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problem in Installing Bio::Seq, Bio::DB::GFF, #36

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amoltej opened this Issue Feb 7, 2016 · 6 comments

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@amoltej

amoltej commented Feb 7, 2016

Hi, I have been trying to install these modules using cpan install command.
I have installed all the dependencies and my bioperl installation says it is up to date.

But when I try to install these modules using following command

sudo cpan install Bio::Seq or Bio::DB::GFF it gives me follwing error message

Test Summary Report

t/RemoteDB/HIV/HIVQuery.t (Wstat: 65280 Tests: 6 Failed: 1)
Failed test: 1
Non-zero exit status: 255
Parse errors: Bad plan. You planned 41 tests but ran 6.
Files=334, Tests=23870, 119 wallclock secs ( 4.48 usr 0.75 sys + 110.06 cusr 6.90 csys = 122.19 CPU)
Result: FAIL
Failed 1/334 test programs. 1/23870 subtests failed.
CJFIELDS/BioPerl-1.6.924.tar.gz
./Build test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
reports CJFIELDS/BioPerl-1.6.924.tar.gz

can someone please help me to solve the issue?
Thank you in advance
Amol

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majensen Feb 7, 2016

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Hi Amol

This failure shouldn't affect what you want to use. I would do
cpan --force install
which will put the modules you need where they need to be.

@cjfields, we should probably pull out the hiv query stuff, I will look into it

Mark

On Sun, Feb 07, 2016 at 7:18 AM, amoltej < notifications@github.com [notifications@github.com] > wrote:
Hi, I have been trying to install these modules using cpan install command
I have installed all the dependencies and my bioperl installation says it is up
to date

But when I try to install these modules using following command

sudo cpan install Bio::Seq or Bio::DB::GFF it gives me follwing error message

TEST SUMMARY REPORT
t/RemoteDB/HIV/HIVQueryt (Wstat: 65280 Tests: 6 Failed: 1)
Failed test: 1
Non-zero exit status: 255
Parse errors: Bad plan You planned 41 tests but ran 6
Files=334, Tests=23870, 119 wallclock secs ( 448 usr 075 sys + 11006 cusr 690
csys = 12219 CPU)
Result: FAIL
Failed 1/334 test programs 1/23870 subtests failed
CJFIELDS/BioPerl-16924targz
/Build test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
reports CJFIELDS/BioPerl-16924targz

can someone please help me to solve the issue?
Thank you in advance
Amol


Reply to this email directly or view it on GitHub [https://github.com/bioperl/bioperl-run/issues/36] .[https://github.com/notifications/beacon/AAFAmYBcfLnhMNJtUsxyv2guBkq5hNshks5phy2ngaJpZM4HVE1B.gif]

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majensen commented Feb 7, 2016

Hi Amol

This failure shouldn't affect what you want to use. I would do
cpan --force install
which will put the modules you need where they need to be.

@cjfields, we should probably pull out the hiv query stuff, I will look into it

Mark

On Sun, Feb 07, 2016 at 7:18 AM, amoltej < notifications@github.com [notifications@github.com] > wrote:
Hi, I have been trying to install these modules using cpan install command
I have installed all the dependencies and my bioperl installation says it is up
to date

But when I try to install these modules using following command

sudo cpan install Bio::Seq or Bio::DB::GFF it gives me follwing error message

TEST SUMMARY REPORT
t/RemoteDB/HIV/HIVQueryt (Wstat: 65280 Tests: 6 Failed: 1)
Failed test: 1
Non-zero exit status: 255
Parse errors: Bad plan You planned 41 tests but ran 6
Files=334, Tests=23870, 119 wallclock secs ( 448 usr 075 sys + 11006 cusr 690
csys = 12219 CPU)
Result: FAIL
Failed 1/334 test programs 1/23870 subtests failed
CJFIELDS/BioPerl-16924targz
/Build test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
reports CJFIELDS/BioPerl-16924targz

can someone please help me to solve the issue?
Thank you in advance
Amol


Reply to this email directly or view it on GitHub [https://github.com/bioperl/bioperl-run/issues/36] .[https://github.com/notifications/beacon/AAFAmYBcfLnhMNJtUsxyv2guBkq5hNshks5phy2ngaJpZM4HVE1B.gif]

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cjfields Feb 7, 2016

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@majensen we can do that. Though those tests shouldn't be run by default, they generally require explicitly asking for network tests, which can be flaky based on network and remote service availability.

@amoltej did you ask for (or were you prompted for) remote tests when installing?

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cjfields commented Feb 7, 2016

@majensen we can do that. Though those tests shouldn't be run by default, they generally require explicitly asking for network tests, which can be flaky based on network and remote service availability.

@amoltej did you ask for (or were you prompted for) remote tests when installing?

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amoltej Feb 7, 2016

@majensen --Force install has worked. Thank you for that. but while installation there were several messages saying command not found. Do I need to worry for that?

@cjfields I believe not, Please see below -

CPAN: Time::HiRes loaded ok (v1.9726)
Configuring C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz with Build.PL
Do you want to run the Bio::DB::GFF or Bio::DB::SeqFeature::Store live database tests? y/n [n] - will not run the BioDBGFF or BioDBSeqFeature live database tests

Install [a]ll BioPerl scripts, [n]one, or choose groups [i]nteractively? [a] - will install all scripts

Do you want to run tests that require connection to servers across the internet
(likely to cause some failures)? y/n [n] - will not run internet-requiring tests
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'BioPerl' version '1.006924'
CJFIELDS/BioPerl-1.6.924.tar.gz
/usr/bin/perl Build.PL -- OK
Running Build for C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz
Building BioPerl
CJFIELDS/BioPerl-1.6.924.tar.gz
./Build -- OK
Running Build test

amoltej commented Feb 7, 2016

@majensen --Force install has worked. Thank you for that. but while installation there were several messages saying command not found. Do I need to worry for that?

@cjfields I believe not, Please see below -

CPAN: Time::HiRes loaded ok (v1.9726)
Configuring C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz with Build.PL
Do you want to run the Bio::DB::GFF or Bio::DB::SeqFeature::Store live database tests? y/n [n] - will not run the BioDBGFF or BioDBSeqFeature live database tests

Install [a]ll BioPerl scripts, [n]one, or choose groups [i]nteractively? [a] - will install all scripts

Do you want to run tests that require connection to servers across the internet
(likely to cause some failures)? y/n [n] - will not run internet-requiring tests
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'BioPerl' version '1.006924'
CJFIELDS/BioPerl-1.6.924.tar.gz
/usr/bin/perl Build.PL -- OK
Running Build for C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz
Building BioPerl
CJFIELDS/BioPerl-1.6.924.tar.gz
./Build -- OK
Running Build test

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@cjfields This is a common problem I think-- when a user wants to just install a module or two, cpan installs the whole distro-- I wonder if there a way to tweak it so that just the desired module is brought down? I.e., without the big reorganization that we all want to do someday.

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majensen commented Feb 8, 2016

@cjfields This is a common problem I think-- when a user wants to just install a module or two, cpan installs the whole distro-- I wonder if there a way to tweak it so that just the desired module is brought down? I.e., without the big reorganization that we all want to do someday.

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Unfortunately not easily. I believe @majensen was looking into this for bioperl-run but I don’t know of any precedent dists that do this in CPAN.

chris

On Feb 8, 2016, at 7:10 AM, Mark Jensen <notifications@github.commailto:notifications@github.com> wrote:

@cjfieldshttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cjfields&d=BQMCaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=vQWdwSIk5RXki4sjPut5QxUjrzDM2mGgZwYQiIZau_s&s=2CmYIVpCd2AK0Y34KD-19bOMUv7lI_fU1O0XHHGi-dQ&e= This is a common problem I think-- when a user wants to just install a module or two, cpan installs the whole distro-- I wonder if there a way to tweak it so that just the desired module is brought down? I.e., without the big reorganization that we all want to do someday.


Reply to this email directly or view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bioperl_bioperl-2Drun_issues_36-23issuecomment-2D181359073&d=BQMCaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=vQWdwSIk5RXki4sjPut5QxUjrzDM2mGgZwYQiIZau_s&s=rS6UxDHVy4_7VaEzo6kFIGjtO-VMKTGo3W-LODKX-ns&e=.

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cjfields commented Feb 8, 2016

Unfortunately not easily. I believe @majensen was looking into this for bioperl-run but I don’t know of any precedent dists that do this in CPAN.

chris

On Feb 8, 2016, at 7:10 AM, Mark Jensen <notifications@github.commailto:notifications@github.com> wrote:

@cjfieldshttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cjfields&d=BQMCaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=vQWdwSIk5RXki4sjPut5QxUjrzDM2mGgZwYQiIZau_s&s=2CmYIVpCd2AK0Y34KD-19bOMUv7lI_fU1O0XHHGi-dQ&e= This is a common problem I think-- when a user wants to just install a module or two, cpan installs the whole distro-- I wonder if there a way to tweak it so that just the desired module is brought down? I.e., without the big reorganization that we all want to do someday.


Reply to this email directly or view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bioperl_bioperl-2Drun_issues_36-23issuecomment-2D181359073&d=BQMCaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=vQWdwSIk5RXki4sjPut5QxUjrzDM2mGgZwYQiIZau_s&s=rS6UxDHVy4_7VaEzo6kFIGjtO-VMKTGo3W-LODKX-ns&e=.

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Hmm, seeing that it was me making the comment, you may be right!

On Mon, Feb 08, 2016 at 8:25 AM, Chris Fields < notifications@github.com [notifications@github.com] > wrote:
Unfortunately not easily. I believe @majensen was looking into this for
bioperl-run but I don’t know of any precedent dists that do this in CPAN.

chris

On Feb 8, 2016, at 7:10 AM, Mark Jensen
<notifications@github.commailto:notifications@github.com> wrote:

@cjfieldshttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cjfields&d=BQMCaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=vQWdwSIk5RXki4sjPut5QxUjrzDM2mGgZwYQiIZau_s&s=2CmYIVpCd2AK0Y34KD-19bOMUv7lI_fU1O0XHHGi-dQ&e=
This is a common problem I think-- when a user wants to just install a module or
two, cpan installs the whole distro-- I wonder if there a way to tweak it so
that just the desired module is brought down? I.e., without the big
reorganization that we all want to do someday.


Reply to this email directly or view it on
GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bioperl_bioperl-2Drun_issues_36-23issuecomment-2D181359073&d=BQMCaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=vQWdwSIk5RXki4sjPut5QxUjrzDM2mGgZwYQiIZau_s&s=rS6UxDHVy4_7VaEzo6kFIGjtO-VMKTGo3W-LODKX-ns&e=.


Reply to this email directly or view it on GitHub
[https://github.com/bioperl/bioperl-run/issues/36#issuecomment-181365558] .[https://github.com/notifications/beacon/AAFAmWPWW8XwLOdFuzpCvgreu7QrTaOfks5piI7igaJpZM4HVE1B.gif]

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majensen commented Feb 8, 2016

Hmm, seeing that it was me making the comment, you may be right!

On Mon, Feb 08, 2016 at 8:25 AM, Chris Fields < notifications@github.com [notifications@github.com] > wrote:
Unfortunately not easily. I believe @majensen was looking into this for
bioperl-run but I don’t know of any precedent dists that do this in CPAN.

chris

On Feb 8, 2016, at 7:10 AM, Mark Jensen
<notifications@github.commailto:notifications@github.com> wrote:

@cjfieldshttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cjfields&d=BQMCaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=vQWdwSIk5RXki4sjPut5QxUjrzDM2mGgZwYQiIZau_s&s=2CmYIVpCd2AK0Y34KD-19bOMUv7lI_fU1O0XHHGi-dQ&e=
This is a common problem I think-- when a user wants to just install a module or
two, cpan installs the whole distro-- I wonder if there a way to tweak it so
that just the desired module is brought down? I.e., without the big
reorganization that we all want to do someday.


Reply to this email directly or view it on
GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bioperl_bioperl-2Drun_issues_36-23issuecomment-2D181359073&d=BQMCaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=vQWdwSIk5RXki4sjPut5QxUjrzDM2mGgZwYQiIZau_s&s=rS6UxDHVy4_7VaEzo6kFIGjtO-VMKTGo3W-LODKX-ns&e=.


Reply to this email directly or view it on GitHub
[https://github.com/bioperl/bioperl-run/issues/36#issuecomment-181365558] .[https://github.com/notifications/beacon/AAFAmWPWW8XwLOdFuzpCvgreu7QrTaOfks5piI7igaJpZM4HVE1B.gif]

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