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itmat / rum

RNA-Seq Unified Mapper
http://cbil.upenn.edu/RUM
MIT License
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Can't locate object method "newdir" via package "File::Temp" #169

Closed karinschlangen closed 11 years ago

karinschlangen commented 11 years ago

Hi everybody,

the alignment with RUM stopped with the following error message:

Error running "perl /PATH/TO/RUM-Pipeline-v2.0.4/bin/../bin/sort_RUM_by_location.pl --ram 6 /PATH/TO/OUTPUT/chunks/RUM_Unique.1 -o /PATH/TO/OUTPUT/chunks/RUM_Unique.sorted.1.tmp.ykkUcgeP >> /PATH/TO/OUTPUT/chunks/chr_counts_u.1.tmp.KsHQolwR"

The stderr from that command is

Can't locate object method "newdir" via package "File::Temp" at /PATH/TO/RUM-Pipeline-v2.0.4/bin/../lib/RUM/Script/SortRumByLocation.pm line 157.

and i don't know how to deal with that. Has anyone an idea?

The error log file ./log/rum_errors.log contains the following:

Thu Mar 21 18:38:27 2013 18618 FATAL RUM::Death - Can't locate object method "newdir" via package "File::Temp" at /PATH/TO/RUM-Pipeline-v2.0.4/bin/../lib/RUM/Script/SortRumByLocation.pm line 157. Thu Mar 21 18:38:27 2013 8440 FATAL RUM::Death - Error running "perl /PATH/TO/OUTPUT/RUM-Pipeline-v2.0.4/bin/../bin/sort_RUM_by_location.pl --ram 6 /PATH/TO/OUTPUT/chunks/RUM_Unique.1 -o /PATH/TO/OUTPUT/chunks/RUM_Unique.sorted.1.tmp.ykkUcgeP >> /PATH/TO/OUTPUT/chunks/chr_counts_u.1.tmp.KsHQolwR"

The stderr from that command is

Can't locate object method "newdir" via package "File::Temp" at /PATH/TO/bin/RUM-Pipeline-v2.0.4/bin/../lib/RUM/Script/SortRumByLocation.pm line 157.

The error log file ./log/rum_errors.log may have more details. ./log/rum_errors.log (END)

mdelaurentis commented 11 years ago

Can you let me know what version of Perl you are using?

On Fri, Mar 22, 2013 at 4:05 AM, karinschlangen notifications@github.comwrote:

Hi everybody,

the alignment with RUM stopped with the following error message:

Error running "perl /PATH/TO/RUM-Pipeline-v2.0.4/bin/../bin/sort_RUM_by_location.pl --ram 6 /PATH/TO/OUTPUT/chunks/RUM_Unique.1 -o /PATH/TO/OUTPUT/chunks/RUM_Unique.sorted.1.tmp.ykkUcgeP >> /PATH/TO/OUTPUT/chunks/chr_counts_u.1.tmp.KsHQolwR"

The stderr from that command is

Can't locate object method "newdir" via package "File::Temp" at /PATH/TO/RUM-Pipeline-v2.0.4/bin/../lib/RUM/Script/SortRumByLocation.pm line 157.

and i don't know how to deal with that. Has anyone an idea?

The error log file ./log/rum_errors.log contains the following:

Thu Mar 21 18:38:27 2013 18618 FATAL RUM::Death - Can't locate object method "newdir" via package "File::Temp" at /PATH/TO/RUM-Pipeline-v2.0.4/bin/../lib/RUM/Script/SortRumByLocation.pm line 157. Thu Mar 21 18:38:27 2013 8440 FATAL RUM::Death - Error running "perl /PATH/TO/OUTPUT/RUM-Pipeline-v2.0.4/bin/../bin/sort_RUM_by_location.pl --ram 6 /PATH/TO/OUTPUT/chunks/RUM_Unique.1 -o /PATH/TO/OUTPUT/chunks/RUM_Unique.sorted.1.tmp.ykkUcgeP >> /PATH/TO/OUTPUT/chunks/chr_counts_u.1.tmp.KsHQolwR"

The stderr from that command is

Can't locate object method "newdir" via package "File::Temp" at /PATH/TO/bin/RUM-Pipeline-v2.0.4/bin/../lib/RUM/Script/SortRumByLocation.pm line 157.

The error log file ./log/rum_errors.log may have more details. ./log/rum_errors.log (END)

— Reply to this email directly or view it on GitHubhttps://github.com/PGFI/rum/issues/169 .

karinschlangen commented 11 years ago

Hi Mike,

i am using perl v5.10.0

running on a mac.

Thanks!

On Fri, Mar 22, 2013 at 3:11 PM, Mike DeLaurentis notifications@github.comwrote:

Can you let me know what version of Perl you are using?

On Fri, Mar 22, 2013 at 4:05 AM, karinschlangen notifications@github.comwrote:

Hi everybody,

the alignment with RUM stopped with the following error message:

Error running "perl /PATH/TO/RUM-Pipeline-v2.0.4/bin/../bin/sort_RUM_by_location.pl --ram 6 /PATH/TO/OUTPUT/chunks/RUM_Unique.1 -o /PATH/TO/OUTPUT/chunks/RUM_Unique.sorted.1.tmp.ykkUcgeP >> /PATH/TO/OUTPUT/chunks/chr_counts_u.1.tmp.KsHQolwR"

The stderr from that command is

Can't locate object method "newdir" via package "File::Temp" at /PATH/TO/RUM-Pipeline-v2.0.4/bin/../lib/RUM/Script/SortRumByLocation.pm line 157.

and i don't know how to deal with that. Has anyone an idea?

The error log file ./log/rum_errors.log contains the following:

Thu Mar 21 18:38:27 2013 18618 FATAL RUM::Death - Can't locate object method "newdir" via package "File::Temp" at /PATH/TO/RUM-Pipeline-v2.0.4/bin/../lib/RUM/Script/SortRumByLocation.pm line 157. Thu Mar 21 18:38:27 2013 8440 FATAL RUM::Death - Error running "perl /PATH/TO/OUTPUT/RUM-Pipeline-v2.0.4/bin/../bin/sort_RUM_by_location.pl --ram 6 /PATH/TO/OUTPUT/chunks/RUM_Unique.1 -o /PATH/TO/OUTPUT/chunks/RUM_Unique.sorted.1.tmp.ykkUcgeP >> /PATH/TO/OUTPUT/chunks/chr_counts_u.1.tmp.KsHQolwR"

The stderr from that command is

Can't locate object method "newdir" via package "File::Temp" at

/PATH/TO/bin/RUM-Pipeline-v2.0.4/bin/../lib/RUM/Script/SortRumByLocation.pm line 157.

The error log file ./log/rum_errors.log may have more details. ./log/rum_errors.log (END)

— Reply to this email directly or view it on GitHub< https://github.com/PGFI/rum/issues/169> .

— Reply to this email directly or view it on GitHubhttps://github.com/PGFI/rum/issues/169#issuecomment-15298541 .

mdelaurentis commented 11 years ago

It looks like I'm accidentally using a feature that was introduced in Perl 5.12. I just committed a change that will fix it, which will be available the next time we tag a release. In the meantime, you can fix it locally by opening lib/RUM/Script/SortRumByLocation.pm and changing the line that contains:

my $tempdir = File::Temp->newdir;

to

my $tempdir = File::Temp::tempdir(CLEANUP => 1);

That should be around line 165 of that file. Can you please let me know if that works for you?

Thanks,

Mike

On Fri, Mar 22, 2013 at 10:24 AM, karinschlangen notifications@github.comwrote:

Hi Mike,

i am using perl v5.10.0

running on a mac.

Thanks!

On Fri, Mar 22, 2013 at 3:11 PM, Mike DeLaurentis notifications@github.comwrote:

Can you let me know what version of Perl you are using?

On Fri, Mar 22, 2013 at 4:05 AM, karinschlangen < notifications@github.com>wrote:

Hi everybody,

the alignment with RUM stopped with the following error message:

Error running "perl /PATH/TO/RUM-Pipeline-v2.0.4/bin/../bin/sort_RUM_by_location.pl --ram 6 /PATH/TO/OUTPUT/chunks/RUM_Unique.1 -o /PATH/TO/OUTPUT/chunks/RUM_Unique.sorted.1.tmp.ykkUcgeP >> /PATH/TO/OUTPUT/chunks/chr_counts_u.1.tmp.KsHQolwR"

The stderr from that command is

Can't locate object method "newdir" via package "File::Temp" at

/PATH/TO/RUM-Pipeline-v2.0.4/bin/../lib/RUM/Script/SortRumByLocation.pm line 157.

and i don't know how to deal with that. Has anyone an idea?

The error log file ./log/rum_errors.log contains the following:

Thu Mar 21 18:38:27 2013 18618 FATAL RUM::Death - Can't locate object method "newdir" via package "File::Temp" at

/PATH/TO/RUM-Pipeline-v2.0.4/bin/../lib/RUM/Script/SortRumByLocation.pm line 157. Thu Mar 21 18:38:27 2013 8440 FATAL RUM::Death - Error running "perl /PATH/TO/OUTPUT/RUM-Pipeline-v2.0.4/bin/../bin/sort_RUM_by_location.pl --ram 6 /PATH/TO/OUTPUT/chunks/RUM_Unique.1 -o /PATH/TO/OUTPUT/chunks/RUM_Unique.sorted.1.tmp.ykkUcgeP >> /PATH/TO/OUTPUT/chunks/chr_counts_u.1.tmp.KsHQolwR"

The stderr from that command is

Can't locate object method "newdir" via package "File::Temp" at

/PATH/TO/bin/RUM-Pipeline-v2.0.4/bin/../lib/RUM/Script/SortRumByLocation.pm

line 157.

The error log file ./log/rum_errors.log may have more details. ./log/rum_errors.log (END)

— Reply to this email directly or view it on GitHub< https://github.com/PGFI/rum/issues/169> .

— Reply to this email directly or view it on GitHub< https://github.com/PGFI/rum/issues/169#issuecomment-15298541> .

— Reply to this email directly or view it on GitHubhttps://github.com/PGFI/rum/issues/169#issuecomment-15299238 .

karinschlangen commented 11 years ago

Hi Mike,

i changed the file and started the mapping again. I will let you know if it works.

Thanks a lot! Karin

On Fri, Mar 22, 2013 at 4:28 PM, Mike DeLaurentis notifications@github.comwrote:

It looks like I'm accidentally using a feature that was introduced in Perl 5.12. I just committed a change that will fix it, which will be available the next time we tag a release. In the meantime, you can fix it locally by opening lib/RUM/Script/SortRumByLocation.pm and changing the line that contains:

my $tempdir = File::Temp->newdir;

to

my $tempdir = File::Temp::tempdir(CLEANUP => 1);

That should be around line 165 of that file. Can you please let me know if that works for you?

Thanks,

Mike

On Fri, Mar 22, 2013 at 10:24 AM, karinschlangen notifications@github.comwrote:

Hi Mike,

i am using perl v5.10.0

running on a mac.

Thanks!

On Fri, Mar 22, 2013 at 3:11 PM, Mike DeLaurentis notifications@github.comwrote:

Can you let me know what version of Perl you are using?

On Fri, Mar 22, 2013 at 4:05 AM, karinschlangen < notifications@github.com>wrote:

Hi everybody,

the alignment with RUM stopped with the following error message:

Error running "perl /PATH/TO/RUM-Pipeline-v2.0.4/bin/../bin/sort_RUM_by_location.pl --ram 6 /PATH/TO/OUTPUT/chunks/RUM_Unique.1 -o /PATH/TO/OUTPUT/chunks/RUM_Unique.sorted.1.tmp.ykkUcgeP >> /PATH/TO/OUTPUT/chunks/chr_counts_u.1.tmp.KsHQolwR"

The stderr from that command is

Can't locate object method "newdir" via package "File::Temp" at

/PATH/TO/RUM-Pipeline-v2.0.4/bin/../lib/RUM/Script/SortRumByLocation.pm line 157.

and i don't know how to deal with that. Has anyone an idea?

The error log file ./log/rum_errors.log contains the following:

Thu Mar 21 18:38:27 2013 18618 FATAL RUM::Death - Can't locate object method "newdir" via package "File::Temp" at

/PATH/TO/RUM-Pipeline-v2.0.4/bin/../lib/RUM/Script/SortRumByLocation.pm line 157. Thu Mar 21 18:38:27 2013 8440 FATAL RUM::Death - Error running "perl

/PATH/TO/OUTPUT/RUM-Pipeline-v2.0.4/bin/../bin/sort_RUM_by_location.pl --ram 6 /PATH/TO/OUTPUT/chunks/RUM_Unique.1 -o /PATH/TO/OUTPUT/chunks/RUM_Unique.sorted.1.tmp.ykkUcgeP >> /PATH/TO/OUTPUT/chunks/chr_counts_u.1.tmp.KsHQolwR"

The stderr from that command is

Can't locate object method "newdir" via package "File::Temp" at

/PATH/TO/bin/RUM-Pipeline-v2.0.4/bin/../lib/RUM/Script/SortRumByLocation.pm

line 157.

The error log file ./log/rum_errors.log may have more details. ./log/rum_errors.log (END)

— Reply to this email directly or view it on GitHub< https://github.com/PGFI/rum/issues/169> .

— Reply to this email directly or view it on GitHub< https://github.com/PGFI/rum/issues/169#issuecomment-15298541> .

— Reply to this email directly or view it on GitHub< https://github.com/PGFI/rum/issues/169#issuecomment-15299238> .

— Reply to this email directly or view it on GitHubhttps://github.com/PGFI/rum/issues/169#issuecomment-15303064 .

karinschlangen commented 11 years ago

Hi Mike,

now it worked!

Thanks again! Karin

On Fri, Mar 22, 2013 at 5:04 PM, Karin Schlangen karinschlangen@gmail.comwrote:

Hi Mike,

i changed the file and started the mapping again. I will let you know if it works.

Thanks a lot! Karin

On Fri, Mar 22, 2013 at 4:28 PM, Mike DeLaurentis < notifications@github.com> wrote:

It looks like I'm accidentally using a feature that was introduced in Perl 5.12. I just committed a change that will fix it, which will be available the next time we tag a release. In the meantime, you can fix it locally by opening lib/RUM/Script/SortRumByLocation.pm and changing the line that contains:

my $tempdir = File::Temp->newdir;

to

my $tempdir = File::Temp::tempdir(CLEANUP => 1);

That should be around line 165 of that file. Can you please let me know if that works for you?

Thanks,

Mike

On Fri, Mar 22, 2013 at 10:24 AM, karinschlangen notifications@github.comwrote:

Hi Mike,

i am using perl v5.10.0

running on a mac.

Thanks!

On Fri, Mar 22, 2013 at 3:11 PM, Mike DeLaurentis notifications@github.comwrote:

Can you let me know what version of Perl you are using?

On Fri, Mar 22, 2013 at 4:05 AM, karinschlangen < notifications@github.com>wrote:

Hi everybody,

the alignment with RUM stopped with the following error message:

Error running "perl /PATH/TO/RUM-Pipeline-v2.0.4/bin/../bin/sort_RUM_by_location.pl --ram 6 /PATH/TO/OUTPUT/chunks/RUM_Unique.1 -o /PATH/TO/OUTPUT/chunks/RUM_Unique.sorted.1.tmp.ykkUcgeP >> /PATH/TO/OUTPUT/chunks/chr_counts_u.1.tmp.KsHQolwR"

The stderr from that command is

Can't locate object method "newdir" via package "File::Temp" at

/PATH/TO/RUM-Pipeline-v2.0.4/bin/../lib/RUM/Script/SortRumByLocation.pm line 157.

and i don't know how to deal with that. Has anyone an idea?

The error log file ./log/rum_errors.log contains the following:

Thu Mar 21 18:38:27 2013 18618 FATAL RUM::Death - Can't locate object method "newdir" via package "File::Temp" at

/PATH/TO/RUM-Pipeline-v2.0.4/bin/../lib/RUM/Script/SortRumByLocation.pm line 157. Thu Mar 21 18:38:27 2013 8440 FATAL RUM::Death - Error running "perl

/PATH/TO/OUTPUT/RUM-Pipeline-v2.0.4/bin/../bin/sort_RUM_by_location.pl --ram 6 /PATH/TO/OUTPUT/chunks/RUM_Unique.1 -o /PATH/TO/OUTPUT/chunks/RUM_Unique.sorted.1.tmp.ykkUcgeP >> /PATH/TO/OUTPUT/chunks/chr_counts_u.1.tmp.KsHQolwR"

The stderr from that command is

Can't locate object method "newdir" via package "File::Temp" at

/PATH/TO/bin/RUM-Pipeline-v2.0.4/bin/../lib/RUM/Script/SortRumByLocation.pm

line 157.

The error log file ./log/rum_errors.log may have more details. ./log/rum_errors.log (END)

— Reply to this email directly or view it on GitHub< https://github.com/PGFI/rum/issues/169> .

— Reply to this email directly or view it on GitHub< https://github.com/PGFI/rum/issues/169#issuecomment-15298541> .

— Reply to this email directly or view it on GitHub< https://github.com/PGFI/rum/issues/169#issuecomment-15299238> .

— Reply to this email directly or view it on GitHubhttps://github.com/PGFI/rum/issues/169#issuecomment-15303064 .