Enhancing non-Perl bioinformatic applications with #Perl: Building novel, component based applications using Object Orientation, PDL, Alien, FFI, Inline and OpenMP - Archive ouverte HAL https://hal.science/hal-04606172v1

Preprint for the #TPRC2024 talk to be delivered in 10days

submitted by /u/ReplacementSlight413
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This might be Perl/docker-perl#161 but if I filed this in the wrong place, let me know. Keeping these things current is the sort of thing I'd pay for.

Pulling perl images locally give the same warnings for old perl versions, although my local docker will still run them:

$ docker pull perl:5.14 5.14: Pulling from library/perl Image docker.io/library/perl:5.14 uses outdated schema1 manifest format. Please upgrade to a schema2 image for better future compatibility. More information at https://docs.docker.com/registry/spec/deprecated-schema-v1/ 

/usr/bin/docker pull perl:5.14 5.14: Pulling from library/perl [DEPRECATION NOTICE] Docker Image Format v1 and Docker Image manifest version 2, schema 1 support is disabled by default and will be removed in an upcoming release. Suggest the author of docker.io/library/perl:5.14 to upgrade the image to the OCI Format or Docker Image manifest v2, schema 2. More information at https://docs.docker.com/go/deprecated-image-specs/ Warning: Docker pull failed with exit code 1, back off 5.148 seconds before retry. /usr/bin/docker pull perl:5.14 5.14: Pulling from library/perl [DEPRECATION NOTICE] Docker Image Format v1 and Docker Image manifest version 2, schema 1 support is disabled by default and will be removed in an upcoming release. Suggest the author of docker.io/library/perl:5.14 to upgrade the image to the OCI Format or Docker Image manifest v2, schema 2. More information at https://docs.docker.com/go/deprecated-image-specs/ Warning: Docker pull failed with exit code 1, back off 4.06 seconds before retry. /usr/bin/docker pull perl:5.14 5.14: Pulling from library/perl [DEPRECATION NOTICE] Docker Image Format v1 and Docker Image manifest version 2, schema 1 support is disabled by default and will be removed in an upcoming release. Suggest the author of docker.io/library/perl:5.14 to upgrade the image to the OCI Format or Docker Image manifest v2, schema 2. More information at https://docs.docker.com/go/deprecated-image-specs/ Error: Docker pull failed with exit code 1 

 matrix: os: - ubuntu-22.04 perl-version: - '5.8' - '5.10' - '5.12' - '5.14' - '5.16' - '5.18' - '5.20' - '5.22' - '5.24' - '5.26' - '5.28' - '5.30' - '5.32' - '5.34' - '5.36' - 'latest' container: image: perl:${{ matrix.perl-version }} 

GitHub Actions says "upgrade the image to the OCI Format or Docker Image manifest v2, schema 2." · Issue #161 · Perl/docker-perl

Today I started seeing this, which means that all of my Perl testing is borked (thanks for the heads up GitHub). I think you are the source I'm pulling from, but if I'm not, do you know where I sho...

^GitHub

I have an input string that has "comments" in it that are in the form of: everything after a ; is considered a comment. I want to remove all comments from the string and get the raw text out. This is a pretty simple regexp replace except for the fact that ; characters are valid non-comments inside of double quoted strings.

How can I improve the remove_comments() function to handle quoted strings with semi-colons in them correctly?

```perl use v5.36;

my $str = 'Raw data ; This is a full-line comment More data ; comment after it Some data "and a quoted string; this is NOT a comment"';

my $clean = remove_comments($str);

print "Before:\n$str\n\nAfter:\n$clean\n";

sub remove_comments { my $in = shift();

$in =~ s/;.*//g; # Remove everything after the ; to EOL return $in; 

submitted by /u/scottchiefbaker
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Hi,

im looking to put my website written in perl that currently runs locally inside apache out on the internet.

I dont want to host myself, and i dont have lots of spare time to config or money to spend for a vps.

Does anyone have experiences and can recommend a webhoster for maybe 10-15 bucks a month where i can just get a simple interface with ssh, where i can put an index.cgi somewhere(dont care if its in cgi-bin or public_html or something else,

i want something where i can just checkout my git repo thta contains index.cgi in its root and just works.

Thank you in advance!

submitted by /u/throwawaybambo
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I am hopeful someone has done this before as I'm stuck... I have a 3TB disk image file and I am trying to find all the different email addresses that I've used over the past 22 years.

I can use hex editor tools to find them but it takes days to look at the data and pick out even a handful of matches.

I use Perl regularly but I normally scan text files and do non binary file actions. That's easy since I can do a line by line search. But binary seems different.

If I want to search for zeropoint@ (no domain because I've used dozens of ISPs over the years and that's why I am trying to figure this out.) inside the entire 3TB file, what's the best way to do that? I can dump the results to a file and then clean it up but the search part has me stuck

Thank you

submitted by /u/zeropointlabs
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Mo utilities for email.

Changes for 0.02 - 2024-04-26T23:02:53+02:00

• Add tests for error parameters.
• Rewrite the tests so that the functional tests are first and then the errors.

Hi! Asking for a wisdom here...

We have a module that modifies signal handler $SIG{__DIE__} to log information and to die afterwards. Hundreds of scripts relied on this module which worked fine in perl 5.10.1.

Recently we had the opportunity to install several Perl versions but unfortunately a large number of scripts that used to work with Perl 5.10.1 now behave differently:

• Failed in 5.14.4: /home/dev/perl-5.14.4/bin/perl -wc test.pl RECEIVED SIGNAL - S_IFFIFO is not a valid Fcntl macro at /home/dev/perl-5.14.4/lib/5.14.4/File/stat.pm line 41
• Worked without changes in 5.26.3: /home/dev/perl-5.26.3/bin/perl -wc test.pl test.pl syntax OK
• Worked without changes in 5.38.2: /home/dev/perl-5.38.2/bin/perl -wc test.pl test.pl syntax OK

Many of the scripts can only be updated to 5.14.4 due to the huge jumps between 5.10 and 3.58; But we are stuck on that failures.

Was there an internal Perl change in 5.14 which cause the failures but works on other recent versions without any update on the scripts?

Cheerio!

submitted by /u/Longjumping_Army_525
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Sanity-check calling context

Changes for 0.04

• (no code changes)
• Switched to MIT license.
• Switched README from POD to Markdown.
• Removed Travis CI.

Sort lines of text by a SortKey module

Changes for 0.001 - 2024-03-07

• First release.

Sort lines of text by a Comparer module

Changes for 0.002 - 2024-03-07

• No functional changes.
• [doc] Mention some related links.

An assortment of date-/time-related CLI utilities

Changes for 0.128 - 2024-03-07

• [clis strftime, strftimeq] Use localtime() instead of gmtime(). We can still show UTC using "TZ=UTC strftime ...".

I understand that many disagree with this statement, but it really makes it easier to build distributions for people who not monks. Wish the documentation was more detailed

submitted by /u/ReplacementSlight413
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Sah schemas related to BCA (Bank Central Asia) bank

Changes for 0.002 - 2024-04-03

• Rename module/dist Sah-Schema{s,Bundle}-* following rename of Sah-Schema{s,Bundle} (for visual clarity and consistency with naming of other bundles).

search nested hashref/arrayref structures using JSONPath

Changes for 1.0.5 - 2024-04-22T16:10:46-05:00

simulating paper and pencil techniques for basic arithmetic operations

Changes for 0.01 - 2024-04

• First version, with the four basic operations, plus square-root, GCD and radix conversion. And HTML rendering

Use a type to validate values in a deep comparison.

Changes for 1.0.1 - 2024-04-22

• Add Test2::Tools::Type

An open source web-based network management tool.

Changes for 2.076000 - 2024-04-22

• NEW FEATURES
• ENHANCEMENTS
• BUG FIXES

Silverpeak Orchestrator REST API client library

Changes for 0.011000 - 2024-04-22T17:58:39+02:00

• add support for version 9.3+ API endpoints

A module that performs semantic similarity in PXF/BFF data structures and beyond (JSON|YAML)

Changes for 0.07 - 2024-04-22T00:00:00Z

• Excluded keys with {} or [] values (e.g. subject.vitalStatus: {})
• Precompiled regex patterns where possible
• Schema validation errors related to weights are now directed to STDERR
• Added support for variables with non-word characters (e.g., "Survey.Timestamp.1")

Pango style markup formatting

Changes for 0.036 - 2024-04-22

• Introducing struts. Update SYNOPOSIS example to modern PDF::API2 conventions. Fix/enhance drawing of brackgrounds. Fix problem with wrongly calculated underlining.

My environment is perl/5.18.2 on CentOs 7

I'm trying to use a SWIG generated module in perl, which has a c plus plus backend. The backend.cpp sets an environment variable, $MY_ENV_VAR =1

But when I try to access this in perl, using $ENV{MY_ENV_VAR} this is undef.

However doing something like print echo $MY_ENV_VAR works

So the variable is set in the process, but it's not reflected automatically since nothing updates the $ENV data structure.

I'm assuming it may work using some getEnv like mechanism, but is there a way to reset/ refresh the $ENV that it rebuilds itself from the current environment?

submitted by /u/sarcasmwala
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By default cpanm drops Perl modules into ~/perl5. How do I tell cpanm to use a different location, such as ~/.local/share/perl5 instead?

submitted by /u/s-ro_mojosa
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Get stock and mutual fund quotes from various exchanges

Changes for 1.61_01 - 2024-04-21T17:50:16-07:00

• YahooWeb.pm - Issue #377. Modified YahooWeb to account for changes from Yahoo.

Sah schemas related to SortKey

Changes for 0.002 - 2024-03-07

• Rename module/dist Sah-Schema{s,Bundle}-SortKey.

Perl Data Language

Changes for 2.088 - 2024-04-22

• Slatec::ch{ic,sp} work arrays now [t]
• add Slatec::bvalu
• add Func::{pchip,spline}, and a demo
• add Ufunc::diff2
• extra ) on end of Pars now an error
• PP dim sizes can be =CALC(...) instead of explicit RedoDimsCode
• PP add loop(n=start:end:inc) idiom to stop not at end and have non-1 inc
• updated README.md - thanks @falsifian
• support T_PTROBJ in typemap

an interactive plotting widget and library for PDL and Prima

Changes for 0.21 - 2024-04-22

• demo now only loads Prima when run, reducing perldl problems

demonstrate PDL::Graphics::PLplot capabilities

Changes for 0.84 - 2024-04-22

• add perldl demo
• fix plFreeGrid to use free that matches the allocator
• pl{Alloc,Free}{,2d}Grid error if not match allocating and freeing routine
• minimum PDL 2.083 due to output OtherPars

Fast Perl SSG: now with automatic Language Translation via OCI and translate.pl. Check it out at

https://github.com/SunStarSys/orion

submitted by /u/joesuf4
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GitHub - SunStarSys/orion: SunStar Systems' Orion Enterprise Wiki SSG

SunStar Systems' Orion Enterprise Wiki SSG. Contribute to SunStarSys/orion development by creating an account on GitHub.

<sup>GitHub</sup>

Tags helper for table view.

Changes for 0.06 - 2024-04-21T17:26:14+02:00

• Fix of setting of table data. Copy in this time.

Tags helper for CPAN::Changes object.

Changes for 0.04 - 2024-04-21T16:06:08+02:00

• Add trivial Changes file and test on it.
• Fix output on ex1.changes test file.

parses .pm file as PAUSE does

Changes for 0.47 - 2024-04-21

• Improve class detection

Plack application for running Tags::HTML objects.

Changes for 0.17 - 2024-04-21T12:34:17+02:00

• Add test for 'css_data'.
• Rewrite examples in doc to version with indented output.

Perl extension for finding the memory usage of Perl variables

Changes for 0.83_50 - 2024-04-21

• patch from Slaven:
• CvOUTSIDE is again set on all cloned subs [CPAN #149902]