problem of install gbrowse2

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problem of install gbrowse2

sam789123
hello all,

It's my first time to install Gbrowse2 and I got some problems.

Before installed Gbrowse2 , I tried to install kent source tree.

unzip jksrc.zip
cd kent/src/lib 
export MACHTYPE=i686 
make 
cd .. 
export KENT_SRC=`pwd`

After that, I installed Bio::DB::BigFile

cpan Bio::DB::BigFile

Please enter the location of Kent source tree:

I gave it the path but it still couldn't find it.

Can anyone give me some suggestion?

Thanks!

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Re: problem of install gbrowse2

Scott Cain
Hi,

When you gave the path to the Kent source, what path did you use?  It has to end in "src".  Also, I assume you are sure there were no errors when compiling?

Scott



On Wed, Feb 12, 2014 at 11:08 PM, Yi-De Xie <[hidden email]> wrote:
hello all,

It's my first time to install Gbrowse2 and I got some problems.

Before installed Gbrowse2 , I tried to install kent source tree.

unzip jksrc.zip
cd kent/src/lib 
export MACHTYPE=i686 
make 
cd .. 
export KENT_SRC=`pwd`

After that, I installed Bio::DB::BigFile

cpan Bio::DB::BigFile

Please enter the location of Kent source tree:

I gave it the path but it still couldn't find it.

Can anyone give me some suggestion?

Thanks!

------------------------------------------------------------------------------
Android apps run on BlackBerry 10
Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
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Re: problem of install gbrowse2

sam789123
Yes,path of Kent source is '/home/yide102/', so I typed /home/yide102/kent/src as it path.

I compiled kent source tree as following steps

unzip jksrc.zip
cd kent/src/lib 
export MACHTYPE=i686 
make 
cd .. 
export KENT_SRC=`pwd`

there were no errors but some warnings like these

pslGenoShow.c: In function ‘pslShowAlignmentStranded2’:
pslGenoShow.c:31:36: warning: variable ‘tcfmEnd’ set but not used [-Wunused-but-set-variable]
pslGenoShow.c:31:16: warning: variable ‘qcfmEnd’ set but not used [-Wunused-but-set-variable]
pslGenoShow.c:30:36: warning: variable ‘tbafEnd’ set but not used [-Wunused-but-set-variable]
pslGenoShow.c:30:16: warning: variable ‘qbafEnd’ set but not used [-Wunused-but-set-variable]

pslShow.c: In function ‘pslShowAlignmentStranded’:
pslShow.c:25:36: warning: variable ‘tcfmEnd’ set but not used [-Wunused-but-set-variable]
pslShow.c:25:16: warning: variable ‘qcfmEnd’ set but not used [-Wunused-but-set-variable]
pslShow.c:24:36: warning: variable ‘tbafEnd’ set but not used [-Wunused-but-set-variable]
pslShow.c:24:16: warning: variable ‘qbafEnd’ set but not used [-Wunused-but-set-variable]

udc.c: In function ‘udcBitmapOpen’:
udc.c:549:8: warning: variable ‘reserved64’ set but not used [-Wunused-but-set-variable]
udc.c:548:8: warning: variable ‘reserved32’ set but not used [-Wunused-but-set-variable]

Did I lost something?

Thanks!


2014-02-14 3:24 GMT+08:00 Yi-De Xie <[hidden email]>:
Yes,path of Kent source is '/home/yide102/', so I typed /home/yide102/kent/src as it path.

I compiled kent source tree as following steps

unzip jksrc.zip
cd kent/src/lib 
export MACHTYPE=i686 
make 
cd .. 
export KENT_SRC=`pwd`

there were no errors but some warnings like these

pslGenoShow.c: In function ‘pslShowAlignmentStranded2’:
pslGenoShow.c:31:36: warning: variable ‘tcfmEnd’ set but not used [-Wunused-but-set-variable]
pslGenoShow.c:31:16: warning: variable ‘qcfmEnd’ set but not used [-Wunused-but-set-variable]
pslGenoShow.c:30:36: warning: variable ‘tbafEnd’ set but not used [-Wunused-but-set-variable]
pslGenoShow.c:30:16: warning: variable ‘qbafEnd’ set but not used [-Wunused-but-set-variable]

pslShow.c: In function ‘pslShowAlignmentStranded’:
pslShow.c:25:36: warning: variable ‘tcfmEnd’ set but not used [-Wunused-but-set-variable]
pslShow.c:25:16: warning: variable ‘qcfmEnd’ set but not used [-Wunused-but-set-variable]
pslShow.c:24:36: warning: variable ‘tbafEnd’ set but not used [-Wunused-but-set-variable]
pslShow.c:24:16: warning: variable ‘qbafEnd’ set but not used [-Wunused-but-set-variable]

udc.c: In function ‘udcBitmapOpen’:
udc.c:549:8: warning: variable ‘reserved64’ set but not used [-Wunused-but-set-variable]
udc.c:548:8: warning: variable ‘reserved32’ set but not used [-Wunused-but-set-variable]

Did I lost something?

Thanks!


2014-02-13 23:58 GMT+08:00 Scott Cain <[hidden email]>:

Hi,

When you gave the path to the Kent source, what path did you use?  It has to end in "src".  Also, I assume you are sure there were no errors when compiling?

Scott



On Wed, Feb 12, 2014 at 11:08 PM, Yi-De Xie <[hidden email]> wrote:
hello all,

It's my first time to install Gbrowse2 and I got some problems.

Before installed Gbrowse2 , I tried to install kent source tree.

unzip jksrc.zip
cd kent/src/lib 
export MACHTYPE=i686 
make 
cd .. 
export KENT_SRC=`pwd`

After that, I installed Bio::DB::BigFile

cpan Bio::DB::BigFile

Please enter the location of Kent source tree:

I gave it the path but it still couldn't find it.

Can anyone give me some suggestion?

Thanks!

------------------------------------------------------------------------------
Android apps run on BlackBerry 10
Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
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Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
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Re: problem of install gbrowse2

sam789123
hi,

I solved the problem because I compiled Kent source tree as 'me' .
But installed Bio::DB::BigFile as 'root' .
After that ,I still got problem of installing Bio::DB::BigFile like this

lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__BigFile_bigWigFileCreate’:
lib/Bio/DB/BigFile.xs:94:3: warning: passing argument 7 of ‘bigWigFileCreate’ makes integer from pointer without a cast [enabled by default]
/home/yide102/kent/src/inc/bigWig.h:30:6: note: expected ‘int’ but argument is of type ‘char *’
lib/Bio/DB/BigFile.xs:94:3: error: too few arguments to function ‘bigWigFileCreate’
/home/yide102/kent/src/inc/bigWig.h:30:6: note: declared here
error building lib/Bio/DB/BigFile.o from 'lib/Bio/DB/BigFile.c' at /usr/share/perl/5.14/ExtUtils/CBuilder/Base.pm line 177.
  LDS/Bio-BigFile-1.07.tar.gz
  ./Build -- NOT OK
Running Build test
  Can't test without successful make
Running Build install
  Make had returned bad status, install seems impossible

So I read  bigWigFileCreate function in kent/src/inc/bigWig.h , it had 9 arguments.
And bigWigFileCreate function in lib/Bio/DB/BigFile.xs only had 7arguments.

Can anyone give me some suggestion?

------------------------------------------------------------------------------
Android apps run on BlackBerry 10
Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
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Re: problem of install gbrowse2

Scott Cain
Chris,

Where you telling me about changes in the Kent source code that would cause problems with Bio::DB::BigFile?  Do you think it's related to this problem?

Thanks,
Scott



On Sun, Feb 16, 2014 at 9:10 PM, Yi-De Xie <[hidden email]> wrote:
hi,

I solved the problem because I compiled Kent source tree as 'me' .
But installed Bio::DB::BigFile as 'root' .
After that ,I still got problem of installing Bio::DB::BigFile like this

lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__BigFile_bigWigFileCreate’:
lib/Bio/DB/BigFile.xs:94:3: warning: passing argument 7 of ‘bigWigFileCreate’ makes integer from pointer without a cast [enabled by default]
/home/yide102/kent/src/inc/bigWig.h:30:6: note: expected ‘int’ but argument is of type ‘char *’
lib/Bio/DB/BigFile.xs:94:3: error: too few arguments to function ‘bigWigFileCreate’
/home/yide102/kent/src/inc/bigWig.h:30:6: note: declared here
error building lib/Bio/DB/BigFile.o from 'lib/Bio/DB/BigFile.c' at /usr/share/perl/5.14/ExtUtils/CBuilder/Base.pm line 177.
  LDS/Bio-BigFile-1.07.tar.gz
  ./Build -- NOT OK
Running Build test
  Can't test without successful make
Running Build install
  Make had returned bad status, install seems impossible

So I read  bigWigFileCreate function in kent/src/inc/bigWig.h , it had 9 arguments.
And bigWigFileCreate function in lib/Bio/DB/BigFile.xs only had 7arguments.

Can anyone give me some suggestion?

------------------------------------------------------------------------------
Android apps run on BlackBerry 10
Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Managing the Performance of Cloud-Based Applications
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Re: problem of install gbrowse2

Fields, Christopher J
Yes, that’s it; this only pops up when using the kent utils from github but I expected it to land to their stable code at some point.  There is a simple branch on github that deals with it:


It’s a pretty small code change, we could probably create a simple patch and post it.

chris

On Feb 17, 2014, at 12:39 PM, Scott Cain <[hidden email]> wrote:

Chris,

Where you telling me about changes in the Kent source code that would cause problems with Bio::DB::BigFile?  Do you think it's related to this problem?

Thanks,
Scott



On Sun, Feb 16, 2014 at 9:10 PM, Yi-De Xie <[hidden email]> wrote:
hi,

I solved the problem because I compiled Kent source tree as 'me' .
But installed Bio::DB::BigFile as 'root' .
After that ,I still got problem of installing Bio::DB::BigFile like this

lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__BigFile_bigWigFileCreate’:
lib/Bio/DB/BigFile.xs:94:3: warning: passing argument 7 of ‘bigWigFileCreate’ makes integer from pointer without a cast [enabled by default]
/home/yide102/kent/src/inc/bigWig.h:30:6: note: expected ‘int’ but argument is of type ‘char *’
lib/Bio/DB/BigFile.xs:94:3: error: too few arguments to function ‘bigWigFileCreate’
/home/yide102/kent/src/inc/bigWig.h:30:6: note: declared here
error building lib/Bio/DB/BigFile.o from 'lib/Bio/DB/BigFile.c' at /usr/share/perl/5.14/ExtUtils/CBuilder/Base.pm line 177.
  LDS/Bio-BigFile-1.07.tar.gz
  ./Build -- NOT OK
Running Build test
  Can't test without successful make
Running Build install
  Make had returned bad status, install seems impossible

So I read  bigWigFileCreate function in kent/src/inc/bigWig.h , it had 9 arguments.
And bigWigFileCreate function in lib/Bio/DB/BigFile.xs only had 7arguments.

Can anyone give me some suggestion?

------------------------------------------------------------------------------
Android apps run on BlackBerry 10
Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
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------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


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Re: problem of install gbrowse2

Timothy Parnell
Hi guys,

I can confirm that downloading the current jksrc.zip from the UCSC website, per the instructions, does not work with the current Bio-DB-BigFile release. It does work with Chris’ modified version on github.

UCSC does not post previous .zip releases on their main website (you will have to dig through their github repo for that), so this will become a more common occurrence going forward. But note that this patch will also break with previously compiled UCSC library installations that people may have kept around for upgrade purposes.

Tim

On Feb 17, 2014, at 12:55 PM, Fields, Christopher J <[hidden email]<mailto:[hidden email]>> wrote:

Yes, that’s it; this only pops up when using the kent utils from github but I expected it to land to their stable code at some point.  There is a simple branch on github that deals with it:

https://github.com/cjfields/GBrowse-Adaptors/commit/bce13df624f703ac7501aaa83f87fe644f187c1a

It’s a pretty small code change, we could probably create a simple patch and post it.

chris

On Feb 17, 2014, at 12:39 PM, Scott Cain <[hidden email]<mailto:[hidden email]>> wrote:

Chris,

Where you telling me about changes in the Kent source code that would cause problems with Bio::DB::BigFile?  Do you think it's related to this problem?

Thanks,
Scott



On Sun, Feb 16, 2014 at 9:10 PM, Yi-De Xie <[hidden email]<mailto:[hidden email]>> wrote:
hi,

I solved the problem because I compiled Kent source tree as 'me' .
But installed Bio::DB::BigFile as 'root' .
After that ,I still got problem of installing Bio::DB::BigFile like this

lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__BigFile_bigWigFileCreate’:
lib/Bio/DB/BigFile.xs:94:3: warning: passing argument 7 of ‘bigWigFileCreate’ makes integer from pointer without a cast [enabled by default]
/home/yide102/kent/src/inc/bigWig.h:30:6: note: expected ‘int’ but argument is of type ‘char *’
lib/Bio/DB/BigFile.xs:94:3: error: too few arguments to function ‘bigWigFileCreate’
/home/yide102/kent/src/inc/bigWig.h:30:6: note: declared here
error building lib/Bio/DB/BigFile.o from 'lib/Bio/DB/BigFile.c' at /usr/share/perl/5.14/ExtUtils/CBuilder/Base.pm line 177.
  LDS/Bio-BigFile-1.07.tar.gz
  ./Build -- NOT OK
Running Build test
  Can't test without successful make
Running Build install
  Make had returned bad status, install seems impossible

So I read  bigWigFileCreate function in kent/src/inc/bigWig.h , it had 9 arguments.
And bigWigFileCreate function in lib/Bio/DB/BigFile.xs only had 7arguments.

Can anyone give me some suggestion?

------------------------------------------------------------------------------
Android apps run on BlackBerry 10
Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
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Re: problem of install gbrowse2

Fields, Christopher J
In reply to this post by Fields, Christopher J
Here’s a patch, apply it using ‘patch -p1 < kent.patch’. 


chris

On Feb 17, 2014, at 1:55 PM, Fields, Christopher J <[hidden email]> wrote:

Yes, that’s it; this only pops up when using the kent utils from github but I expected it to land to their stable code at some point.  There is a simple branch on github that deals with it:


It’s a pretty small code change, we could probably create a simple patch and post it.

chris

On Feb 17, 2014, at 12:39 PM, Scott Cain <[hidden email]> wrote:

Chris,

Where you telling me about changes in the Kent source code that would cause problems with Bio::DB::BigFile?  Do you think it's related to this problem?

Thanks,
Scott



On Sun, Feb 16, 2014 at 9:10 PM, Yi-De Xie <[hidden email]> wrote:
hi,

I solved the problem because I compiled Kent source tree as 'me' .
But installed Bio::DB::BigFile as 'root' .
After that ,I still got problem of installing Bio::DB::BigFile like this

lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__BigFile_bigWigFileCreate’:
lib/Bio/DB/BigFile.xs:94:3: warning: passing argument 7 of ‘bigWigFileCreate’ makes integer from pointer without a cast [enabled by default]
/home/yide102/kent/src/inc/bigWig.h:30:6: note: expected ‘int’ but argument is of type ‘char *’
lib/Bio/DB/BigFile.xs:94:3: error: too few arguments to function ‘bigWigFileCreate’
/home/yide102/kent/src/inc/bigWig.h:30:6: note: declared here
error building lib/Bio/DB/BigFile.o from 'lib/Bio/DB/BigFile.c' at /usr/share/perl/5.14/ExtUtils/CBuilder/Base.pm line 177.
  LDS/Bio-BigFile-1.07.tar.gz
  ./Build -- NOT OK
Running Build test
  Can't test without successful make
Running Build install
  Make had returned bad status, install seems impossible

So I read  bigWigFileCreate function in kent/src/inc/bigWig.h , it had 9 arguments.
And bigWigFileCreate function in lib/Bio/DB/BigFile.xs only had 7arguments.

Can anyone give me some suggestion?

------------------------------------------------------------------------------
Android apps run on BlackBerry 10
Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk
_______________________________________________
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
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Re: problem of install gbrowse2

Scott Cain
In reply to this post by Timothy Parnell
Which is really nice, since they don't appear to provide a way to check versions :-/



On Mon, Feb 17, 2014 at 12:30 PM, Timothy Parnell <[hidden email]> wrote:
Hi guys,

I can confirm that downloading the current jksrc.zip from the UCSC website, per the instructions, does not work with the current Bio-DB-BigFile release. It does work with Chris’ modified version on github.

UCSC does not post previous .zip releases on their main website (you will have to dig through their github repo for that), so this will become a more common occurrence going forward. But note that this patch will also break with previously compiled UCSC library installations that people may have kept around for upgrade purposes.

Tim

On Feb 17, 2014, at 12:55 PM, Fields, Christopher J <[hidden email]<mailto:[hidden email]>> wrote:

Yes, that’s it; this only pops up when using the kent utils from github but I expected it to land to their stable code at some point.  There is a simple branch on github that deals with it:

https://github.com/cjfields/GBrowse-Adaptors/commit/bce13df624f703ac7501aaa83f87fe644f187c1a

It’s a pretty small code change, we could probably create a simple patch and post it.

chris

On Feb 17, 2014, at 12:39 PM, Scott Cain <[hidden email]<mailto:[hidden email]>> wrote:

Chris,

Where you telling me about changes in the Kent source code that would cause problems with Bio::DB::BigFile?  Do you think it's related to this problem?

Thanks,
Scott



On Sun, Feb 16, 2014 at 9:10 PM, Yi-De Xie <[hidden email]<mailto:[hidden email]>> wrote:
hi,

I solved the problem because I compiled Kent source tree as 'me' .
But installed Bio::DB::BigFile as 'root' .
After that ,I still got problem of installing Bio::DB::BigFile like this

lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__BigFile_bigWigFileCreate’:
lib/Bio/DB/BigFile.xs:94:3: warning: passing argument 7 of ‘bigWigFileCreate’ makes integer from pointer without a cast [enabled by default]
/home/yide102/kent/src/inc/bigWig.h:30:6: note: expected ‘int’ but argument is of type ‘char *’
lib/Bio/DB/BigFile.xs:94:3: error: too few arguments to function ‘bigWigFileCreate’
/home/yide102/kent/src/inc/bigWig.h:30:6: note: declared here
error building lib/Bio/DB/BigFile.o from 'lib/Bio/DB/BigFile.c' at /usr/share/perl/5.14/ExtUtils/CBuilder/Base.pm line 177.
  LDS/Bio-BigFile-1.07.tar.gz
  ./Build -- NOT OK
Running Build test
  Can't test without successful make
Running Build install
  Make had returned bad status, install seems impossible

So I read  bigWigFileCreate function in kent/src/inc/bigWig.h , it had 9 arguments.
And bigWigFileCreate function in lib/Bio/DB/BigFile.xs only had 7arguments.

Can anyone give me some suggestion?

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Re: problem of install gbrowse2

Fields, Christopher J
Actually, there is (in /kent/src/hg/inc/versionInfo.h):

#define CGI_VERSION “293"

Not perfect but it’s something.

chris

On Feb 17, 2014, at 2:34 PM, Scott Cain <[hidden email]> wrote:

Which is really nice, since they don't appear to provide a way to check versions :-/



On Mon, Feb 17, 2014 at 12:30 PM, Timothy Parnell <[hidden email]> wrote:
Hi guys,

I can confirm that downloading the current jksrc.zip from the UCSC website, per the instructions, does not work with the current Bio-DB-BigFile release. It does work with Chris’ modified version on github.

UCSC does not post previous .zip releases on their main website (you will have to dig through their github repo for that), so this will become a more common occurrence going forward. But note that this patch will also break with previously compiled UCSC library installations that people may have kept around for upgrade purposes.

Tim

On Feb 17, 2014, at 12:55 PM, Fields, Christopher J <[hidden email]<mailto:[hidden email]>> wrote:

Yes, that’s it; this only pops up when using the kent utils from github but I expected it to land to their stable code at some point.  There is a simple branch on github that deals with it:

https://github.com/cjfields/GBrowse-Adaptors/commit/bce13df624f703ac7501aaa83f87fe644f187c1a

It’s a pretty small code change, we could probably create a simple patch and post it.

chris

On Feb 17, 2014, at 12:39 PM, Scott Cain <[hidden email]<mailto:[hidden email]>> wrote:

Chris,

Where you telling me about changes in the Kent source code that would cause problems with Bio::DB::BigFile?  Do you think it's related to this problem?

Thanks,
Scott



On Sun, Feb 16, 2014 at 9:10 PM, Yi-De Xie <[hidden email]<mailto:[hidden email]>> wrote:
hi,

I solved the problem because I compiled Kent source tree as 'me' .
But installed Bio::DB::BigFile as 'root' .
After that ,I still got problem of installing Bio::DB::BigFile like this

lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__BigFile_bigWigFileCreate’:
lib/Bio/DB/BigFile.xs:94:3: warning: passing argument 7 of ‘bigWigFileCreate’ makes integer from pointer without a cast [enabled by default]
/home/yide102/kent/src/inc/bigWig.h:30:6: note: expected ‘int’ but argument is of type ‘char *’
lib/Bio/DB/BigFile.xs:94:3: error: too few arguments to function ‘bigWigFileCreate’
/home/yide102/kent/src/inc/bigWig.h:30:6: note: declared here
error building lib/Bio/DB/BigFile.o from 'lib/Bio/DB/BigFile.c' at /usr/share/perl/5.14/ExtUtils/CBuilder/Base.pm line 177.
  LDS/Bio-BigFile-1.07.tar.gz
  ./Build -- NOT OK
Running Build test
  Can't test without successful make
Running Build install
  Make had returned bad status, install seems impossible

So I read  bigWigFileCreate function in kent/src/inc/bigWig.h , it had 9 arguments.
And bigWigFileCreate function in lib/Bio/DB/BigFile.xs only had 7arguments.

Can anyone give me some suggestion?

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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="&#43;12163923087">216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


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Re: problem of install gbrowse2

Keiran Raine
Hi,

Just thought I'd mention that there are a couple of new programs for generating BigWigs in the new source tree.  Rather than generate the BW from the complete BAM file you can now generate each ref/chr in turn and then merge them.  There's a couple of advantages:

1. Overall less memory is required
2. The bamToGbrowse.pl script could track each successfully completed ref/chr so it can complete faster should a problem occur (network glitches etc).

I can't remember the exact names, but I was planning to submit a patch when I had a chance,

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 17 Feb 2014, at 20:40, "Fields, Christopher J" <[hidden email]> wrote:

Actually, there is (in /kent/src/hg/inc/versionInfo.h):

#define CGI_VERSION “293"

Not perfect but it’s something.

chris

On Feb 17, 2014, at 2:34 PM, Scott Cain <[hidden email]> wrote:

Which is really nice, since they don't appear to provide a way to check versions :-/



On Mon, Feb 17, 2014 at 12:30 PM, Timothy Parnell <[hidden email]> wrote:
Hi guys,

I can confirm that downloading the current jksrc.zip from the UCSC website, per the instructions, does not work with the current Bio-DB-BigFile release. It does work with Chris’ modified version on github.

UCSC does not post previous .zip releases on their main website (you will have to dig through their github repo for that), so this will become a more common occurrence going forward. But note that this patch will also break with previously compiled UCSC library installations that people may have kept around for upgrade purposes.

Tim

On Feb 17, 2014, at 12:55 PM, Fields, Christopher J <[hidden email]<mailto:[hidden email]>> wrote:

Yes, that’s it; this only pops up when using the kent utils from github but I expected it to land to their stable code at some point.  There is a simple branch on github that deals with it:

https://github.com/cjfields/GBrowse-Adaptors/commit/bce13df624f703ac7501aaa83f87fe644f187c1a

It’s a pretty small code change, we could probably create a simple patch and post it.

chris

On Feb 17, 2014, at 12:39 PM, Scott Cain <[hidden email]<mailto:[hidden email]>> wrote:

Chris,

Where you telling me about changes in the Kent source code that would cause problems with Bio::DB::BigFile?  Do you think it's related to this problem?

Thanks,
Scott



On Sun, Feb 16, 2014 at 9:10 PM, Yi-De Xie <[hidden email]<mailto:[hidden email]>> wrote:
hi,

I solved the problem because I compiled Kent source tree as 'me' .
But installed Bio::DB::BigFile as 'root' .
After that ,I still got problem of installing Bio::DB::BigFile like this

lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__BigFile_bigWigFileCreate’:
lib/Bio/DB/BigFile.xs:94:3: warning: passing argument 7 of ‘bigWigFileCreate’ makes integer from pointer without a cast [enabled by default]
/home/yide102/kent/src/inc/bigWig.h:30:6: note: expected ‘int’ but argument is of type ‘char *’
lib/Bio/DB/BigFile.xs:94:3: error: too few arguments to function ‘bigWigFileCreate’
/home/yide102/kent/src/inc/bigWig.h:30:6: note: declared here
error building lib/Bio/DB/BigFile.o from 'lib/Bio/DB/BigFile.c' at /usr/share/perl/5.14/ExtUtils/CBuilder/Base.pm line 177.
  LDS/Bio-BigFile-1.07.tar.gz
  ./Build -- NOT OK
Running Build test
  Can't test without successful make
Running Build install
  Make had returned bad status, install seems impossible

So I read  bigWigFileCreate function in kent/src/inc/bigWig.h , it had 9 arguments.
And bigWigFileCreate function in lib/Bio/DB/BigFile.xs only had 7arguments.

Can anyone give me some suggestion?

------------------------------------------------------------------------------
Android apps run on BlackBerry 10
Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk
_______________________________________________
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk_______________________________________________



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
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-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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Re: problem of install gbrowse2

sam789123
Hi all,

I forgot to say thanks, it worked.
Thank you.

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