dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake

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dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake

Bai, Youhuang
Hi

I can run Apollo, but got error when I wanna to add annotations:

Here is the error info:

Xiaozhuans-MacBook-Pro:Apollo-2.1.0 xiaozhuandai$ tools/data/add_features_from_gff3_to_annotations.pl -h

Attempting to create directory /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib
dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake
  Referenced from: /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
  Expected in: flat namespace

dyld: Symbol not found: _Perl_xs_handshake
  Referenced from: /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
  Expected in: flat namespace

Abort trap: 6

Best
Youhuang Bai





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Re: dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake

nathandunn

Unfortunately Perl + Mac has become more problematic.  

I’m assuming you’re using home-brew perl? 

I’ll look at some better solutions this week and reply here.  

Some workarounds:

1 - use docker or another linux-based system to install apollo with the proper dependencies and run the web services through that.   Seems to be less problematic than the Mac.

2 - try installing in the same way that you install JBrowse ( brew install --build-from-source perl).  

3 - lots of info online about re-installing perl packages if you are using homebrew on the Mac.  

Again, I’ll follow-up when I have a better solution for you this week, but possibly someone else has already run into this. 

Nathan


On Jul 27, 2018, at 3:03 PM, Bai, Youhuang <[hidden email]> wrote:

Hi

I can run Apollo, but got error when I wanna to add annotations:

Here is the error info:

Xiaozhuans-MacBook-Pro:Apollo-2.1.0 xiaozhuandai$ tools/data/add_features_from_gff3_to_annotations.pl -h

Attempting to create directory /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib
dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake
  Referenced from: /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
  Expected in: flat namespace

dyld: Symbol not found: _Perl_xs_handshake
  Referenced from: /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
  Expected in: flat namespace

Abort trap: 6

Best
Youhuang Bai




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 





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Re: [Gmod-ajax] dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake

nathandunn

That’s right.  It installs using npm (against 1.12.5-apollo) and then runs the setup.sh script.  

I’m wondering if either the local cpanm commands are out of sync, or not run, or just missing dependencies.  

I seem to have no issues when running this on a linux de novo system.

I’m going to keep poking around.   I sense a rebuild of home-brew might be part of the issue based on googling around, but I’m unsure.   

Nathan


On Jul 29, 2018, at 7:39 PM, Robert Buels <[hidden email]> wrote:

Sounds like you definitely need to try reinstalling the things in the JBrowse extlib/ directory.  I'm not sure how it's wired in Apollo, but I'd recommend deleting jbrowse-download/extlib and re-running setup.sh or the Apollo equivalent.  Nathan, is setup.sh the right thing to run for a clean install?


On Sun, Jul 29, 2018 at 6:14 PM Nathan Dunn <[hidden email]> wrote:

Unfortunately Perl + Mac has become more problematic.  

I’m assuming you’re using home-brew perl? 

I’ll look at some better solutions this week and reply here.  

Some workarounds:

1 - use docker or another linux-based system to install apollo with the proper dependencies and run the web services through that.   Seems to be less problematic than the Mac.

2 - try installing in the same way that you install JBrowse ( brew install --build-from-source perl).  

3 - lots of info online about re-installing perl packages if you are using homebrew on the Mac.  

Again, I’ll follow-up when I have a better solution for you this week, but possibly someone else has already run into this. 

Nathan


On Jul 27, 2018, at 3:03 PM, Bai, Youhuang <[hidden email]> wrote:

Hi

I can run Apollo, but got error when I wanna to add annotations:

Here is the error info:

Xiaozhuans-MacBook-Pro:Apollo-2.1.0 xiaozhuandai$ tools/data/add_features_from_gff3_to_annotations.pl -h

Attempting to create directory /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib
dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake
  Referenced from: /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
  Expected in: flat namespace

dyld: Symbol not found: _Perl_xs_handshake
  Referenced from: /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
  Expected in: flat namespace

Abort trap: 6

Best
Youhuang Bai




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 

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答复: [Gmod-ajax] dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake

Bai, Youhuang
Thanks guys
Here I used conda to build Apollo, so I think it was not home-brew perl. 

# Name                    Version                   Build  Channel

apache-tomcat            7.0.88                       0    birdhouse

ca-certificates          2018.4.16                    0    conda-forge

curl                     7.61.0              h93b3f91_1    conda-forge

expat                    2.2.5               hfc679d8_1    conda-forge

gettext                  0.19.8.1                     0    conda-forge

git                      2.18.0         pl526hbb17d3c_1    conda-forge

krb5                     1.14.6                       0    conda-forge

libgcc                   4.8.5              hdbeacc1_10  

libgfortran              3.0.1               h93005f0_2  

libiconv                 1.15                h470a237_1    conda-forge

libssh2                  1.8.0               h5b517e9_2    conda-forge

nodejs                   10.4.1                       0    conda-forge

openjdk                  8.0.121                      1  

openssl                  1.0.2o               h470a237_1    conda-forge

perl                     5.26.2              h16c6ff1_0    conda-forge

perl-bioperl             1.6.924                      4    bioconda

perl-threaded            5.22.0                      10    bioconda

perl-yaml                 1.26                    pl526_0    bioconda

tk                       8.6.8                        0    conda-forge

zlib                     1.2.11              h470a237_3    conda-forge

 
But when Apollo install Jbrowse automatically, it takes much long time. So I think it may miss some dependencies.

Best
Youhuang


发件人: [hidden email] [[hidden email]] 代表 Nathan Dunn [[hidden email]]
发送时间: 2018年7月30日 1:02
收件人: Robert Buels
抄送: Apollo List; gmod-ajax
主题: Re: [apollo] [Gmod-ajax] dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake


That’s right.  It installs using npm (against 1.12.5-apollo) and then runs the setup.sh script.  

I’m wondering if either the local cpanm commands are out of sync, or not run, or just missing dependencies.  

I seem to have no issues when running this on a linux de novo system.

I’m going to keep poking around.   I sense a rebuild of home-brew might be part of the issue based on googling around, but I’m unsure.   

Nathan


On Jul 29, 2018, at 7:39 PM, Robert Buels <[hidden email]> wrote:

Sounds like you definitely need to try reinstalling the things in the JBrowse extlib/ directory.  I'm not sure how it's wired in Apollo, but I'd recommend deleting jbrowse-download/extlib and re-running setup.sh or the Apollo equivalent.  Nathan, is setup.sh the right thing to run for a clean install?


On Sun, Jul 29, 2018 at 6:14 PM Nathan Dunn <[hidden email]> wrote:

Unfortunately Perl + Mac has become more problematic.  

I’m assuming you’re using home-brew perl? 

I’ll look at some better solutions this week and reply here.  

Some workarounds:

1 - use docker or another linux-based system to install apollo with the proper dependencies and run the web services through that.   Seems to be less problematic than the Mac.

2 - try installing in the same way that you install JBrowse ( brew install --build-from-source perl).  

3 - lots of info online about re-installing perl packages if you are using homebrew on the Mac.  

Again, I’ll follow-up when I have a better solution for you this week, but possibly someone else has already run into this. 

Nathan


On Jul 27, 2018, at 3:03 PM, Bai, Youhuang <[hidden email]> wrote:

Hi

I can run Apollo, but got error when I wanna to add annotations:

Here is the error info:

Xiaozhuans-MacBook-Pro:Apollo-2.1.0 xiaozhuandai$ tools/data/add_features_from_gff3_to_annotations.pl -h

Attempting to create directory /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib
dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake
  Referenced from: /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
  Expected in: flat namespace

dyld: Symbol not found: _Perl_xs_handshake
  Referenced from: /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
  Expected in: flat namespace

Abort trap: 6

Best
Youhuang Bai




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/gmod-ajax





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: 答复: [Gmod-ajax] dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake

Colin
The bioconda list posts suggest that, at least for jbrowse, there may have been a fix as recently as 3 days ago. I don't have bioconda experience but maybe you must update the formula and then try to install


-Colin

On Mon, Jul 30, 2018 at 8:52 AM Bai, Youhuang <[hidden email]> wrote:
Thanks guys
Here I used conda to build Apollo, so I think it was not home-brew perl. 

# Name                    Version                   Build  Channel

apache-tomcat            7.0.88                       0    birdhouse

ca-certificates          2018.4.16                    0    conda-forge

curl                     7.61.0              h93b3f91_1    conda-forge

expat                    2.2.5               hfc679d8_1    conda-forge

gettext                  0.19.8.1                     0    conda-forge

git                      2.18.0         pl526hbb17d3c_1    conda-forge

krb5                     1.14.6                       0    conda-forge

libgcc                   4.8.5              hdbeacc1_10  

libgfortran              3.0.1               h93005f0_2  

libiconv                 1.15                h470a237_1    conda-forge

libssh2                  1.8.0               h5b517e9_2    conda-forge

nodejs                   10.4.1                       0    conda-forge

openjdk                  8.0.121                      1  

openssl                  1.0.2o               h470a237_1    conda-forge

perl                     5.26.2              h16c6ff1_0    conda-forge

perl-bioperl             1.6.924                      4    bioconda

perl-threaded            5.22.0                      10    bioconda

perl-yaml                 1.26                    pl526_0    bioconda

tk                       8.6.8                        0    conda-forge

zlib                     1.2.11              h470a237_3    conda-forge

 
But when Apollo install Jbrowse automatically, it takes much long time. So I think it may miss some dependencies.

Best
Youhuang


发件人: [hidden email] [[hidden email]] 代表 Nathan Dunn [[hidden email]]
发送时间: 2018年7月30日 1:02
收件人: Robert Buels
抄送: Apollo List; gmod-ajax
主题: Re: [apollo] [Gmod-ajax] dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake


That’s right.  It installs using npm (against 1.12.5-apollo) and then runs the setup.sh script.  

I’m wondering if either the local cpanm commands are out of sync, or not run, or just missing dependencies.  

I seem to have no issues when running this on a linux de novo system.

I’m going to keep poking around.   I sense a rebuild of home-brew might be part of the issue based on googling around, but I’m unsure.   

Nathan


On Jul 29, 2018, at 7:39 PM, Robert Buels <[hidden email]> wrote:

Sounds like you definitely need to try reinstalling the things in the JBrowse extlib/ directory.  I'm not sure how it's wired in Apollo, but I'd recommend deleting jbrowse-download/extlib and re-running setup.sh or the Apollo equivalent.  Nathan, is setup.sh the right thing to run for a clean install?


On Sun, Jul 29, 2018 at 6:14 PM Nathan Dunn <[hidden email]> wrote:

Unfortunately Perl + Mac has become more problematic.  

I’m assuming you’re using home-brew perl? 

I’ll look at some better solutions this week and reply here.  

Some workarounds:

1 - use docker or another linux-based system to install apollo with the proper dependencies and run the web services through that.   Seems to be less problematic than the Mac.

2 - try installing in the same way that you install JBrowse ( brew install --build-from-source perl).  

3 - lots of info online about re-installing perl packages if you are using homebrew on the Mac.  

Again, I’ll follow-up when I have a better solution for you this week, but possibly someone else has already run into this. 

Nathan


On Jul 27, 2018, at 3:03 PM, Bai, Youhuang <[hidden email]> wrote:

Hi

I can run Apollo, but got error when I wanna to add annotations:

Here is the error info:

Xiaozhuans-MacBook-Pro:Apollo-2.1.0 xiaozhuandai$ tools/data/add_features_from_gff3_to_annotations.pl -h

Attempting to create directory /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib
dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake
  Referenced from: /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
  Expected in: flat namespace

dyld: Symbol not found: _Perl_xs_handshake
  Referenced from: /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
  Expected in: flat namespace

Abort trap: 6

Best
Youhuang Bai




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
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This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: 答复: [Gmod-ajax] dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake

Colin
It does seems there are a lot of perl changes in the bioconda repo so any solution may still remain in flux...unless bioconda needed you might try a traditional install approach :)

-Colin

On Mon, Jul 30, 2018 at 7:18 PM Colin <[hidden email]> wrote:
The bioconda list posts suggest that, at least for jbrowse, there may have been a fix as recently as 3 days ago. I don't have bioconda experience but maybe you must update the formula and then try to install


-Colin

On Mon, Jul 30, 2018 at 8:52 AM Bai, Youhuang <[hidden email]> wrote:
Thanks guys
Here I used conda to build Apollo, so I think it was not home-brew perl. 

# Name                    Version                   Build  Channel

apache-tomcat            7.0.88                       0    birdhouse

ca-certificates          2018.4.16                    0    conda-forge

curl                     7.61.0              h93b3f91_1    conda-forge

expat                    2.2.5               hfc679d8_1    conda-forge

gettext                  0.19.8.1                     0    conda-forge

git                      2.18.0         pl526hbb17d3c_1    conda-forge

krb5                     1.14.6                       0    conda-forge

libgcc                   4.8.5              hdbeacc1_10  

libgfortran              3.0.1               h93005f0_2  

libiconv                 1.15                h470a237_1    conda-forge

libssh2                  1.8.0               h5b517e9_2    conda-forge

nodejs                   10.4.1                       0    conda-forge

openjdk                  8.0.121                      1  

openssl                  1.0.2o               h470a237_1    conda-forge

perl                     5.26.2              h16c6ff1_0    conda-forge

perl-bioperl             1.6.924                      4    bioconda

perl-threaded            5.22.0                      10    bioconda

perl-yaml                 1.26                    pl526_0    bioconda

tk                       8.6.8                        0    conda-forge

zlib                     1.2.11              h470a237_3    conda-forge

 
But when Apollo install Jbrowse automatically, it takes much long time. So I think it may miss some dependencies.

Best
Youhuang


发件人: [hidden email] [[hidden email]] 代表 Nathan Dunn [[hidden email]]
发送时间: 2018年7月30日 1:02
收件人: Robert Buels
抄送: Apollo List; gmod-ajax
主题: Re: [apollo] [Gmod-ajax] dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake


That’s right.  It installs using npm (against 1.12.5-apollo) and then runs the setup.sh script.  

I’m wondering if either the local cpanm commands are out of sync, or not run, or just missing dependencies.  

I seem to have no issues when running this on a linux de novo system.

I’m going to keep poking around.   I sense a rebuild of home-brew might be part of the issue based on googling around, but I’m unsure.   

Nathan


On Jul 29, 2018, at 7:39 PM, Robert Buels <[hidden email]> wrote:

Sounds like you definitely need to try reinstalling the things in the JBrowse extlib/ directory.  I'm not sure how it's wired in Apollo, but I'd recommend deleting jbrowse-download/extlib and re-running setup.sh or the Apollo equivalent.  Nathan, is setup.sh the right thing to run for a clean install?


On Sun, Jul 29, 2018 at 6:14 PM Nathan Dunn <[hidden email]> wrote:

Unfortunately Perl + Mac has become more problematic.  

I’m assuming you’re using home-brew perl? 

I’ll look at some better solutions this week and reply here.  

Some workarounds:

1 - use docker or another linux-based system to install apollo with the proper dependencies and run the web services through that.   Seems to be less problematic than the Mac.

2 - try installing in the same way that you install JBrowse ( brew install --build-from-source perl).  

3 - lots of info online about re-installing perl packages if you are using homebrew on the Mac.  

Again, I’ll follow-up when I have a better solution for you this week, but possibly someone else has already run into this. 

Nathan


On Jul 27, 2018, at 3:03 PM, Bai, Youhuang <[hidden email]> wrote:

Hi

I can run Apollo, but got error when I wanna to add annotations:

Here is the error info:

Xiaozhuans-MacBook-Pro:Apollo-2.1.0 xiaozhuandai$ tools/data/add_features_from_gff3_to_annotations.pl -h

Attempting to create directory /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib
dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake
  Referenced from: /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
  Expected in: flat namespace

dyld: Symbol not found: _Perl_xs_handshake
  Referenced from: /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
  Expected in: flat namespace

Abort trap: 6

Best
Youhuang Bai




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
Gmod-ajax mailing list
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Re: [Gmod-ajax] dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake

nathandunn

So, I think the best solution until we move this script away from perl is to use the dockerized version of the tool:

docker run -it quay.io/gmod/docker-apollo:latest /apollo/tools/data/add_features_from_gff3_to_annotations.pl

Eventually this should be a service from within Apollo, or moved to the groovy JVM language or built into the command-line package: https://github.com/galaxy-genome-annotation/python-apollo

I added a ticket here, but not sure when I’ll have time to get to it. 

Nathan


On Jul 30, 2018, at 4:22 PM, Colin <[hidden email]> wrote:

It does seems there are a lot of perl changes in the bioconda repo so any solution may still remain in flux...unless bioconda needed you might try a traditional install approach :)

-Colin

On Mon, Jul 30, 2018 at 7:18 PM Colin <[hidden email]> wrote:
The bioconda list posts suggest that, at least for jbrowse, there may have been a fix as recently as 3 days ago. I don't have bioconda experience but maybe you must update the formula and then try to install


-Colin

On Mon, Jul 30, 2018 at 8:52 AM Bai, Youhuang <[hidden email]> wrote:
Thanks guys
Here I used conda to build Apollo, so I think it was not home-brew perl. 

# Name                    Version                   Build  Channel
apache-tomcat            7.0.88                       0    birdhouse
ca-certificates          2018.4.16                    0    conda-forge
curl                     7.61.0              h93b3f91_1    conda-forge
expat                    2.2.5               hfc679d8_1    conda-forge
gettext                  0.19.8.1                     0    conda-forge
git                      2.18.0         pl526hbb17d3c_1    conda-forge
krb5                     1.14.6                       0    conda-forge
libgcc                   4.8.5              hdbeacc1_10  
libgfortran              3.0.1               h93005f0_2  
libiconv                 1.15                h470a237_1    conda-forge
libssh2                  1.8.0               h5b517e9_2    conda-forge
nodejs                   10.4.1                       0    conda-forge
openjdk                  8.0.121                      1  
openssl                  1.0.2o               h470a237_1    conda-forge
perl                     5.26.2              h16c6ff1_0    conda-forge
perl-bioperl             1.6.924                      4    bioconda
perl-threaded            5.22.0                      10    bioconda
perl-yaml                 1.26                    pl526_0    bioconda
tk                       8.6.8                        0    conda-forge
zlib                     1.2.11              h470a237_3    conda-forge
 
But when Apollo install Jbrowse automatically, it takes much long time. So I think it may miss some dependencies.

Best
Youhuang


发件人: [hidden email] [[hidden email]] 代表 Nathan Dunn [[hidden email]]
发送时间: 2018年7月30日 1:02
收件人: Robert Buels
抄送: Apollo List; gmod-ajax
主题: Re: [apollo] [Gmod-ajax] dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake


That’s right.  It installs using npm (against 1.12.5-apollo) and then runs the setup.sh script.  

I’m wondering if either the local cpanm commands are out of sync, or not run, or just missing dependencies.  

I seem to have no issues when running this on a linux de novo system.

I’m going to keep poking around.   I sense a rebuild of home-brew might be part of the issue based on googling around, but I’m unsure.   

Nathan


On Jul 29, 2018, at 7:39 PM, Robert Buels <[hidden email]> wrote:

Sounds like you definitely need to try reinstalling the things in the JBrowse extlib/ directory.  I'm not sure how it's wired in Apollo, but I'd recommend deleting jbrowse-download/extlib and re-running setup.sh or the Apollo equivalent.  Nathan, is setup.sh the right thing to run for a clean install?


On Sun, Jul 29, 2018 at 6:14 PM Nathan Dunn <[hidden email]> wrote:

Unfortunately Perl + Mac has become more problematic.  

I’m assuming you’re using home-brew perl? 

I’ll look at some better solutions this week and reply here.  

Some workarounds:

1 - use docker or another linux-based system to install apollo with the proper dependencies and run the web services through that.   Seems to be less problematic than the Mac.

2 - try installing in the same way that you install JBrowse ( brew install --build-from-source perl).  

3 - lots of info online about re-installing perl packages if you are using homebrew on the Mac.  

Again, I’ll follow-up when I have a better solution for you this week, but possibly someone else has already run into this. 

Nathan


On Jul 27, 2018, at 3:03 PM, Bai, Youhuang <[hidden email]> wrote:

Hi

I can run Apollo, but got error when I wanna to add annotations:

Here is the error info:

Xiaozhuans-MacBook-Pro:Apollo-2.1.0 xiaozhuandai$ tools/data/add_features_from_gff3_to_annotations.pl -h

Attempting to create directory /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib
dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake
  Referenced from: /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
  Expected in: flat namespace

dyld: Symbol not found: _Perl_xs_handshake
  Referenced from: /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
  Expected in: flat namespace

Abort trap: 6

Best
Youhuang Bai




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