file included from /usr/lib64/perl5/CORE/perl.h:976:0,
from XS.xs:3:
XS.c: In function ‘XS_Heap__Simple__XS__key_absorb’:
/usr/lib64/perl5/CORE/embed.h:3251:37: warning: ‘key’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define sv_setnv(a,b) Perl_sv_setnv(aTHX_ a,b)
^
XS.xs:1859:21: note: ‘key’ was declared here
SV *heap1_ref, *key, *value;
^
In file included from /usr/lib64/perl5/CORE/perl.h:976:0,
from XS.xs:3:
/usr/lib64/perl5/CORE/embed.h:3251:37: warning: ‘value’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define sv_setnv(a,b) Perl_sv_setnv(aTHX_ a,b)
^
XS.xs:1859:27: note: ‘value’ was declared here
SV *heap1_ref, *key, *value;
^
XS.c: In function ‘XS_Heap__Simple__XS_merge_arrays’:
XS.xs:2309:17: warning: ‘av’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ptr = av_fetch(av, k0, 0);
^
XS.xs:2275:9: note: ‘av’ was declared here
AV *av, *work_av;
^
rm -f blib/arch/auto/Heap/Simple/XS/XS.so
gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic XS.o -o blib/arch/auto/Heap/Simple/XS/XS.so
\

chmod 755 blib/arch/auto/Heap/Simple/XS/XS.so
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- XS.bs blib/arch/auto/Heap/Simple/XS/XS.bs 644
Manifying 1 pod document
Running Mkbootstrap for Heap::Simple::XS ()
chmod 644 "XS.bs"
Manifying 1 pod document
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/auto/Heap/Simple/XS/XS.so
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/Heap/Simple/XS.pm
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/Heap/Simple/XS/Package.pm
Installing /public/home/zpxu/jbrowse/extlib/man/man3/Heap::Simple::XS.3pm
Appending installation info to /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/perllocal.pod
OK
Successfully installed Heap-Simple-XS-0.10
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/.meta/Heap-Simple-XS-0.10/install.json
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/.meta/Heap-Simple-XS-0.10/MYMETA.json
Searching Devel::Size (0) on cpanmetadb ...
Unpacking Devel-Size-0.82.tar.gz
--> Working on Devel::Size
Fetching http://www.cpan.org/authors/id/N/NW/NWCLARK/Devel-Size-0.82.tar.gz ... OK
Devel-Size-0.82/
Devel-Size-0.82/META.yml
Devel-Size-0.82/META.json
Devel-Size-0.82/Size.xs
Devel-Size-0.82/ppport.h
Devel-Size-0.82/MANIFEST
Devel-Size-0.82/MANIFEST.SKIP
Devel-Size-0.82/lib/
Devel-Size-0.82/lib/Devel/
Devel-Size-0.82/lib/Devel/Size.pm
Devel-Size-0.82/Makefile.PL
Devel-Size-0.82/t/
Devel-Size-0.82/t/pvbm.t
Devel-Size-0.82/t/pod.t
Devel-Size-0.82/t/warnings.t
Devel-Size-0.82/t/code.t
Devel-Size-0.82/t/globs.t
Devel-Size-0.82/t/magic.t
Devel-Size-0.82/t/basic.t
Devel-Size-0.82/t/recurse.t
Devel-Size-0.82/t/pod_cov.t
Devel-Size-0.82/CHANGES
Devel-Size-0.82/typemap
Devel-Size-0.82/README
Entering Devel-Size-0.82
Checking configure dependencies from META.json
Checking if you have ExtUtils::MakeMaker 6.58 ... Yes (7.10)
Running Makefile.PL
Configuring Devel-Size-0.82 ... Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Devel::Size
Writing MYMETA.yml and MYMETA.json
Checking dependencies from MYMETA.json ...
Checking if you have Test::More 0 ... Yes (1.001014)
Checking if you have XSLoader 0 ... Yes (0.22)
Checking if you have ExtUtils::MakeMaker 0 ... Yes (7.10)
OK
Building Devel-Size-0.82 ... cp lib/Devel/Size.pm blib/lib/Devel/Size.pm
Running Mkbootstrap for Devel::Size ()
chmod 644 "Size.bs"
"/usr/bin/perl" "/usr/share/perl5/ExtUtils/xsubpp" -typemap "/usr/share/perl5/ExtUtils/typemap" -typemap "typemap" Size.xs > Size.xsc && mv Size.xsc Size.c
gcc -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DVERSION="0.82" -DXS_VERSION="0.82" -fPIC "-I/usr/lib64/perl5/CORE" -DALIGN_BITS=3 Size.c
Size.xs: In function ‘check_new’:
Size.xs:115:20: warning: unused variable ‘c’ [-Wunused-variable]
const char c = (const char )p;
^
In file included from Size.xs:6:0:
Size.c: In function ‘XS_Devel__Size_size’:
/usr/lib64/perl5/CORE/perl.h:362:39: warning: unused variable ‘Perl___notused’ [-Wunused-variable]
#define dNOOP extern int /
@unused@
/ Perl___notused PERL_UNUSED_DECL
^
/usr/lib64/perl5/CORE/perl.h:180:17: note: in expansion of macro ‘dNOOP’

define dVAR dNOOP

             ^

Size.c:1153:5: note: in expansion of macro ‘dVAR’
dVAR; dXSARGS;
^
Size.c: In function ‘boot_Devel__Size’:
/usr/lib64/perl5/CORE/perl.h:362:39: warning: unused variable ‘Perl___notused’ [-Wunused-variable]
#define dNOOP extern int /@unused@/ Perl___notused PERL_UNUSED_DECL
^
/usr/lib64/perl5/CORE/perl.h:180:17: note: in expansion of macro ‘dNOOP’

define dVAR dNOOP

             ^

Size.c:1192:5: note: in expansion of macro ‘dVAR’
dVAR; dXSARGS;
^
rm -f blib/arch/auto/Devel/Size/Size.so
gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic Size.o -o blib/arch/auto/Devel/Size/Size.so
\

chmod 755 blib/arch/auto/Devel/Size/Size.so
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- Size.bs blib/arch/auto/Devel/Size/Size.bs 644
Manifying 1 pod document
Running Mkbootstrap for Devel::Size ()
chmod 644 "Size.bs"
Manifying 1 pod document
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/auto/Devel/Size/Size.so
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/Devel/Size.pm
Installing /public/home/zpxu/jbrowse/extlib/man/man3/Devel::Size.3pm
Appending installation info to /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/perllocal.pod
OK
Successfully installed Devel-Size-0.82
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/.meta/Devel-Size-0.82/install.json
Installing /public/home/zpxu/jbrowse/extlib/lib/perl5/x86_64-linux-thread-multi/.meta/Devel-Size-0.82/MYMETA.json
<== Installed dependencies for .. Finishing.
3 distributions installed

  • bin/cpanm -v --notest -l extlib/ --installdeps .
    cpanm (App::cpanminus) 1.7043 on perl 5.010001 built for x86_64-linux-thread-multi
    Work directory is /public/home/zpxu/.cpanm/work/1533608572.11696
    You have make /usr/bin/make
    You have LWP 5.833
    You have /bin/tar: tar (GNU tar) 1.23
    Copyright (C) 2010 Free Software Foundation, Inc.
    License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html.
    This is free software: you are free to change and redistribute it.
    There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
You have /usr/bin/unzip
Entering /public/home/zpxu/jbrowse
Running Makefile.PL
--> Working on .
Configuring /public/home/zpxu/jbrowse ... Can't parse version 'dev'
Can't parse version 'dev'
Generating a Unix-style Makefile
Writing Makefile for JBrowse
Writing MYMETA.yml and MYMETA.json
Checking dependencies from MYMETA.json ...
Checking if you have Capture::Tiny 0 ... Yes (0.30)
Checking if you have Pod::Usage 0 ... Yes (1.36)
Checking if you have Storable 0 ... Yes (2.20)
Checking if you have JSON::XS 0 ... Yes (3.04)
Checking if you have List::Util 0 ... Yes (1.46)
Checking if you have PerlIO::gzip 0 ... Yes (0.19)
Checking if you have Digest::Crc32 0 ... Yes (0.01)
Checking if you have File::Path 2 ... Yes (2.08)
Checking if you have local::lib 0 ... Yes (2.000024)
Checking if you have List::MoreUtils 0.28 ... Yes (0.416)
Checking if you have Bio::FeatureIO 0 ... Yes (1.6.905)
Checking if you have DBI 0 ... Yes (1.641)
Checking if you have Getopt::Long 0 ... Yes (2.38)
Checking if you have warnings 0 ... Yes (1.06)
Checking if you have base 0 ... Yes (2.14)
Checking if you have IO::File 0 ... Yes (1.14)
Checking if you have Data::Dumper 0 ... Yes (2.154)
Checking if you have Bio::GFF3::LowLevel 1.8 ... Yes (2.0)
Checking if you have Bio::Index::Fasta 0 ... Yes (undef)
Checking if you have DB_File 0 ... Yes (1.820)
Checking if you have Bio::Root::Version 1.006000 ... Yes (1.007001)
Checking if you have Bio::Annotation::SimpleValue 0 ... Yes (undef)
Checking if you have vars 0 ... Yes (1.01)
Checking if you have Parse::RecDescent 0 ... Yes (1.967015)
Checking if you have Test::More 0 ... Yes (1.001014)
Checking if you have strict 0 ... Yes (1.04)
Checking if you have File::Temp 0 ... Yes (0.22)
Checking if you have File::Copy::Recursive 0 ... Yes (0.44)
Checking if you have Scalar::Util 0 ... Yes (1.46)
Checking if you have FindBin 0 ... Yes (1.50)
Checking if you have DBD::SQLite 0 ... Yes (1.27)
Checking if you have URI::Escape 0 ... Yes (3.31)
Checking if you have File::Spec 0 ... Yes (3.30)
Checking if you have Heap::Simple 0 ... Yes (0.13)
Checking if you have Heap::Simple::XS 0 ... Yes (0.10)
Checking if you have Fcntl 0 ... Yes (1.06)
Checking if you have POSIX 0 ... Yes (1.17)
Checking if you have Devel::Size 0 ... Yes (0.82)
Checking if you have File::Spec::Functions 0 ... Yes (3.30)
Checking if you have Bio::SeqFeature::Lite 0 ... Yes (undef)
Checking if you have Bio::GFF3::LowLevel::Parser 1.8 ... Yes (2.0)
Checking if you have IO::Uncompress::Gunzip 0 ... Yes (2.021)
Checking if you have Hash::Merge 0 ... Yes (0.300)
Checking if you have constant 0 ... Yes (1.17)
Checking if you have Exporter 0 ... Yes (5.63)
Checking if you have Bio::OntologyIO 0 ... Yes (undef)
Checking if you have Bio::SeqFeature::Annotated 0 ... Yes (1.6.905)
Checking if you have Carp 0 ... Yes (1.38)
Checking if you have Test::Warn 0 ... Yes (0.30)
Checking if you have File::Next 0 ... Yes (1.16)
Checking if you have File::Basename 0 ... Yes (2.77)
Checking if you have JSON 2 ... Yes (2.97001)
Checking if you have Cwd 0 ... Yes (3.30)
OK
<== Installed dependencies for .. Finishing.

  • set -e
  • bin/cpanm -v --notest -l extlib/ --installdeps .
    cpanm (App::cpanminus) 1.7043 on perl 5.010001 built for x86_64-linux-thread-multi
    Work directory is /public/home/zpxu/.cpanm/work/1533608573.11731
    You have make /usr/bin/make
    You have LWP 5.833
    You have /bin/tar: tar (GNU tar) 1.23
    Copyright (C) 2010 Free Software Foundation, Inc.
    License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html.
    This is free software: you are free to change and redistribute it.
    There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
You have /usr/bin/unzip
Entering /public/home/zpxu/jbrowse
Running Makefile.PL
--> Working on .
Configuring /public/home/zpxu/jbrowse ... Can't parse version 'dev'
Can't parse version 'dev'
Generating a Unix-style Makefile
Writing Makefile for JBrowse
Writing MYMETA.yml and MYMETA.json
Checking dependencies from MYMETA.json ...
Checking if you have Capture::Tiny 0 ... Yes (0.30)
Checking if you have Pod::Usage 0 ... Yes (1.36)
Checking if you have Storable 0 ... Yes (2.20)
Checking if you have JSON::XS 0 ... Yes (3.04)
Checking if you have List::Util 0 ... Yes (1.46)
Checking if you have PerlIO::gzip 0 ... Yes (0.19)
Checking if you have Digest::Crc32 0 ... Yes (0.01)
Checking if you have File::Path 2 ... Yes (2.08)
Checking if you have local::lib 0 ... Yes (2.000024)
Checking if you have List::MoreUtils 0.28 ... Yes (0.416)
Checking if you have Bio::FeatureIO 0 ... Yes (1.6.905)
Checking if you have DBI 0 ... Yes (1.641)
Checking if you have Getopt::Long 0 ... Yes (2.38)
Checking if you have warnings 0 ... Yes (1.06)
Checking if you have base 0 ... Yes (2.14)
Checking if you have IO::File 0 ... Yes (1.14)
Checking if you have Data::Dumper 0 ... Yes (2.154)
Checking if you have Bio::GFF3::LowLevel 1.8 ... Yes (2.0)
Checking if you have Bio::Index::Fasta 0 ... Yes (undef)
Checking if you have DB_File 0 ... Yes (1.820)
Checking if you have Bio::Root::Version 1.006000 ... Yes (1.007001)
Checking if you have Bio::Annotation::SimpleValue 0 ... Yes (undef)
Checking if you have vars 0 ... Yes (1.01)
Checking if you have Parse::RecDescent 0 ... Yes (1.967015)
Checking if you have Test::More 0 ... Yes (1.001014)
Checking if you have strict 0 ... Yes (1.04)
Checking if you have File::Temp 0 ... Yes (0.22)
Checking if you have File::Copy::Recursive 0 ... Yes (0.44)
Checking if you have Scalar::Util 0 ... Yes (1.46)
Checking if you have FindBin 0 ... Yes (1.50)
Checking if you have DBD::SQLite 0 ... Yes (1.27)
Checking if you have URI::Escape 0 ... Yes (3.31)
Checking if you have File::Spec 0 ... Yes (3.30)
Checking if you have Heap::Simple 0 ... Yes (0.13)
Checking if you have Heap::Simple::XS 0 ... Yes (0.10)
Checking if you have Fcntl 0 ... Yes (1.06)
Checking if you have POSIX 0 ... Yes (1.17)
Checking if you have Devel::Size 0 ... Yes (0.82)
Checking if you have File::Spec::Functions 0 ... Yes (3.30)
Checking if you have Bio::SeqFeature::Lite 0 ... Yes (undef)
Checking if you have Bio::GFF3::LowLevel::Parser 1.8 ... Yes (2.0)
Checking if you have IO::Uncompress::Gunzip 0 ... Yes (2.021)
Checking if you have Hash::Merge 0 ... Yes (0.300)
Checking if you have constant 0 ... Yes (1.17)
Checking if you have Exporter 0 ... Yes (5.63)
Checking if you have Bio::OntologyIO 0 ... Yes (undef)
Checking if you have Bio::SeqFeature::Annotated 0 ... Yes (1.6.905)
Checking if you have Carp 0 ... Yes (1.38)
Checking if you have Test::Warn 0 ... Yes (0.30)
Checking if you have File::Next 0 ... Yes (1.16)
Checking if you have File::Basename 0 ... Yes (2.77)
Checking if you have JSON 2 ... Yes (2.97001)
Checking if you have Cwd 0 ... Yes (3.30)
OK
<== Installed dependencies for .. Finishing.

done.

Formatting Volvox example data ...

  • rm -rf sample_data/json/volvox
  • bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa --out sample_data/json/volvox
  • '[' 0 -eq 1 ']'
  • bin/biodb-to-json.pl -v --conf docs/tutorial/conf_files/volvox.json --out sample_data/json/volvox

working on refseq ctgA
working on track ExampleFeatures
mergedTrackCfg: $VAR1 = {
'feature' => [
'remark'
],
'autocomplete' => 'all',
'track' => 'ExampleFeatures',
'style' => {
'className' => 'feature2'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - Example Features'
};
searching for features of type: remark
working on track NameTest
mergedTrackCfg: $VAR1 = {
'feature' => [
'protein_coding_primary_transcript',
'polypeptide'
],
'autocomplete' => 'all',
'track' => 'NameTest',
'style' => {
'className' => 'feature2'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - Name test track has a really long track label'
};
searching for features of type: protein_coding_primary_transcript, polypeptide
working on track snps
mergedTrackCfg: $VAR1 = {
'feature' => [
'SNP'
],
'autocomplete' => 'all',
'track' => 'snps',
'style' => {
'className' => 'triangle hgred'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - SNPs'
};
searching for features of type: SNP
working on track Motifs
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Motifs',
'style' => {
'className' => 'feature3',
'label' => 'function(feature) { return feature.get('Name')+' (via JS callback)' }',
'description' => 'function(feature) { return feature.get('Name')+': '+feature.get('Note'); }'
},
'description' => 1,
'key' => 'HTMLFeatures - Example motifs',
'feature' => [
'polypeptide_domain'
],
'compress' => 0,
'category' => 'Miscellaneous'
};
searching for features of type: polypeptide_domain
working on track malformed_alignments
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'malformed_alignments',
'style' => {
'className' => 'feature4'
},
'menuTemplate' => [
{
'children' => [
{
'children' => [
{
'iconClass' => 'dijitIconBookmark',
'url' => 'http://wiki.trin.org.au/{name}-{start}-{end}',
'action' => 'newWindow',
'label' => 'Query trin for {name}'
},
{
'iconClass' => 'dijitIconSearch',
'url' => 'http://example.com/{name}-{start}-{end}',
'label' => 'Query example.com for {name}'
}
],
'label' => 'Check gene on databases'
},
{
'label' => '2nd child of demo'
},
{
'label' => '3rd child: this is a track'
}
],
'label' => 'Item with submenu'
},
{
'iconClass' => 'dijitIconDatabase',
'url' => 'http://www.example.com?featurename={name}',
'action' => 'iframeDialog',
'title' => 'The magnificent example.com (feature {name})',
'label' => 'Open example.com in an iframe popup'
},
{
'iconClass' => 'dijitIconDatabase',
'url' => 'sample_data/test_snippet.html?featurename={name}:{start}-{end}',
'action' => 'xhrDialog',
'title' => 'function(track,feature,div) { return 'Random XHR HTML '+Math.random()+' title!'; }',
'label' => 'Open popup with XHR HTML snippet (btw this is feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => 'function(track,feature,div) { return '

'+feature.get('name')+'

This is some test content!

This message brought to you by the number '+Math.round(Math.random()*100)+'.

';} ',
'action' => 'contentDialog',
'title' => 'function(track,feature,div) { return 'Random content snippet '+Math.random()+' title!'; }',
'label' => 'Popup with content snippet from a function (feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => '

{name}

This is some test content about {name}, which goes from {start} to {end} on the {strand} strand.

',
'action' => 'contentDialog',
'title' => '{randomNumberTitle}',
'label' => 'Popup with content snippet from string (feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'action' => '{exampleFeatureClick}',
'label' => '{randomNumberLabel}'
}
],
'hooks' => {
'modify' => 'function( track, feature, div ) { div.style.backgroundColor = ['green','blue','red','orange','purple'][Math.round(Math.random()5)];}'
},
'key' => 'HTMLFeatures - Features with right-click menus',
'feature' => [
'match'
],
'shortDescription' => 'Features with customized right-click menus',
'compress' => 0,
'metadata' => {
'category' => 'Miscellaneous',
'Description' => 'Features with extensively customized right-click menus, and with their colors set at random by a JavaScript callback.'
}
};
searching for features of type: match
working on track Genes
mergedTrackCfg: $VAR1 = {
'fmtDetailValue_Name' => 'function(name,feature) { if(feature.get('type')=='gene') { return name + ' <a href=http://www.ncbi.nlm.nih.gov/gquery/?term=\'+name+\'>[NCBI custom link]'; } else { return name; } }',
'fmtMetaDescription_Name' => 'function(name) { return '[Custom description]'; }',
'fmtMetaValue_Name' => 'function(name) { return name+' [Track with custom callbacks for About track popup]'; }',
'key' => 'CanvasFeatures - Protein-coding genes',
'onClick' => {
'action' => 'defaultDialog',
'title' => '{type} {name}',
'label' => '<div style='font:normal 12px Univers,Helvetica,Arial,sans-serif'><div style='font-weight:bold'>Custom tooltip<div style='color:blue;'>Feature name: {name}
Feature start: {start}
Feature end: {end}'
},
'feature' => [
'gene'
],
'fmtDetailField_Name' => 'function(name,feature) { if(feature.get('type')=='gene') { return 'Gene Name'; } else { return name; } }',
'fmtMetaField_Name' => 'function(name) { return 'Track Name'; }',
'fmtDetailField_Load_id' => 'function(name,feature) { /
remove field from dialog box */ return null; }',
'category' => 'Transcripts',
'metadata' => {
'ncbi_submission_model' => 'Generic',
'insdc_first_public' => '2018-05-15T00:00:00Z',
'Link: ENA study page' => 'http://www.ebi.ac.uk/ena/',
'library_total_amount_of_reads' => '3349981',
'insdc_secondary_accession' => 'SRS12345678',
'insdc_center_name' => 'INSDC Sample',
'ncbi_submission_package' => 'Generic.1.0',
'sample_name' => 'GSM12345678',
'ENA first public' => '2018-05-16',
'study' => 'SRP12345678 a study of volvox',
'organism' => 'Volvox',
'library_size_approx' => '1-5mln',
'Link: RNASeq-er analysis results' => 'ftp://ftp.ebi.ac.uk/pub/databases/arrayexpress/',
'insdc_last_update' => '2018-05-15T01:18:23.110Z',
'insdc_status' => 'live',
'developmental_stage' => 'stage 6- 330 min',
'mapping_quality_approx' => 'under 50%',
'tissue' => 'embryo',
'source_name' => 'Volvox 6- 330 min',
'mapping_fraction_of_uniquely_mapped_reads' => '0.429',
'ENA last update' => '2018-05-16',
'description_title' => 'Volvox_mRNA_rep_2_6'
},
'autocomplete' => 'all',
'track' => 'Genes',
'style' => {
'className' => 'feature5'
},
'menuTemplate' => [
{
'label' => 'View details'
},
{
'label' => 'Zoom this gene'
},
{
'label' => 'Highlight this gene'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => '

{name}

This is some test content about {type} {name}, which goes from {start} to {end} on the {strand} strand.',
'action' => 'contentDialog',
'title' => '{randomNumberTitle}',
'label' => 'Popup with content snippet from string (feature {name})'
}
],
'trackType' => 'NeatCanvasFeatures/View/Track/NeatFeatures',
'compress' => 0
};
searching for features of type: gene
working on track ReadingFrame
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'ReadingFrame',
'style' => {
'className' => 'cds'
},
'key' => 'HTMLFeatures - mRNAs',
'onClick' => {
'url' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}',
'title' => 'NCBI search box',
'label' => 'Search for {name} at NCBI
Feature start {start}
Feature end {end}'
},
'feature' => [
'mRNA'
],
'trackType' => 'NeatHTMLFeatures/View/Track/NeatFeatures',
'phase' => 1,
'compress' => 0,
'category' => 'Transcripts'
};
searching for features of type: mRNA
working on track CDS
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'CDS',
'style' => {
'className' => 'cds',
'linkTemplate' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}-{start}-{end}'
},
'key' => 'CanvasFeatures - mixed mRNAs and CDSs',
'feature' => [
'CDS:bare_predicted',
'mRNA:exonerate',
'mRNA:predicted'
],
'trackType' => 'CanvasFeatures',
'compress' => 0,
'category' => 'Transcripts'
};
searching for features of type: CDS:bare_predicted, mRNA:exonerate, mRNA:predicted
working on track Transcript
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Transcript',
'style' => {
'className' => 'feature',
'color' => '#E32A3A',
'description' => 'customdescription'
},
'description' => 1,
'key' => 'CanvasFeatures - transcripts',
'onClick' => '{exampleFeatureClick}',
'feature' => [
'mRNA:exonerate'
],
'trackType' => 'JBrowse/View/Track/CanvasFeatures',
'compress' => 0,
'category' => 'Transcripts',
'showNoteInAttributes' => bless( do{(my $o = 1)}, 'JSON::PP::Boolean' ),
'subfeatures' => $VAR1->{'showNoteInAttributes'}
};
searching for features of type: mRNA:exonerate
working on track Clones
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Clones',
'style' => {
'className' => 'exon'
},
'description' => 1,
'key' => 'HTMLFeatures - Fingerprinted BACs',
'feature' => [
'BAC'
],
'compress' => 0,
'category' => 'Miscellaneous'
};
searching for features of type: BAC
working on track EST
mergedTrackCfg: $VAR1 = {
'feature' => [
'EST_match:est'
],
'autocomplete' => 'all',
'track' => 'EST',
'style' => {
'className' => 'est'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - ESTs'
};
searching for features of type: EST_match:est

working on refseq ctgB
working on track ExampleFeatures
mergedTrackCfg: $VAR1 = {
'feature' => [
'remark'
],
'autocomplete' => 'all',
'track' => 'ExampleFeatures',
'style' => {
'className' => 'feature2'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - Example Features'
};
searching for features of type: remark
working on track NameTest
mergedTrackCfg: $VAR1 = {
'feature' => [
'protein_coding_primary_transcript',
'polypeptide'
],
'autocomplete' => 'all',
'track' => 'NameTest',
'style' => {
'className' => 'feature2'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - Name test track has a really long track label'
};
searching for features of type: protein_coding_primary_transcript, polypeptide
working on track snps
mergedTrackCfg: $VAR1 = {
'feature' => [
'SNP'
],
'autocomplete' => 'all',
'track' => 'snps',
'style' => {
'className' => 'triangle hgred'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - SNPs'
};
searching for features of type: SNP
working on track Motifs
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Motifs',
'style' => {
'className' => 'feature3',
'label' => 'function(feature) { return feature.get('Name')+' (via JS callback)' }',
'description' => 'function(feature) { return feature.get('Name')+': '+feature.get('Note'); }'
},
'description' => 1,
'key' => 'HTMLFeatures - Example motifs',
'feature' => [
'polypeptide_domain'
],
'compress' => 0,
'category' => 'Miscellaneous'
};
searching for features of type: polypeptide_domain
working on track malformed_alignments
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'malformed_alignments',
'style' => {
'className' => 'feature4'
},
'menuTemplate' => [
{
'children' => [
{
'children' => [
{
'iconClass' => 'dijitIconBookmark',
'url' => 'http://wiki.trin.org.au/{name}-{start}-{end}',
'action' => 'newWindow',
'label' => 'Query trin for {name}'
},
{
'iconClass' => 'dijitIconSearch',
'url' => 'http://example.com/{name}-{start}-{end}',
'label' => 'Query example.com for {name}'
}
],
'label' => 'Check gene on databases'
},
{
'label' => '2nd child of demo'
},
{
'label' => '3rd child: this is a track'
}
],
'label' => 'Item with submenu'
},
{
'iconClass' => 'dijitIconDatabase',
'url' => 'http://www.example.com?featurename={name}',
'action' => 'iframeDialog',
'title' => 'The magnificent example.com (feature {name})',
'label' => 'Open example.com in an iframe popup'
},
{
'iconClass' => 'dijitIconDatabase',
'url' => 'sample_data/test_snippet.html?featurename={name}:{start}-{end}',
'action' => 'xhrDialog',
'title' => 'function(track,feature,div) { return 'Random XHR HTML '+Math.random()+' title!'; }',
'label' => 'Open popup with XHR HTML snippet (btw this is feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => 'function(track,feature,div) { return '

'+feature.get('name')+'

This is some test content!

This message brought to you by the number '+Math.round(Math.random()*100)+'.

';} ',
'action' => 'contentDialog',
'title' => 'function(track,feature,div) { return 'Random content snippet '+Math.random()+' title!'; }',
'label' => 'Popup with content snippet from a function (feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => '

{name}

This is some test content about {name}, which goes from {start} to {end} on the {strand} strand.

',
'action' => 'contentDialog',
'title' => '{randomNumberTitle}',
'label' => 'Popup with content snippet from string (feature {name})'
},
{
'iconClass' => 'dijitIconDatabase',
'action' => '{exampleFeatureClick}',
'label' => '{randomNumberLabel}'
}
],
'hooks' => {
'modify' => 'function( track, feature, div ) { div.style.backgroundColor = ['green','blue','red','orange','purple'][Math.round(Math.random()5)];}'
},
'key' => 'HTMLFeatures - Features with right-click menus',
'feature' => [
'match'
],
'shortDescription' => 'Features with customized right-click menus',
'compress' => 0,
'metadata' => {
'category' => 'Miscellaneous',
'Description' => 'Features with extensively customized right-click menus, and with their colors set at random by a JavaScript callback.'
}
};
searching for features of type: match
working on track Genes
mergedTrackCfg: $VAR1 = {
'fmtDetailValue_Name' => 'function(name,feature) { if(feature.get('type')=='gene') { return name + ' <a href=http://www.ncbi.nlm.nih.gov/gquery/?term=\'+name+\'>[NCBI custom link]'; } else { return name; } }',
'fmtMetaDescription_Name' => 'function(name) { return '[Custom description]'; }',
'fmtMetaValue_Name' => 'function(name) { return name+' [Track with custom callbacks for About track popup]'; }',
'key' => 'CanvasFeatures - Protein-coding genes',
'onClick' => {
'action' => 'defaultDialog',
'title' => '{type} {name}',
'label' => '<div style='font:normal 12px Univers,Helvetica,Arial,sans-serif'><div style='font-weight:bold'>Custom tooltip<div style='color:blue;'>Feature name: {name}
Feature start: {start}
Feature end: {end}'
},
'feature' => [
'gene'
],
'fmtDetailField_Name' => 'function(name,feature) { if(feature.get('type')=='gene') { return 'Gene Name'; } else { return name; } }',
'fmtMetaField_Name' => 'function(name) { return 'Track Name'; }',
'fmtDetailField_Load_id' => 'function(name,feature) { /
remove field from dialog box */ return null; }',
'category' => 'Transcripts',
'metadata' => {
'ncbi_submission_model' => 'Generic',
'insdc_first_public' => '2018-05-15T00:00:00Z',
'Link: ENA study page' => 'http://www.ebi.ac.uk/ena/',
'library_total_amount_of_reads' => '3349981',
'insdc_secondary_accession' => 'SRS12345678',
'insdc_center_name' => 'INSDC Sample',
'ncbi_submission_package' => 'Generic.1.0',
'sample_name' => 'GSM12345678',
'ENA first public' => '2018-05-16',
'study' => 'SRP12345678 a study of volvox',
'organism' => 'Volvox',
'library_size_approx' => '1-5mln',
'Link: RNASeq-er analysis results' => 'ftp://ftp.ebi.ac.uk/pub/databases/arrayexpress/',
'insdc_last_update' => '2018-05-15T01:18:23.110Z',
'insdc_status' => 'live',
'developmental_stage' => 'stage 6- 330 min',
'mapping_quality_approx' => 'under 50%',
'tissue' => 'embryo',
'source_name' => 'Volvox 6- 330 min',
'mapping_fraction_of_uniquely_mapped_reads' => '0.429',
'ENA last update' => '2018-05-16',
'description_title' => 'Volvox_mRNA_rep_2_6'
},
'autocomplete' => 'all',
'track' => 'Genes',
'style' => {
'className' => 'feature5'
},
'menuTemplate' => [
{
'label' => 'View details'
},
{
'label' => 'Zoom this gene'
},
{
'label' => 'Highlight this gene'
},
{
'iconClass' => 'dijitIconDatabase',
'content' => '

{name}

This is some test content about {type} {name}, which goes from {start} to {end} on the {strand} strand.',
'action' => 'contentDialog',
'title' => '{randomNumberTitle}',
'label' => 'Popup with content snippet from string (feature {name})'
}
],
'trackType' => 'NeatCanvasFeatures/View/Track/NeatFeatures',
'compress' => 0
};
searching for features of type: gene
working on track ReadingFrame
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'ReadingFrame',
'style' => {
'className' => 'cds'
},
'key' => 'HTMLFeatures - mRNAs',
'onClick' => {
'url' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}',
'title' => 'NCBI search box',
'label' => 'Search for {name} at NCBI
Feature start {start}
Feature end {end}'
},
'feature' => [
'mRNA'
],
'trackType' => 'NeatHTMLFeatures/View/Track/NeatFeatures',
'phase' => 1,
'compress' => 0,
'category' => 'Transcripts'
};
searching for features of type: mRNA
working on track CDS
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'CDS',
'style' => {
'className' => 'cds',
'linkTemplate' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}-{start}-{end}'
},
'key' => 'CanvasFeatures - mixed mRNAs and CDSs',
'feature' => [
'CDS:bare_predicted',
'mRNA:exonerate',
'mRNA:predicted'
],
'trackType' => 'CanvasFeatures',
'compress' => 0,
'category' => 'Transcripts'
};
searching for features of type: CDS:bare_predicted, mRNA:exonerate, mRNA:predicted
working on track Transcript
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Transcript',
'style' => {
'className' => 'feature',
'color' => '#E32A3A',
'description' => 'customdescription'
},
'description' => 1,
'key' => 'CanvasFeatures - transcripts',
'onClick' => '{exampleFeatureClick}',
'feature' => [
'mRNA:exonerate'
],
'trackType' => 'JBrowse/View/Track/CanvasFeatures',
'compress' => 0,
'category' => 'Transcripts',
'showNoteInAttributes' => bless( do{(my $o = 1)}, 'JSON::PP::Boolean' ),
'subfeatures' => $VAR1->{'showNoteInAttributes'}
};
searching for features of type: mRNA:exonerate
working on track Clones
mergedTrackCfg: $VAR1 = {
'autocomplete' => 'all',
'track' => 'Clones',
'style' => {
'className' => 'exon'
},
'description' => 1,
'key' => 'HTMLFeatures - Fingerprinted BACs',
'feature' => [
'BAC'
],
'compress' => 0,
'category' => 'Miscellaneous'
};
searching for features of type: BAC
working on track EST
mergedTrackCfg: $VAR1 = {
'feature' => [
'EST_match:est'
],
'autocomplete' => 'all',
'track' => 'EST',
'style' => {
'className' => 'est'
},
'compress' => 0,
'category' => 'Miscellaneous',
'key' => 'HTMLFeatures - ESTs'
};
searching for features of type: EST_match:est

  • cat docs/tutorial/data_files/volvox_microarray.bw.conf docs/tutorial/data_files/volvox_sine.bw.conf docs/tutorial/data_files/volvox-sorted.bam.conf docs/tutorial/data_files/volvox-sorted.bam.coverage.conf docs/tutorial/data_files/volvox-paired.bam.conf docs/tutorial/data_files/volvox.vcf.conf docs/tutorial/data_files/volvox_fromconfig.conf docs/tutorial/data_files/volvox.gff3.conf docs/tutorial/data_files/volvox.gtf.conf docs/tutorial/data_files/volvox.sort.gff3.gz.conf docs/tutorial/data_files/volvox.sort.gff3.gz.htmlfeatures.conf docs/tutorial/data_files/volvox.sort.bed.gz.conf docs/tutorial/data_files/gvcf.vcf.gz.conf docs/tutorial/data_files/bookmarks.conf docs/tutorial/data_files/volvox.subsubparts.gff3.conf docs/tutorial/data_files/volvox-long-reads.fastq.sorted.bam.conf docs/tutorial/data_files/volvox-long-reads.fastq.sorted.cram.conf docs/tutorial/data_files/volvox.bb.conf docs/tutorial/data_files/volvox-sorted.cram.conf
  • bin/add-json.pl '{ "dataset_id": "volvox", "include": [ "../../raw/volvox/functions.conf" ] }' sample_data/json/volvox/trackList.json
  • bin/add-json.pl '{ "dataset_id": "volvox", "plugins": [ "HideTrackLabels", "NeatCanvasFeatures", "NeatHTMLFeatures" ] }' sample_data/json/volvox/trackList.json
  • bin/flatfile-to-json.pl --bed docs/tutorial/data_files/volvox_segment.bed --out sample_data/json/volvox --trackLabel ChromHMM --trackType CanvasFeatures --clientConfig '{"color": "{chromHMM}", "strandArrow": false}' --config '{"displayMode": "collapsed", "enableCollapsedMouseover": true, "category": "Miscellaneous" }'
  • bin/generate-names.pl --safeMode -v --out sample_data/json/volvox
    Tracks:
    CDS
    ChromHMM
    Clones
    DNA
    EST
    ExampleFeatures
    Genes
    Motifs
    NameTest
    ReadingFrame
    Transcript
    fromconfig
    malformed_alignments
    snps
    volvox-long_reads
    volvox-long_reads-cram
    volvox-paired_bam
    volvox-sorted-vcf
    volvox-sorted_bam
    volvox-sorted_bam_coverage
    volvox-sorted_cram
    volvox_bb
    volvox_bed_tabix
    volvox_gff3
    volvox_gff3_subsubparts
    volvox_gff3_tabix
    volvox_gff3_tabix_html
    volvox_gtf
    volvox_gvcf_test
    volvox_microarray_bw_density
    volvox_microarray_bw_xyplot
    volvox_sine_density
    volvox_sine_xyplot
    volvox_vcf_test
    Sampled input stats:
    avg record text bytes 2201.79498861048
    name input records 847
    operation stream estimated count 736
    record stream estimated count 184
    total namerec bytes 1933176
    total input bytes 407148
    operations made 4325
    namerecs buffered 878
    namerecs converted to operations 878
    Removing existing contents of target dir sample_data/json/volvox/names
    Hash store cache size: 2684 buckets
    Using 1 chars for sort log names (16 sort logs)
  • mkdir -p sample_data/raw
  • '[' '!' -e sample_data/raw/volvox ']'
  • ln -sf ../../docs/tutorial/conf_files/volvox.json sample_data/raw/
  • touch sample_data/json/volvox/successfully_run

done.

Formatting Yeast example data ...

  • rm -rf sample_data/json/yeast/
  • bin/prepare-refseqs.pl --fasta sample_data/raw/yeast_scaffolds/chr1.fa.gz --fasta sample_data/raw/yeast_scaffolds/chr2.fa.gzip --out sample_data/json/yeast/
  • gunzip -c sample_data/raw/yeast_scaffolds/chr1.fa.gz sample_data/raw/yeast_scaffolds/chr2.fa.gzip
  • '[' 0 -eq 1 ']'
  • bin/biodb-to-json.pl --conf sample_data/raw/yeast.json --out sample_data/json/yeast/

working on refseq chrI
working on track Genes
working on track transcript_with_no_features

working on refseq chrII
working on track Genes
working on track transcript_with_no_features

  • bin/add-json.pl '{ "dataset_id": "yeast" }' sample_data/json/yeast/trackList.json
  • bin/add-json.pl '{ "dataset_id": "yeast", "plugins": [ "NeatHTMLFeatures","NeatCanvasFeatures","HideTrackLabels" ] }' sample_data/json/yeast/trackList.json
  • bin/generate-names.pl --dir sample_data/json/yeast/

done.

</details>
@cmdcolin

This comment has been minimized.

Show comment
Hide comment
@cmdcolin

cmdcolin Aug 7, 2018

Contributor

Do you have any output from the javascript console? It does appear to have successfully compiled via setup.sh!

Contributor

cmdcolin commented Aug 7, 2018

Do you have any output from the javascript console? It does appear to have successfully compiled via setup.sh!

@tiramisutes

This comment has been minimized.

Show comment
Hide comment
@tiramisutes

tiramisutes Aug 8, 2018

Just a blank page with Loading... (picture)

tiramisutes commented Aug 8, 2018

Just a blank page with Loading... (picture)

@cmdcolin

This comment has been minimized.

Show comment
Hide comment
@cmdcolin

cmdcolin Aug 8, 2018

Contributor

I am looking for info in this thing called the "console log", here are some instructions to open it

https://developer.mozilla.org/en-US/docs/Tools/Browser_Console

Thanks for your patience :)

Contributor

cmdcolin commented Aug 8, 2018

I am looking for info in this thing called the "console log", here are some instructions to open it

https://developer.mozilla.org/en-US/docs/Tools/Browser_Console

Thanks for your patience :)

@tiramisutes

This comment has been minimized.

Show comment
Hide comment
@tiramisutes

tiramisutes Aug 8, 2018

Yes, I check the Browser Console and find some error.

Failed to load native module at path '/usr/lib64/firefox/components/libxpcomsample.so': (80004005) /usr/lib64/firefox/components/libxpcomsample.so: cannot open shared object file: No such file or directory
Could not read chrome manifest 'file:///usr/lib64/firefox/browser/extensions/%7B972ce4c6-7e08-4474-a285-3208198ce6fd%7D/chrome.manifest'.
The character encoding of the HTML document was not declared. The document will render with garbled text in some browser configurations if the document contains characters from outside the US-ASCII range. The character encoding of the page must be declared in the document or in the transfer protocol. index.html
Content Security Policy: Couldn't process unknown directive 'worker-src' <unknown>
Content Security Policy: Couldn't process unknown directive 'block-all-mixed-content' <unknown>
Key event not available on some keyboard layouts: key="r" modifiers="accel,alt" browser.xul
Key event not available on some keyboard layouts: key="c" modifiers="accel,alt" browser.xul
calling a builtin ArrayBuffer constructor without new is deprecated and will be forbidden in ES6 main.bundle.js:3306:4
calling a builtin typed array constructor without new is deprecated and will be forbidden in ES6 main.bundle.js:1540:6
SyntaxError: missing } after property list 0.bundle.js:40373:25
Error: Loading chunk 0 failed.
Stack trace:
onScriptComplete@http://localhost:3000/dist/main.bundle.js:99:24
 main.bundle.js:142:51

"Unhandled promise rejection" Error: Loading chunk 0 failed.
Stack trace:
onScriptComplete@http://localhost:3000/dist/main.bundle.js:99:24
 main.bundle.js:8873:10

reflow: 3.59ms function fillInPageTooltip, popup.xml line 618

tiramisutes commented Aug 8, 2018

Yes, I check the Browser Console and find some error.

Failed to load native module at path '/usr/lib64/firefox/components/libxpcomsample.so': (80004005) /usr/lib64/firefox/components/libxpcomsample.so: cannot open shared object file: No such file or directory
Could not read chrome manifest 'file:///usr/lib64/firefox/browser/extensions/%7B972ce4c6-7e08-4474-a285-3208198ce6fd%7D/chrome.manifest'.
The character encoding of the HTML document was not declared. The document will render with garbled text in some browser configurations if the document contains characters from outside the US-ASCII range. The character encoding of the page must be declared in the document or in the transfer protocol. index.html
Content Security Policy: Couldn't process unknown directive 'worker-src' <unknown>
Content Security Policy: Couldn't process unknown directive 'block-all-mixed-content' <unknown>
Key event not available on some keyboard layouts: key="r" modifiers="accel,alt" browser.xul
Key event not available on some keyboard layouts: key="c" modifiers="accel,alt" browser.xul
calling a builtin ArrayBuffer constructor without new is deprecated and will be forbidden in ES6 main.bundle.js:3306:4
calling a builtin typed array constructor without new is deprecated and will be forbidden in ES6 main.bundle.js:1540:6
SyntaxError: missing } after property list 0.bundle.js:40373:25
Error: Loading chunk 0 failed.
Stack trace:
onScriptComplete@http://localhost:3000/dist/main.bundle.js:99:24
 main.bundle.js:142:51

"Unhandled promise rejection" Error: Loading chunk 0 failed.
Stack trace:
onScriptComplete@http://localhost:3000/dist/main.bundle.js:99:24
 main.bundle.js:8873:10

reflow: 3.59ms function fillInPageTooltip, popup.xml line 618
@cmdcolin

This comment has been minimized.

Show comment
Hide comment
@cmdcolin

cmdcolin Aug 8, 2018

Contributor

Thanks for checking. It looks like somehow the JavaScript had a syntax error. This seems unlikely because webpack would have caught basic syntax errors so it seems like corruption

To fix you could

(a) check out a stable release tag if you are using git e g. git checkout 1.15.0-release or git checkout master
(b) remove package-lock.json, and maybe the entire node_modules folder, because I see in the setup.log file that it didn't like file existing
(c) re-run setup.sh

Contributor

cmdcolin commented Aug 8, 2018

Thanks for checking. It looks like somehow the JavaScript had a syntax error. This seems unlikely because webpack would have caught basic syntax errors so it seems like corruption

To fix you could

(a) check out a stable release tag if you are using git e g. git checkout 1.15.0-release or git checkout master
(b) remove package-lock.json, and maybe the entire node_modules folder, because I see in the setup.log file that it didn't like file existing
(c) re-run setup.sh

@cmdcolin

This comment has been minimized.

Show comment
Hide comment
@cmdcolin

cmdcolin Aug 8, 2018

Contributor

Another thing to add to that list is clear cache in browser

Contributor

cmdcolin commented Aug 8, 2018

Another thing to add to that list is clear cache in browser

@cmdcolin

This comment has been minimized.

Show comment
Hide comment
@cmdcolin

cmdcolin Aug 14, 2018

Contributor

Are there any updates @tiramisutes ? I may close this for now as it is likely a weird setup bug and probably not a true issue with jbrowse itself. Potentially more error handling could be done for chunk loading failures but it's a little tricky

Contributor

cmdcolin commented Aug 14, 2018

Are there any updates @tiramisutes ? I may close this for now as it is likely a weird setup bug and probably not a true issue with jbrowse itself. Potentially more error handling could be done for chunk loading failures but it's a little tricky

@cmdcolin cmdcolin closed this Aug 14, 2018

@cmdcolin

This comment has been minimized.

Show comment
Hide comment
@cmdcolin

cmdcolin Aug 14, 2018

Contributor

Feel free to post back here if you have any continued issues with the setup, I am just triaging issues :)

Contributor

cmdcolin commented Aug 14, 2018

Feel free to post back here if you have any continued issues with the setup, I am just triaging issues :)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment