Packaging pycurl on toolshed

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Packaging pycurl on toolshed

saketkc
My attempt to 'package' pycurl on testtoolshed fails with the following error:

src/pycurl.c: In function ‘do_multi_info_read’: src/pycurl.c:3549:15:
warning: call to ‘_curl_easy_getinfo_err_string’ declared with
attribute warning: curl_easy_getinfo expects a pointer to char * for
this info [enabled by default] src/pycurl.c: In function
‘do_curl_getinfo’: src/pycurl.c:2888:19: warning: call to
‘_curl_easy_getinfo_err_curl_slist’ declared with attribute warning:
curl_easy_getinfo expects a pointer to struct curl_slist * for this
info [enabled by default] error: could not create
'/usr/local/share/doc': Permission denied


A local install worked fine. Is this because of libcurl-devel missing
on toolshed instance?

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Re: Packaging pycurl on toolshed

saketkc
Any comments on this?
http://testtoolshed.g2.bx.psu.edu/view/saketkc/package_pycurl_7_19_3_1

On 17 April 2014 19:54, Saket Choudhary <[hidden email]> wrote:

> My attempt to 'package' pycurl on testtoolshed fails with the following error:
>
> src/pycurl.c: In function ‘do_multi_info_read’: src/pycurl.c:3549:15:
> warning: call to ‘_curl_easy_getinfo_err_string’ declared with
> attribute warning: curl_easy_getinfo expects a pointer to char * for
> this info [enabled by default] src/pycurl.c: In function
> ‘do_curl_getinfo’: src/pycurl.c:2888:19: warning: call to
> ‘_curl_easy_getinfo_err_curl_slist’ declared with attribute warning:
> curl_easy_getinfo expects a pointer to struct curl_slist * for this
> info [enabled by default] error: could not create
> '/usr/local/share/doc': Permission denied
>
>
> A local install worked fine. Is this because of libcurl-devel missing
> on toolshed instance?

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Re: Packaging pycurl on toolshed

Björn Grüning-3
Hi Saket,

is there any script installed with that package? --install-scripts may
be needed. Also I'm wondering if there is no dependency on curl-lib?

Cheers,
Bjoern

Am 29.04.2014 19:16, schrieb Saket Choudhary:

> Any comments on this?
> http://testtoolshed.g2.bx.psu.edu/view/saketkc/package_pycurl_7_19_3_1
>
> On 17 April 2014 19:54, Saket Choudhary <[hidden email]> wrote:
>> My attempt to 'package' pycurl on testtoolshed fails with the following error:
>>
>> src/pycurl.c: In function ‘do_multi_info_read’: src/pycurl.c:3549:15:
>> warning: call to ‘_curl_easy_getinfo_err_string’ declared with
>> attribute warning: curl_easy_getinfo expects a pointer to char * for
>> this info [enabled by default] src/pycurl.c: In function
>> ‘do_curl_getinfo’: src/pycurl.c:2888:19: warning: call to
>> ‘_curl_easy_getinfo_err_curl_slist’ declared with attribute warning:
>> curl_easy_getinfo expects a pointer to struct curl_slist * for this
>> info [enabled by default] error: could not create
>> '/usr/local/share/doc': Permission denied
>>
>>
>> A local install worked fine. Is this because of libcurl-devel missing
>> on toolshed instance?
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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Re: Packaging pycurl on toolshed

saketkc
Hi Bjoern,

There is no script installed, I generally just do this on my local system
$ python setup.py build --with-ssl
$ python setup.py install

The documentation mentions the following options:
PycURL Unix options:
 --curl-config=/path/to/curl-config  use specified curl-config binary
 --openssl-dir=/path/to/openssl/dir  path to OpenSSL headers and libraries
 --with-ssl                          libcurl is linked against OpenSSL
 --with-gnutls                       libcurl is linked against GnuTLS
 --with-nss                          libcurl is linked against NSS


Saket

On 29 April 2014 23:31, Björn Grüning <[hidden email]> wrote:

> Hi Saket,
>
> is there any script installed with that package? --install-scripts may be
> needed. Also I'm wondering if there is no dependency on curl-lib?
>
> Cheers,
> Bjoern
>
> Am 29.04.2014 19:16, schrieb Saket Choudhary:
>>
>> Any comments on this?
>> http://testtoolshed.g2.bx.psu.edu/view/saketkc/package_pycurl_7_19_3_1
>>
>> On 17 April 2014 19:54, Saket Choudhary <[hidden email]> wrote:
>>>
>>> My attempt to 'package' pycurl on testtoolshed fails with the following
>>> error:
>>>
>>> src/pycurl.c: In function ‘do_multi_info_read’: src/pycurl.c:3549:15:
>>> warning: call to ‘_curl_easy_getinfo_err_string’ declared with
>>> attribute warning: curl_easy_getinfo expects a pointer to char * for
>>> this info [enabled by default] src/pycurl.c: In function
>>> ‘do_curl_getinfo’: src/pycurl.c:2888:19: warning: call to
>>> ‘_curl_easy_getinfo_err_curl_slist’ declared with attribute warning:
>>> curl_easy_getinfo expects a pointer to struct curl_slist * for this
>>> info [enabled by default] error: could not create
>>> '/usr/local/share/doc': Permission denied
>>>
>>>
>>> A local install worked fine. Is this because of libcurl-devel missing
>>> on toolshed instance?
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>    http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>    http://galaxyproject.org/search/mailinglists/
>>
>

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Re: Packaging pycurl on toolshed

Greg Von Kuster
Hello Saket,

I'm not a system-level expert, so please ignore my attempt at helping if it is incorrect.  Your recipe for installing and compiling pycurl may be assuming that certain dependencies exist in the Galaxy environment into which it is being installed for testing, but they do not.  Galaxy tools and tool dependency recipes can only assume the following dependencies are available in the Galaxy environment into which they will be installed (this list is available in the Tool Shed wiki on this page: https://wiki.galaxyproject.org/InstallAndTestCertification).  In your case, a recipe should probably also be installing the libcurl-devel package (and possibly others??).

Recipes need to be created for dependencies that are not on the following list, and then relationships can be defined between repositories that contain them and repositories that contain tools that depend upon them.  The reason the following list is short is because starting up a new Galaxy instance should be as simple as cloning it and starting it up with run.sh.  

  • autoconf
  • automake
  • autotools-dev
  • build-essential
  • cmake
  • git-core
  • libatlas-base-dev
  • libblas-dev
  • liblapack-dev
  • libc6-dev
  • mercurial
  • python2.6
  • python2.6-dev
  • pkg-config
  • subversion
  • python-dev
  • python-pip

  • Greg Von Kuster


    On Apr 29, 2014, at 4:34 PM, Saket Choudhary <[hidden email]> wrote:

    Hi Bjoern,

    There is no script installed, I generally just do this on my local system
    $ python setup.py build --with-ssl
    $ python setup.py install

    The documentation mentions the following options:
    PycURL Unix options:
    --curl-config=/path/to/curl-config  use specified curl-config binary
    --openssl-dir=/path/to/openssl/dir  path to OpenSSL headers and libraries
    --with-ssl                          libcurl is linked against OpenSSL
    --with-gnutls                       libcurl is linked against GnuTLS
    --with-nss                          libcurl is linked against NSS


    Saket

    On 29 April 2014 23:31, Björn Grüning <[hidden email]> wrote:
    Hi Saket,

    is there any script installed with that package? --install-scripts may be
    needed. Also I'm wondering if there is no dependency on curl-lib?

    Cheers,
    Bjoern

    Am 29.04.2014 19:16, schrieb Saket Choudhary:

    Any comments on this?
    http://testtoolshed.g2.bx.psu.edu/view/saketkc/package_pycurl_7_19_3_1

    On 17 April 2014 19:54, Saket Choudhary <[hidden email]> wrote:

    My attempt to 'package' pycurl on testtoolshed fails with the following
    error:

    src/pycurl.c: In function ‘do_multi_info_read’: src/pycurl.c:3549:15:
    warning: call to ‘_curl_easy_getinfo_err_string’ declared with
    attribute warning: curl_easy_getinfo expects a pointer to char * for
    this info [enabled by default] src/pycurl.c: In function
    ‘do_curl_getinfo’: src/pycurl.c:2888:19: warning: call to
    ‘_curl_easy_getinfo_err_curl_slist’ declared with attribute warning:
    curl_easy_getinfo expects a pointer to struct curl_slist * for this
    info [enabled by default] error: could not create
    '/usr/local/share/doc': Permission denied


    A local install worked fine. Is this because of libcurl-devel missing
    on toolshed instance?


    ___________________________________________________________
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    and other Galaxy lists, please use the interface at:
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    ___________________________________________________________
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    ___________________________________________________________
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    Re: Packaging pycurl on toolshed

    saketkc
    Thanks Greg & Bjoern,

    I get your point now. I will reconfigure my tool to take into account
    the other dependencies.

    Thanks once again,
    Saket


    On 30 April 2014 02:30, Greg Von Kuster <[hidden email]> wrote:

    > Hello Saket,
    >
    > I'm not a system-level expert, so please ignore my attempt at helping if it
    > is incorrect.  Your recipe for installing and compiling pycurl may be
    > assuming that certain dependencies exist in the Galaxy environment into
    > which it is being installed for testing, but they do not.  Galaxy tools and
    > tool dependency recipes can only assume the following dependencies are
    > available in the Galaxy environment into which they will be installed (this
    > list is available in the Tool Shed wiki on this page:
    > https://wiki.galaxyproject.org/InstallAndTestCertification).  In your case,
    > a recipe should probably also be installing the libcurl-devel package (and
    > possibly others??).
    >
    > Recipes need to be created for dependencies that are not on the following
    > list, and then relationships can be defined between repositories that
    > contain them and repositories that contain tools that depend upon them.  The
    > reason the following list is short is because starting up a new Galaxy
    > instance should be as simple as cloning it and starting it up with run.sh.
    >
    > autoconf
    > automake
    > autotools-dev
    > build-essential
    > cmake
    > git-core
    > libatlas-base-dev
    > libblas-dev
    > liblapack-dev
    > libc6-dev
    > mercurial
    > python2.6
    > python2.6-dev
    > pkg-config
    > subversion
    > python-dev
    > python-pip
    >
    >
    > Greg Von Kuster
    >
    >
    > On Apr 29, 2014, at 4:34 PM, Saket Choudhary <[hidden email]> wrote:
    >
    > Hi Bjoern,
    >
    > There is no script installed, I generally just do this on my local system
    > $ python setup.py build --with-ssl
    > $ python setup.py install
    >
    > The documentation mentions the following options:
    > PycURL Unix options:
    > --curl-config=/path/to/curl-config  use specified curl-config binary
    > --openssl-dir=/path/to/openssl/dir  path to OpenSSL headers and libraries
    > --with-ssl                          libcurl is linked against OpenSSL
    > --with-gnutls                       libcurl is linked against GnuTLS
    > --with-nss                          libcurl is linked against NSS
    >
    >
    > Saket
    >
    > On 29 April 2014 23:31, Björn Grüning <[hidden email]> wrote:
    >
    > Hi Saket,
    >
    > is there any script installed with that package? --install-scripts may be
    > needed. Also I'm wondering if there is no dependency on curl-lib?
    >
    > Cheers,
    > Bjoern
    >
    > Am 29.04.2014 19:16, schrieb Saket Choudhary:
    >
    >
    > Any comments on this?
    > http://testtoolshed.g2.bx.psu.edu/view/saketkc/package_pycurl_7_19_3_1
    >
    > On 17 April 2014 19:54, Saket Choudhary <[hidden email]> wrote:
    >
    >
    > My attempt to 'package' pycurl on testtoolshed fails with the following
    > error:
    >
    > src/pycurl.c: In function ‘do_multi_info_read’: src/pycurl.c:3549:15:
    > warning: call to ‘_curl_easy_getinfo_err_string’ declared with
    > attribute warning: curl_easy_getinfo expects a pointer to char * for
    > this info [enabled by default] src/pycurl.c: In function
    > ‘do_curl_getinfo’: src/pycurl.c:2888:19: warning: call to
    > ‘_curl_easy_getinfo_err_curl_slist’ declared with attribute warning:
    > curl_easy_getinfo expects a pointer to struct curl_slist * for this
    > info [enabled by default] error: could not create
    > '/usr/local/share/doc': Permission denied
    >
    >
    > A local install worked fine. Is this because of libcurl-devel missing
    > on toolshed instance?
    >
    >
    >
    > ___________________________________________________________
    > Please keep all replies on the list by using "reply all"
    > in your mail client.  To manage your subscriptions to this
    > and other Galaxy lists, please use the interface at:
    >   http://lists.bx.psu.edu/
    >
    > To search Galaxy mailing lists use the unified search at:
    >   http://galaxyproject.org/search/mailinglists/
    >
    >
    >
    > ___________________________________________________________
    > Please keep all replies on the list by using "reply all"
    > in your mail client.  To manage your subscriptions to this
    > and other Galaxy lists, please use the interface at:
    >  http://lists.bx.psu.edu/
    >
    > To search Galaxy mailing lists use the unified search at:
    >  http://galaxyproject.org/search/mailinglists/
    >
    >

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    Re: Packaging pycurl on toolshed

    saketkc
    So far I have been trying to avoid this, but I would like to see
    packaged pycurl on the toolshed now.

    This is where my package sits:
    https://testtoolshed.g2.bx.psu.edu/repository?repository_id=534efefdbab02103

    and this is the error:

    Traceback (most recent call last): File "setup.py", line 563, in
    <module> ext = get_extension() File "setup.py", line 368, in
    get_extension ext_config = ExtensionConfiguration() File "setup.py",
    line 65, in __init__ self.configure() File "setup.py", line 93, in
    configure_unix CURL_CONFIG = scan_argv("--curl-config=", CURL_CONFIG)
    File "setup.py", line 42, in scan_argv assert p, arg AssertionError:
    --curl-config=

    and this is why it should be arising:

       python setup.py build --with-ssl --curl-config=$CURL &amp;&amp;

    $CURL being empty.

    A local installation with the commands as in the tool_dependencies.xml
    doe generate $INSTALL_DIR/install-destination/bin/curl-config which
    should then be set to $CURL.

    Is there a way to check the logs, something I attempted by doing this:
        <action type="shell_command">echo $INSTALL_DIR</action>
         <action type="shell_command">echo $CURL</action>

    Or any alternate way to debug?


    On 29 April 2014 14:25, Saket Choudhary <[hidden email]> wrote:

    > Thanks Greg & Bjoern,
    >
    > I get your point now. I will reconfigure my tool to take into account
    > the other dependencies.
    >
    > Thanks once again,
    > Saket
    >
    >
    > On 30 April 2014 02:30, Greg Von Kuster <[hidden email]> wrote:
    >> Hello Saket,
    >>
    >> I'm not a system-level expert, so please ignore my attempt at helping if it
    >> is incorrect.  Your recipe for installing and compiling pycurl may be
    >> assuming that certain dependencies exist in the Galaxy environment into
    >> which it is being installed for testing, but they do not.  Galaxy tools and
    >> tool dependency recipes can only assume the following dependencies are
    >> available in the Galaxy environment into which they will be installed (this
    >> list is available in the Tool Shed wiki on this page:
    >> https://wiki.galaxyproject.org/InstallAndTestCertification).  In your case,
    >> a recipe should probably also be installing the libcurl-devel package (and
    >> possibly others??).
    >>
    >> Recipes need to be created for dependencies that are not on the following
    >> list, and then relationships can be defined between repositories that
    >> contain them and repositories that contain tools that depend upon them.  The
    >> reason the following list is short is because starting up a new Galaxy
    >> instance should be as simple as cloning it and starting it up with run.sh.
    >>
    >> autoconf
    >> automake
    >> autotools-dev
    >> build-essential
    >> cmake
    >> git-core
    >> libatlas-base-dev
    >> libblas-dev
    >> liblapack-dev
    >> libc6-dev
    >> mercurial
    >> python2.6
    >> python2.6-dev
    >> pkg-config
    >> subversion
    >> python-dev
    >> python-pip
    >>
    >>
    >> Greg Von Kuster
    >>
    >>
    >> On Apr 29, 2014, at 4:34 PM, Saket Choudhary <[hidden email]> wrote:
    >>
    >> Hi Bjoern,
    >>
    >> There is no script installed, I generally just do this on my local system
    >> $ python setup.py build --with-ssl
    >> $ python setup.py install
    >>
    >> The documentation mentions the following options:
    >> PycURL Unix options:
    >> --curl-config=/path/to/curl-config  use specified curl-config binary
    >> --openssl-dir=/path/to/openssl/dir  path to OpenSSL headers and libraries
    >> --with-ssl                          libcurl is linked against OpenSSL
    >> --with-gnutls                       libcurl is linked against GnuTLS
    >> --with-nss                          libcurl is linked against NSS
    >>
    >>
    >> Saket
    >>
    >> On 29 April 2014 23:31, Björn Grüning <[hidden email]> wrote:
    >>
    >> Hi Saket,
    >>
    >> is there any script installed with that package? --install-scripts may be
    >> needed. Also I'm wondering if there is no dependency on curl-lib?
    >>
    >> Cheers,
    >> Bjoern
    >>
    >> Am 29.04.2014 19:16, schrieb Saket Choudhary:
    >>
    >>
    >> Any comments on this?
    >> http://testtoolshed.g2.bx.psu.edu/view/saketkc/package_pycurl_7_19_3_1
    >>
    >> On 17 April 2014 19:54, Saket Choudhary <[hidden email]> wrote:
    >>
    >>
    >> My attempt to 'package' pycurl on testtoolshed fails with the following
    >> error:
    >>
    >> src/pycurl.c: In function ‘do_multi_info_read’: src/pycurl.c:3549:15:
    >> warning: call to ‘_curl_easy_getinfo_err_string’ declared with
    >> attribute warning: curl_easy_getinfo expects a pointer to char * for
    >> this info [enabled by default] src/pycurl.c: In function
    >> ‘do_curl_getinfo’: src/pycurl.c:2888:19: warning: call to
    >> ‘_curl_easy_getinfo_err_curl_slist’ declared with attribute warning:
    >> curl_easy_getinfo expects a pointer to struct curl_slist * for this
    >> info [enabled by default] error: could not create
    >> '/usr/local/share/doc': Permission denied
    >>
    >>
    >> A local install worked fine. Is this because of libcurl-devel missing
    >> on toolshed instance?
    >>
    >>
    >>
    >> ___________________________________________________________
    >> Please keep all replies on the list by using "reply all"
    >> in your mail client.  To manage your subscriptions to this
    >> and other Galaxy lists, please use the interface at:
    >>   http://lists.bx.psu.edu/
    >>
    >> To search Galaxy mailing lists use the unified search at:
    >>   http://galaxyproject.org/search/mailinglists/
    >>
    >>
    >>
    >> ___________________________________________________________
    >> Please keep all replies on the list by using "reply all"
    >> in your mail client.  To manage your subscriptions to this
    >> and other Galaxy lists, please use the interface at:
    >>  http://lists.bx.psu.edu/
    >>
    >> To search Galaxy mailing lists use the unified search at:
    >>  http://galaxyproject.org/search/mailinglists/
    >>
    >>

    ___________________________________________________________
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