From bix at sendu.me.uk Wed Dec 6 17:39:49 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 06 Dec 2006 22:39:49 +0000 Subject: [Bioperl-announce-l] Bioperl 1.5.2 Release Message-ID: <457746B5.2020006@sendu.me.uk> I am proud to announce the final release of Bioperl 1.5.2. http://www.bioperl.org/wiki/Release_1.5.2 bioperl (core): cpan>install S/SE/SENDU/bioperl-1.5.2_100.tar.gz http://bioperl.org/DIST/bioperl-1.5.2_100.tar.gz http://bioperl.org/DIST/bioperl-1.5.2_100.tar.bz2 http://bioperl.org/DIST/bioperl-1.5.2_100.zip bioperl-run: cpan>install S/SE/SENDU/bioperl-run-1.5.2_100.tar.gz http://bioperl.org/DIST/bioperl-run-1.5.2_100.tar.gz http://bioperl.org/DIST/bioperl-run-1.5.2_100.tar.bz2 http://bioperl.org/DIST/bioperl-run-1.5.2_100.zip bioperl-db: cpan>install S/SE/SENDU/bioperl-db-1.5.2_100.tar.gz http://bioperl.org/DIST/bioperl-db-1.5.2_100.tar.gz http://bioperl.org/DIST/bioperl-db-1.5.2_100.tar.bz2 http://bioperl.org/DIST/bioperl-db-1.5.2_100.zip bioperl-network: cpan>install S/SE/SENDU/bioperl-network-1.5.2_100.tar.gz http://bioperl.org/DIST/bioperl-network-1.5.2_100.tar.gz http://bioperl.org/DIST/bioperl-network-1.5.2_100.tar.bz2 http://bioperl.org/DIST/bioperl-network-1.5.2_100.zip http://bioperl.org/DIST/SIGNATURES.md5 (all are also available via CVS, and for Windows users, using the Perl Package Manager - see the wiki for details) The other bioperl packages (bioperl-ext, bioperl-gui, bioperl-pedigree and bioperl-pipeline) did not see a unified release for 1.5.2. This release represents a developer release which has been thoroughly tested. We consider it the most stable (in terms of bugs) version of Bioperl and believe it to be suitable for most people. It is marked 'developer' or even 'unstable' because its API may change on short notice. It will also not be maintained or supported beyond the next bioperl release. 1.5.2 introduces the following new (core) features: * Taxonomy (Bio::Species) overhaul * Bio::Map improvements * Bio::SearchIO speedup * Build.PL installation For details, and a complete change log, see the wiki. API documentation is available here: http://doc.bioperl.org/ Acknowledgements: Enumerable thanks are due for the tireless efforts of Christopher Fields (bug fixing, testing, documentation, discussion), Nathan Haigh (Windows&pre-requisite issues, testing) and Mauricio Herrera Cuadra (testing, documentation, support). Feedback and ideas provided by Hilmar Lapp, Jason Stajich, Torsten Seemann and others on the mailing list and elsewhere proved invaluable. None of this would have been possible without the behind-the-scenes work of the open-bio support team. I'd also like to acknowledge Andreas J. Koenig for his help with CPAN matters. Finally, thank you to everyone who tried out the release candidates, and especially those that took the time to file bug reports or report problems. Remember, Bioperl can only go from strength to strength with /your/ help. If you'd like to experience the fame and fortune that naturally follow becoming a Bioperl developer (?!), become one! http://www.bioperl.org/wiki/Becoming_a_developer On behalf of the Bioperl team, Sendu Bala. From cjfields at uiuc.edu Wed Dec 6 21:30:44 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Dec 2006 20:30:44 -0600 Subject: [Bioperl-announce-l] [Bioperl-l] Bioperl 1.5.2 Release In-Reply-To: <457746B5.2020006@sendu.me.uk> Message-ID: <000001c719a7$b48beb90$15327e82@pyrimidine> Great job Sendu! A bit of icing on the cake: all the WinXP PPMs (core, db, network, run) installed w/o a hitch following normal instructions using PPM4 (GUI and command line shell) using clean ActiveState installations. Looks like all the correct prereqs were installed with shell (only XML::SAX::ExpatXS was left out in the GUI installation for reasons outlined before). I'll run more tests tomorrow to see if tests pass with the installed bioperl (this should catch any prereq issues with PPM installation we missed). chris > I am proud to announce the final release of Bioperl 1.5.2. > > http://www.bioperl.org/wiki/Release_1.5.2 > > bioperl (core): > cpan>install S/SE/SENDU/bioperl-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-1.5.2_100.tar.bz2 > http://bioperl.org/DIST/bioperl-1.5.2_100.zip > > bioperl-run: > cpan>install S/SE/SENDU/bioperl-run-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-run-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-run-1.5.2_100.tar.bz2 > http://bioperl.org/DIST/bioperl-run-1.5.2_100.zip > > bioperl-db: > cpan>install S/SE/SENDU/bioperl-db-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-db-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-db-1.5.2_100.tar.bz2 > http://bioperl.org/DIST/bioperl-db-1.5.2_100.zip > > bioperl-network: > cpan>install S/SE/SENDU/bioperl-network-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-network-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-network-1.5.2_100.tar.bz2 > http://bioperl.org/DIST/bioperl-network-1.5.2_100.zip > > http://bioperl.org/DIST/SIGNATURES.md5 > > (all are also available via CVS, and for Windows users, using > the Perl Package Manager - see the wiki for details) > > The other bioperl packages (bioperl-ext, bioperl-gui, > bioperl-pedigree and bioperl-pipeline) did not see a unified > release for 1.5.2. > > > > This release represents a developer release which has been thoroughly > tested. We consider it the most stable (in terms of bugs) version of > Bioperl and believe it to be suitable for most people. It is marked > 'developer' or even 'unstable' because its API may change on short > notice. It will also not be maintained or supported beyond the next > bioperl release. > > 1.5.2 introduces the following new (core) features: > > * Taxonomy (Bio::Species) overhaul > * Bio::Map improvements > * Bio::SearchIO speedup > * Build.PL installation > > For details, and a complete change log, see the wiki. > > API documentation is available here: http://doc.bioperl.org/ > > > Acknowledgements: > Enumerable thanks are due for the tireless efforts of > Christopher Fields > (bug fixing, testing, documentation, discussion), Nathan Haigh > (Windows&pre-requisite issues, testing) and Mauricio Herrera Cuadra > (testing, documentation, support). Feedback and ideas > provided by Hilmar > Lapp, Jason Stajich, Torsten Seemann and others on the > mailing list and > elsewhere proved invaluable. None of this would have been possible > without the behind-the-scenes work of the open-bio support team. I'd > also like to acknowledge Andreas J. Koenig for his help with > CPAN matters. > > Finally, thank you to everyone who tried out the release > candidates, and > especially those that took the time to file bug reports or > report problems. > > > Remember, Bioperl can only go from strength to strength with /your/ > help. If you'd like to experience the fame and fortune that naturally > follow becoming a Bioperl developer (?!), become one! > http://www.bioperl.org/wiki/Becoming_a_developer > > On behalf of the Bioperl team, > Sendu Bala. From arareko at campus.iztacala.unam.mx Wed Dec 6 22:53:21 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Wed, 06 Dec 2006 21:53:21 -0600 Subject: [Bioperl-announce-l] [Bioperl-l] Bioperl 1.5.2 Release In-Reply-To: <457746B5.2020006@sendu.me.uk> References: <457746B5.2020006@sendu.me.uk> Message-ID: <45779031.3050202@campus.iztacala.unam.mx> This has been a great effort. Congrats and thanks to everyone involved! Mauricio. Sendu Bala wrote: > I am proud to announce the final release of Bioperl 1.5.2. > > http://www.bioperl.org/wiki/Release_1.5.2 > > bioperl (core): > cpan>install S/SE/SENDU/bioperl-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-1.5.2_100.tar.bz2 > http://bioperl.org/DIST/bioperl-1.5.2_100.zip > > bioperl-run: > cpan>install S/SE/SENDU/bioperl-run-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-run-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-run-1.5.2_100.tar.bz2 > http://bioperl.org/DIST/bioperl-run-1.5.2_100.zip > > bioperl-db: > cpan>install S/SE/SENDU/bioperl-db-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-db-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-db-1.5.2_100.tar.bz2 > http://bioperl.org/DIST/bioperl-db-1.5.2_100.zip > > bioperl-network: > cpan>install S/SE/SENDU/bioperl-network-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-network-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-network-1.5.2_100.tar.bz2 > http://bioperl.org/DIST/bioperl-network-1.5.2_100.zip > > http://bioperl.org/DIST/SIGNATURES.md5 > > (all are also available via CVS, and for Windows users, using the Perl > Package Manager - see the wiki for details) > > The other bioperl packages (bioperl-ext, bioperl-gui, bioperl-pedigree > and bioperl-pipeline) did not see a unified release for 1.5.2. > > > > This release represents a developer release which has been thoroughly > tested. We consider it the most stable (in terms of bugs) version of > Bioperl and believe it to be suitable for most people. It is marked > 'developer' or even 'unstable' because its API may change on short > notice. It will also not be maintained or supported beyond the next > bioperl release. > > 1.5.2 introduces the following new (core) features: > > * Taxonomy (Bio::Species) overhaul > * Bio::Map improvements > * Bio::SearchIO speedup > * Build.PL installation > > For details, and a complete change log, see the wiki. > > API documentation is available here: http://doc.bioperl.org/ > > > Acknowledgements: > Enumerable thanks are due for the tireless efforts of Christopher Fields > (bug fixing, testing, documentation, discussion), Nathan Haigh > (Windows&pre-requisite issues, testing) and Mauricio Herrera Cuadra > (testing, documentation, support). Feedback and ideas provided by Hilmar > Lapp, Jason Stajich, Torsten Seemann and others on the mailing list and > elsewhere proved invaluable. None of this would have been possible > without the behind-the-scenes work of the open-bio support team. I'd > also like to acknowledge Andreas J. Koenig for his help with CPAN matters. > > Finally, thank you to everyone who tried out the release candidates, and > especially those that took the time to file bug reports or report problems. > > > Remember, Bioperl can only go from strength to strength with /your/ > help. If you'd like to experience the fame and fortune that naturally > follow becoming a Bioperl developer (?!), become one! > http://www.bioperl.org/wiki/Becoming_a_developer > > On behalf of the Bioperl team, > Sendu Bala. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From bix at sendu.me.uk Wed Dec 6 22:39:49 2006 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 06 Dec 2006 22:39:49 +0000 Subject: [Bioperl-announce-l] Bioperl 1.5.2 Release Message-ID: <457746B5.2020006@sendu.me.uk> I am proud to announce the final release of Bioperl 1.5.2. http://www.bioperl.org/wiki/Release_1.5.2 bioperl (core): cpan>install S/SE/SENDU/bioperl-1.5.2_100.tar.gz http://bioperl.org/DIST/bioperl-1.5.2_100.tar.gz http://bioperl.org/DIST/bioperl-1.5.2_100.tar.bz2 http://bioperl.org/DIST/bioperl-1.5.2_100.zip bioperl-run: cpan>install S/SE/SENDU/bioperl-run-1.5.2_100.tar.gz http://bioperl.org/DIST/bioperl-run-1.5.2_100.tar.gz http://bioperl.org/DIST/bioperl-run-1.5.2_100.tar.bz2 http://bioperl.org/DIST/bioperl-run-1.5.2_100.zip bioperl-db: cpan>install S/SE/SENDU/bioperl-db-1.5.2_100.tar.gz http://bioperl.org/DIST/bioperl-db-1.5.2_100.tar.gz http://bioperl.org/DIST/bioperl-db-1.5.2_100.tar.bz2 http://bioperl.org/DIST/bioperl-db-1.5.2_100.zip bioperl-network: cpan>install S/SE/SENDU/bioperl-network-1.5.2_100.tar.gz http://bioperl.org/DIST/bioperl-network-1.5.2_100.tar.gz http://bioperl.org/DIST/bioperl-network-1.5.2_100.tar.bz2 http://bioperl.org/DIST/bioperl-network-1.5.2_100.zip http://bioperl.org/DIST/SIGNATURES.md5 (all are also available via CVS, and for Windows users, using the Perl Package Manager - see the wiki for details) The other bioperl packages (bioperl-ext, bioperl-gui, bioperl-pedigree and bioperl-pipeline) did not see a unified release for 1.5.2. This release represents a developer release which has been thoroughly tested. We consider it the most stable (in terms of bugs) version of Bioperl and believe it to be suitable for most people. It is marked 'developer' or even 'unstable' because its API may change on short notice. It will also not be maintained or supported beyond the next bioperl release. 1.5.2 introduces the following new (core) features: * Taxonomy (Bio::Species) overhaul * Bio::Map improvements * Bio::SearchIO speedup * Build.PL installation For details, and a complete change log, see the wiki. API documentation is available here: http://doc.bioperl.org/ Acknowledgements: Enumerable thanks are due for the tireless efforts of Christopher Fields (bug fixing, testing, documentation, discussion), Nathan Haigh (Windows&pre-requisite issues, testing) and Mauricio Herrera Cuadra (testing, documentation, support). Feedback and ideas provided by Hilmar Lapp, Jason Stajich, Torsten Seemann and others on the mailing list and elsewhere proved invaluable. None of this would have been possible without the behind-the-scenes work of the open-bio support team. I'd also like to acknowledge Andreas J. Koenig for his help with CPAN matters. Finally, thank you to everyone who tried out the release candidates, and especially those that took the time to file bug reports or report problems. Remember, Bioperl can only go from strength to strength with /your/ help. If you'd like to experience the fame and fortune that naturally follow becoming a Bioperl developer (?!), become one! http://www.bioperl.org/wiki/Becoming_a_developer On behalf of the Bioperl team, Sendu Bala. From cjfields at uiuc.edu Thu Dec 7 02:30:44 2006 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Dec 2006 20:30:44 -0600 Subject: [Bioperl-announce-l] [Bioperl-l] Bioperl 1.5.2 Release In-Reply-To: <457746B5.2020006@sendu.me.uk> Message-ID: <000001c719a7$b48beb90$15327e82@pyrimidine> Great job Sendu! A bit of icing on the cake: all the WinXP PPMs (core, db, network, run) installed w/o a hitch following normal instructions using PPM4 (GUI and command line shell) using clean ActiveState installations. Looks like all the correct prereqs were installed with shell (only XML::SAX::ExpatXS was left out in the GUI installation for reasons outlined before). I'll run more tests tomorrow to see if tests pass with the installed bioperl (this should catch any prereq issues with PPM installation we missed). chris > I am proud to announce the final release of Bioperl 1.5.2. > > http://www.bioperl.org/wiki/Release_1.5.2 > > bioperl (core): > cpan>install S/SE/SENDU/bioperl-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-1.5.2_100.tar.bz2 > http://bioperl.org/DIST/bioperl-1.5.2_100.zip > > bioperl-run: > cpan>install S/SE/SENDU/bioperl-run-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-run-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-run-1.5.2_100.tar.bz2 > http://bioperl.org/DIST/bioperl-run-1.5.2_100.zip > > bioperl-db: > cpan>install S/SE/SENDU/bioperl-db-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-db-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-db-1.5.2_100.tar.bz2 > http://bioperl.org/DIST/bioperl-db-1.5.2_100.zip > > bioperl-network: > cpan>install S/SE/SENDU/bioperl-network-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-network-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-network-1.5.2_100.tar.bz2 > http://bioperl.org/DIST/bioperl-network-1.5.2_100.zip > > http://bioperl.org/DIST/SIGNATURES.md5 > > (all are also available via CVS, and for Windows users, using > the Perl Package Manager - see the wiki for details) > > The other bioperl packages (bioperl-ext, bioperl-gui, > bioperl-pedigree and bioperl-pipeline) did not see a unified > release for 1.5.2. > > > > This release represents a developer release which has been thoroughly > tested. We consider it the most stable (in terms of bugs) version of > Bioperl and believe it to be suitable for most people. It is marked > 'developer' or even 'unstable' because its API may change on short > notice. It will also not be maintained or supported beyond the next > bioperl release. > > 1.5.2 introduces the following new (core) features: > > * Taxonomy (Bio::Species) overhaul > * Bio::Map improvements > * Bio::SearchIO speedup > * Build.PL installation > > For details, and a complete change log, see the wiki. > > API documentation is available here: http://doc.bioperl.org/ > > > Acknowledgements: > Enumerable thanks are due for the tireless efforts of > Christopher Fields > (bug fixing, testing, documentation, discussion), Nathan Haigh > (Windows&pre-requisite issues, testing) and Mauricio Herrera Cuadra > (testing, documentation, support). Feedback and ideas > provided by Hilmar > Lapp, Jason Stajich, Torsten Seemann and others on the > mailing list and > elsewhere proved invaluable. None of this would have been possible > without the behind-the-scenes work of the open-bio support team. I'd > also like to acknowledge Andreas J. Koenig for his help with > CPAN matters. > > Finally, thank you to everyone who tried out the release > candidates, and > especially those that took the time to file bug reports or > report problems. > > > Remember, Bioperl can only go from strength to strength with /your/ > help. If you'd like to experience the fame and fortune that naturally > follow becoming a Bioperl developer (?!), become one! > http://www.bioperl.org/wiki/Becoming_a_developer > > On behalf of the Bioperl team, > Sendu Bala. From arareko at campus.iztacala.unam.mx Thu Dec 7 03:53:21 2006 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Wed, 06 Dec 2006 21:53:21 -0600 Subject: [Bioperl-announce-l] [Bioperl-l] Bioperl 1.5.2 Release In-Reply-To: <457746B5.2020006@sendu.me.uk> References: <457746B5.2020006@sendu.me.uk> Message-ID: <45779031.3050202@campus.iztacala.unam.mx> This has been a great effort. Congrats and thanks to everyone involved! Mauricio. Sendu Bala wrote: > I am proud to announce the final release of Bioperl 1.5.2. > > http://www.bioperl.org/wiki/Release_1.5.2 > > bioperl (core): > cpan>install S/SE/SENDU/bioperl-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-1.5.2_100.tar.bz2 > http://bioperl.org/DIST/bioperl-1.5.2_100.zip > > bioperl-run: > cpan>install S/SE/SENDU/bioperl-run-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-run-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-run-1.5.2_100.tar.bz2 > http://bioperl.org/DIST/bioperl-run-1.5.2_100.zip > > bioperl-db: > cpan>install S/SE/SENDU/bioperl-db-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-db-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-db-1.5.2_100.tar.bz2 > http://bioperl.org/DIST/bioperl-db-1.5.2_100.zip > > bioperl-network: > cpan>install S/SE/SENDU/bioperl-network-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-network-1.5.2_100.tar.gz > http://bioperl.org/DIST/bioperl-network-1.5.2_100.tar.bz2 > http://bioperl.org/DIST/bioperl-network-1.5.2_100.zip > > http://bioperl.org/DIST/SIGNATURES.md5 > > (all are also available via CVS, and for Windows users, using the Perl > Package Manager - see the wiki for details) > > The other bioperl packages (bioperl-ext, bioperl-gui, bioperl-pedigree > and bioperl-pipeline) did not see a unified release for 1.5.2. > > > > This release represents a developer release which has been thoroughly > tested. We consider it the most stable (in terms of bugs) version of > Bioperl and believe it to be suitable for most people. It is marked > 'developer' or even 'unstable' because its API may change on short > notice. It will also not be maintained or supported beyond the next > bioperl release. > > 1.5.2 introduces the following new (core) features: > > * Taxonomy (Bio::Species) overhaul > * Bio::Map improvements > * Bio::SearchIO speedup > * Build.PL installation > > For details, and a complete change log, see the wiki. > > API documentation is available here: http://doc.bioperl.org/ > > > Acknowledgements: > Enumerable thanks are due for the tireless efforts of Christopher Fields > (bug fixing, testing, documentation, discussion), Nathan Haigh > (Windows&pre-requisite issues, testing) and Mauricio Herrera Cuadra > (testing, documentation, support). Feedback and ideas provided by Hilmar > Lapp, Jason Stajich, Torsten Seemann and others on the mailing list and > elsewhere proved invaluable. None of this would have been possible > without the behind-the-scenes work of the open-bio support team. I'd > also like to acknowledge Andreas J. Koenig for his help with CPAN matters. > > Finally, thank you to everyone who tried out the release candidates, and > especially those that took the time to file bug reports or report problems. > > > Remember, Bioperl can only go from strength to strength with /your/ > help. If you'd like to experience the fame and fortune that naturally > follow becoming a Bioperl developer (?!), become one! > http://www.bioperl.org/wiki/Becoming_a_developer > > On behalf of the Bioperl team, > Sendu Bala. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM