From 19d887359ff4640d9b23ca1f2e57fc980d5c5561 Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Fri, 11 Oct 2019 14:31:32 +0200 Subject: [PATCH 1/7] perl: Remove Remove perl from /usr/local/... --- perl-5.12.1-2.bee | 51 ----------------------------------------------- 1 file changed, 51 deletions(-) delete mode 100755 perl-5.12.1-2.bee diff --git a/perl-5.12.1-2.bee b/perl-5.12.1-2.bee deleted file mode 100755 index b594aaab0..000000000 --- a/perl-5.12.1-2.bee +++ /dev/null @@ -1,51 +0,0 @@ -#!/bin/env beesh - -PGRP=( uncategorized ) - -SRCURL[0]="http://cpan.org/src/5.0/perl-5.12.1.tar.bz2" - -PATCHES[0]="" - -# EXCLUDE="" - -B=${S} - -PREFIX=/usr/local - -USRBIN=/usr/bin - -mee_patch() { - bee_patch - - - sed -i -e "s|BUILD_ZLIB\s*= True|BUILD_ZLIB = False|" \ - -e "s|INCLUDE\s*= ./zlib-src|INCLUDE = /usr/include|" \ - -e "s|LIB\s*= ./zlib-src|LIB = /usr/lib|" \ - cpan/Compress-Raw-Zlib/config.in - -} - -mee_configure() { - sh Configure -des \ - -Dprefix=${PREFIX} \ - -Dvendorprefix=${PREFIX} \ - -Dman1dir=${MANDIR}/man1 \ - -Dman3dir=${MANDIR}/man3 \ - -Dpager="/usr/bin/less -isR" \ - -Duseithreads \ - -Accflags='-fPIC' -} - -mee_build() { - bee_build - make test -} - -mee_install() { - bee_install - - mkdir -pv ${D}${USRBIN} - - ln -sf ${BINDIR}/perl ${D}${USRBIN}/perl -} - From 1fb2671355dfa844658c17c12a84f266bf759931 Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Fri, 11 Oct 2019 14:45:55 +0200 Subject: [PATCH 2/7] perl: Remove perl modules Remove bee packages which either installed perl modules only or which provided commands which are availabe from the packaged perl. We keep some bee modules for now, which also installed into /usr/local/lib/perl5, but which provided more functionality, e.g. libraries, include files or command not available from the packaged perl: - rrdtool-1.6.0-1.x86_64 - subversion-1.6.16-1.x86_64 - wakeonlan-0.41-0.x86_64 --- Donald.be0 | 31 --------- HTTP-DAV-0.48-0.bee | 85 ----------------------- IO-Tty-1.10-0.bee | 31 --------- Linux-Inotify2-1.22-0.bee | 83 ---------------------- Linux-USBKeyboard-0.04_p1_f541008-0.bee | 83 ---------------------- Mojolicious-2.36-0.bee | 33 --------- Net-SNMP-6.0.1-0.bee | 33 --------- Term-ReadLine-Gnu-1.20-0.bee | 31 --------- Time-Period-1.24-0.bee | 83 ---------------------- Tk-804.029-0.bee | 33 --------- WWW-Dict-Leo-Org.be0 | 91 ------------------------- 11 files changed, 617 deletions(-) delete mode 100755 Donald.be0 delete mode 100755 HTTP-DAV-0.48-0.bee delete mode 100755 IO-Tty-1.10-0.bee delete mode 100755 Linux-Inotify2-1.22-0.bee delete mode 100755 Linux-USBKeyboard-0.04_p1_f541008-0.bee delete mode 100755 Mojolicious-2.36-0.bee delete mode 100755 Net-SNMP-6.0.1-0.bee delete mode 100755 Term-ReadLine-Gnu-1.20-0.bee delete mode 100755 Time-Period-1.24-0.bee delete mode 100755 Tk-804.029-0.bee delete mode 100755 WWW-Dict-Leo-Org.be0 diff --git a/Donald.be0 b/Donald.be0 deleted file mode 100755 index 41b265935..000000000 --- a/Donald.be0 +++ /dev/null @@ -1,31 +0,0 @@ -#!/usr/bin/env beesh - -# BEE_VERSION Donald-1.05-1 - -SRCURL[0]="https://github.molgen.mpg.de/donald/Donald/archive/1.05.tar.gz Donald-1.05.tar.gz" - -# PATCHURL+=() - -# build_in_sourcedir - -# sourcesubdir_append src - -#mee_extract() { -# bee_extract "${@}" -#} - -#mee_patch() { -# bee_patch "${@}" -#} - -#mee_configure() { -# bee_configure -#} - -#mee_build() { -# bee_build -#} - -#mee_install() { -# bee_install -#} diff --git a/HTTP-DAV-0.48-0.bee b/HTTP-DAV-0.48-0.bee deleted file mode 100755 index 46adbcdba..000000000 --- a/HTTP-DAV-0.48-0.bee +++ /dev/null @@ -1,85 +0,0 @@ -#!/usr/bin/env beesh - -## this file was created by bee init and should be executed to build a -## bee-package. (Additional hints are located at the end of this file.) - -############################################################################### -## The source URL(s) define the location of the sources that will be -## downloaded. Version variables may be used to simplify reuse of this bee-file. -SRCURL[0]="http://search.cpan.org/CPAN/authors/id/C/CO/COSIMO/HTTP-DAV-${PKGVERSION}.tar.gz" -############################################################################### -## Add URLs/pathes to patch files to the PATCHURL array. -## The sources will be patched in the order of the array. - -# PATCHURL+=() - -############################################################################### -## Add filename patterns to the EXCLUDE array of files that should not -## be added to you package but may be present in the image directory. - -# EXCLUDE+=() - -############################################################################### -## Uncomment the next statement, if the software may not be able to be build -## outside the source directory and need to be build inside the source -## directory. - -# build_in_sourcedir - -############################################################################### -## bee cannot detect buildtypes specified in subdirectories. -## Sometimes packages "hide" the real sources in a subdirectory named -## 'src' or 'cmake' or .. -## use 'sourcesubdir_append' to specify this directory if known. - -# sourcesubdir_append src - - -############################################################################### -## Change the default (auto-detected) steps to -## extract, patch, configure/setup, build and install the software. -## Make sure the mee_install function does install everything to the -## image directory "${D}" - -#mee_extract() { -# bee_extract "${@}" -#} - -#mee_patch() { -# bee_patch "${@}" -#} - -mee_configure() { - perl Makefile.PL DESTDIR=${D} -} - -#mee_build() { -# bee_build -#} - -#mee_install() { -# bee_install -#} -mee_install_post() { - rm ${D}/usr/local/lib/perl5/5.12.1/x86_64-linux-thread-multi/perllocal.pod - mv ${D}/usr/local/bin ${D}/usr -} -## by default this may be 'make install DESTDIR="${D}"' - -############################################################################### -## -## Additional hints: -## -## The name of this bee-file should follow the following naming convention: -## pkgname-pkgversion-pkgrevision.bee -## -## You may remove all comments as long as SRCURL[0] is set. -## -## Everything in this file will be executed in a bash environment. -## -## Build the package by executing -## './pkg-version-N.bee' or -## 'beesh ./pkg-version-N.bee' -## -## see http://beezinga.org/ -## diff --git a/IO-Tty-1.10-0.bee b/IO-Tty-1.10-0.bee deleted file mode 100755 index 7cfaa15b4..000000000 --- a/IO-Tty-1.10-0.bee +++ /dev/null @@ -1,31 +0,0 @@ -#!/usr/bin/env beesh - -SRCURL[0]="http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/IO-Tty-${PKGVERSION}.tar.gz" - -PATCHURL[0]="" - -# BEE_CONFIGURE=compat - -# EXCLUDE="" - - - -#mee_extract() { -# bee_extract ${@} -#} - -#mee_patch() { -# bee_patch ${@} -#} - -#mee_configure() { -# bee_configure -#} - -#mee_build() { -# bee_build -#} - -#mee_install() { -# bee_install -#} diff --git a/Linux-Inotify2-1.22-0.bee b/Linux-Inotify2-1.22-0.bee deleted file mode 100755 index cae5854cc..000000000 --- a/Linux-Inotify2-1.22-0.bee +++ /dev/null @@ -1,83 +0,0 @@ -#!/usr/bin/env beesh - -## this file was created by bee init and should be executed to build a -## bee-package. (Additional hints are located at the end of this file.) - -############################################################################### -## The source URL(s) define the location of the sources that will be -## downloaded. Version variables may be used to simplify reuse of this bee-file. - -SRCURL[0]="http://search.cpan.org/CPAN/authors/id/M/ML/MLEHMANN/Linux-Inotify2-${PKGVERSION}.tar.gz" - -############################################################################### -## Add URLs/pathes to patch files to the PATCHURL array. -## The sources will be patched in the order of the array. - -# PATCHURL+=() - -############################################################################### -## Add filename patterns to the EXCLUDE array of files that should not -## be added to you package but may be present in the image directory. - -# EXCLUDE+=() - -############################################################################### -## Uncomment the next statement, if the software may not be able to be build -## outside the source directory and need to be build inside the source -## directory. - -# build_in_sourcedir - -############################################################################### -## bee cannot detect buildtypes specified in subdirectories. -## Sometimes packages "hide" the real sources in a subdirectory named -## 'src' or 'cmake' or .. -## use 'sourcesubdir_append' to specify this directory if known. - -# sourcesubdir_append src - - -############################################################################### -## Change the default (auto-detected) steps to -## extract, patch, configure/setup, build and install the software. -## Make sure the mee_install function does install everything to the -## image directory "${D}" - -#mee_extract() { -# bee_extract "${@}" -#} - -#mee_patch() { -# bee_patch "${@}" -#} - -#mee_configure() { -# bee_configure -#} - -#mee_build() { -# bee_build -#} - -#mee_install() { -# bee_install -#} -## by default this may be 'make install DESTDIR="${D}"' - -############################################################################### -## -## Additional hints: -## -## The name of this bee-file should follow the following naming convention: -## pkgname-pkgversion-pkgrevision.bee -## -## You may remove all comments as long as SRCURL[0]="" is set. -## -## Everything in this file will be executed in a bash environment. -## -## Build the package by executing -## './pkg-version-N.bee' or -## 'beesh ./pkg-version-N.bee' -## -## see http://beezinga.org/ -## diff --git a/Linux-USBKeyboard-0.04_p1_f541008-0.bee b/Linux-USBKeyboard-0.04_p1_f541008-0.bee deleted file mode 100755 index 6e4aa11df..000000000 --- a/Linux-USBKeyboard-0.04_p1_f541008-0.bee +++ /dev/null @@ -1,83 +0,0 @@ -#!/usr/bin/env beesh - -## this file was created by bee init and should be executed to build a -## bee-package. (Additional hints are located at the end of this file.) - -############################################################################### -## The source URL(s) define the location of the sources that will be -## downloaded. Version variables may be used to simplify reuse of this bee-file. - -SRCURL[0]="/src/mariux/beeroot/downloads/Linux-USBKeyboard-${PKGVERSION}_p1_f541008.tar.bz2" - -############################################################################### -## Add URLs/pathes to patch files to the PATCHURL array. -## The sources will be patched in the order of the array. - -# PATCHURL+=() - -############################################################################### -## Add filename patterns to the EXCLUDE array of files that should not -## be added to you package but may be present in the image directory. - -# EXCLUDE+=() - -############################################################################### -## Uncomment the next statement, if the software may not be able to be build -## outside the source directory and need to be build inside the source -## directory. - -# build_in_sourcedir - -############################################################################### -## bee cannot detect buildtypes specified in subdirectories. -## Sometimes packages "hide" the real sources in a subdirectory named -## 'src' or 'cmake' or .. -## use 'sourcesubdir_append' to specify this directory if known. - -# sourcesubdir_append src - - -############################################################################### -## Change the default (auto-detected) steps to -## extract, patch, configure/setup, build and install the software. -## Make sure the mee_install function does install everything to the -## image directory "${D}" - -#mee_extract() { -# bee_extract "${@}" -#} - -#mee_patch() { -# bee_patch "${@}" -#} - -#mee_configure() { -# bee_configure -#} - -#mee_build() { -# bee_build -#} - -#mee_install() { -# bee_install -#} -## by default this may be 'make install DESTDIR="${D}"' - -############################################################################### -## -## Additional hints: -## -## The name of this bee-file should follow the following naming convention: -## pkgname-pkgversion-pkgrevision.bee -## -## You may remove all comments as long as SRCURL[0]="" is set. -## -## Everything in this file will be executed in a bash environment. -## -## Build the package by executing -## './pkg-version-N.bee' or -## 'beesh ./pkg-version-N.bee' -## -## see http://beezinga.org/ -## diff --git a/Mojolicious-2.36-0.bee b/Mojolicious-2.36-0.bee deleted file mode 100755 index c8a42f828..000000000 --- a/Mojolicious-2.36-0.bee +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env beesh - -SRCURL[0]="http://cpan.metacpan.org/authors/id/S/SR/SRI/Mojolicious-${PKGVERSION}.tar.gz" - -PATCHURL[0]="" - -# BEE_CONFIGURE=compat - -# BEE_BUILDTYPE= - -# EXCLUDE="" - - - -#mee_extract() { -# bee_extract ${@} -#} - -#mee_patch() { -# bee_patch ${@} -#} - -#mee_configure() { -# bee_configure -#} - -#mee_build() { -# bee_build -#} - -#mee_install() { -# bee_install -#} diff --git a/Net-SNMP-6.0.1-0.bee b/Net-SNMP-6.0.1-0.bee deleted file mode 100755 index fa4602e7b..000000000 --- a/Net-SNMP-6.0.1-0.bee +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env beesh - -SRCURL[0]="http://search.cpan.org/CPAN/authors/id/D/DT/DTOWN/Net-SNMP-v${PKGVERSION}.tar.gz" - -PATCHURL[0]="" - -# BEE_CONFIGURE=compat - -# BEE_BUILDTYPE= - -# EXCLUDE="" - - - -#mee_extract() { -# bee_extract ${@} -#} - -#mee_patch() { -# bee_patch ${@} -#} - -#mee_configure() { -# bee_configure -#} - -#mee_build() { -# bee_build -#} - -#mee_install() { -# bee_install -#} diff --git a/Term-ReadLine-Gnu-1.20-0.bee b/Term-ReadLine-Gnu-1.20-0.bee deleted file mode 100755 index 8b98bceff..000000000 --- a/Term-ReadLine-Gnu-1.20-0.bee +++ /dev/null @@ -1,31 +0,0 @@ -#!/usr/bin/env beesh - -SRCURL[0]="http://search.cpan.org/CPAN/authors/id/H/HA/HAYASHI/Term-ReadLine-Gnu-${PKGVERSION}.tar.gz" - -PATCHURL[0]="" - -# BEE_CONFIGURE=compat - -# EXCLUDE="" - - - -#mee_extract() { -# bee_extract ${@} -#} - -#mee_patch() { -# bee_patch ${@} -#} - -#mee_configure() { -# bee_configure -#} - -#mee_build() { -# bee_build -#} - -#mee_install() { -# bee_install -#} diff --git a/Time-Period-1.24-0.bee b/Time-Period-1.24-0.bee deleted file mode 100755 index 7a0a3075e..000000000 --- a/Time-Period-1.24-0.bee +++ /dev/null @@ -1,83 +0,0 @@ -#!/usr/bin/env beesh - -## this file was created by bee init and should be executed to build a -## bee-package. (Additional hints are located at the end of this file.) - -############################################################################### -## The source URL(s) define the location of the sources that will be -## downloaded. Version variables may be used to simplify reuse of this bee-file. - -SRCURL[0]="http://search.cpan.org/CPAN/authors/id/P/PB/PBOYD/Time-Period-${PKGVERSION}.tar.gz" - -############################################################################### -## Add URLs/pathes to patch files to the PATCHURL array. -## The sources will be patched in the order of the array. - -# PATCHURL+=() - -############################################################################### -## Add filename patterns to the EXCLUDE array of files that should not -## be added to you package but may be present in the image directory. - -# EXCLUDE+=() - -############################################################################### -## Uncomment the next statement, if the software may not be able to be build -## outside the source directory and need to be build inside the source -## directory. - -# build_in_sourcedir - -############################################################################### -## bee cannot detect buildtypes specified in subdirectories. -## Sometimes packages "hide" the real sources in a subdirectory named -## 'src' or 'cmake' or .. -## use 'sourcesubdir_append' to specify this directory if known. - -# sourcesubdir_append src - - -############################################################################### -## Change the default (auto-detected) steps to -## extract, patch, configure/setup, build and install the software. -## Make sure the mee_install function does install everything to the -## image directory "${D}" - -#mee_extract() { -# bee_extract "${@}" -#} - -#mee_patch() { -# bee_patch "${@}" -#} - -#mee_configure() { -# bee_configure -#} - -#mee_build() { -# bee_build -#} - -#mee_install() { -# bee_install -#} -## by default this may be 'make install DESTDIR="${D}"' - -############################################################################### -## -## Additional hints: -## -## The name of this bee-file should follow the following naming convention: -## pkgname-pkgversion-pkgrevision.bee -## -## You may remove all comments as long as SRCURL[0]="" is set. -## -## Everything in this file will be executed in a bash environment. -## -## Build the package by executing -## './pkg-version-N.bee' or -## 'beesh ./pkg-version-N.bee' -## -## see http://beezinga.org/ -## diff --git a/Tk-804.029-0.bee b/Tk-804.029-0.bee deleted file mode 100755 index 25b49869f..000000000 --- a/Tk-804.029-0.bee +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env beesh - -SRCURL[0]="http://search.cpan.org/CPAN/authors/id/S/SR/SREZIC/Tk-${PKGVERSION}.tar.gz" - -PATCHURL[0]="" - -# BEE_CONFIGURE=compat - -# BEE_BUILDTYPE= - -# EXCLUDE="" - - - -#mee_extract() { -# bee_extract ${@} -#} - -#mee_patch() { -# bee_patch ${@} -#} - -#mee_configure() { -# bee_configure -#} - -#mee_build() { -# bee_build -#} - -#mee_install() { -# bee_install -#} diff --git a/WWW-Dict-Leo-Org.be0 b/WWW-Dict-Leo-Org.be0 deleted file mode 100755 index 031b6c427..000000000 --- a/WWW-Dict-Leo-Org.be0 +++ /dev/null @@ -1,91 +0,0 @@ -#!/usr/bin/env beesh - -# BEE_VERSION WWW-Dict-Leo-Org-1.40-0 - -## this file was created by bee init and should be executed to build a -## bee-package. (Additional hints are located at the end of this file.) - -############################################################################### -## The source URL(s) define the location of the sources that will be -## downloaded. Version variables may be used to simplify reuse of this bee-file. - -SRCURL[0]="https://cpan.metacpan.org/authors/id/T/TL/TLINDEN/WWW-Dict-Leo-Org-${PKGVERSION}.tar.gz" - -############################################################################### -## Add URLs/pathes to patch files to the PATCHURL array. -## The sources will be patched in the order of the array. - -# PATCHURL+=() - -############################################################################### -## Add filename patterns to the EXCLUDE array of files that should not -## be added to you package but may be present in the image directory. - -# EXCLUDE+=() - -############################################################################### -## Uncomment the next statement, if the software may not be able to be built -## outside the source directory and needs to be built inside the source -## directory. - -# build_in_sourcedir - -############################################################################### -## bee cannot detect buildtypes specified in subdirectories. -## Sometimes packages "hide" the real sources in a subdirectory named -## 'src' or 'cmake' or .. -## use 'sourcesubdir_append' to specify this directory if known. - -# sourcesubdir_append src - - -############################################################################### -## Change the default (auto-detected) steps to -## extract, patch, configure/setup, build and install the software. -## Make sure the mee_install function does install everything to the -## image directory "${D}" - -#mee_extract() { -# bee_extract "${@}" -#} - -#mee_patch() { -# bee_patch "${@}" -#} - -#mee_configure() { -# bee_configure -#} - -#mee_build() { -# bee_build -#} - -#mee_install() { -# bee_install -#} -## by default this may be 'make install DESTDIR="${D}"' - -mee_install_post() { - rm ${D}/usr/local/lib/perl5/5.12.1/x86_64-linux-thread-multi/perllocal.pod - rmdir ${D}/usr/local/lib/perl5/5.12.1/x86_64-linux-thread-multi/ - rmdir ${D}/usr/local/lib/perl5/5.12.1/ -} - -############################################################################### -## -## Additional hints: -## -## The name of this bee-file should follow the following naming convention: -## pkgname-pkgversion-pkgrevision.bee -## -## You may remove all comments as long as SRCURL[0] is set. -## -## Everything in this file will be executed in a bash environment. -## -## Build the package by executing -## './pkg-version-N.bee' or -## 'beesh ./pkg-version-N.bee' -## -## see http://beezinga.org/ -## From ac53df8f97c97931a8a121b86108a457a192f0a8 Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Fri, 11 Oct 2019 15:09:40 +0200 Subject: [PATCH 3/7] perl-wrapper: Install version 1.1 Install wrapper for commands provided by packaged perl. Note: This commit was cherry-picked from 95d5bdbf7e5f ("perl-wrapper: Install version 1.0") which was applied and later reverted. In contradiction to the commit message title, the initial version was "1.1" not "1.0". We don't correct that so that versions continue to increase. --- perl-wrapper.be0 | 135 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 135 insertions(+) create mode 100755 perl-wrapper.be0 diff --git a/perl-wrapper.be0 b/perl-wrapper.be0 new file mode 100755 index 000000000..dc9434e91 --- /dev/null +++ b/perl-wrapper.be0 @@ -0,0 +1,135 @@ +#!/usr/bin/env beesh + +# BEE_VERSION perl-wrapper-1.1-0 + +## this file was created by bee init and should be executed to build a +## bee-package. (Additional hints are located at the end of this file.) + +############################################################################### +## The source URL(s) define the location of the sources that will be +## downloaded. Version variables may be used to simplify reuse of this bee-file. + +SRCURL[0]="" + +############################################################################### +## Add URLs/pathes to patch files to the PATCHURL array. +## The sources will be patched in the order of the array. + +# PATCHURL+=() + +############################################################################### +## Add filename patterns to the EXCLUDE array of files that should not +## be added to you package but may be present in the image directory. + +# EXCLUDE+=() + +############################################################################### +## Uncomment the next statement, if the software may not be able to be built +## outside the source directory and needs to be built inside the source +## directory. + +# build_in_sourcedir + +############################################################################### +## bee cannot detect buildtypes specified in subdirectories. +## Sometimes packages "hide" the real sources in a subdirectory named +## 'src' or 'cmake' or .. +## use 'sourcesubdir_append' to specify this directory if known. + +# sourcesubdir_append src + + +############################################################################### +## Change the default (auto-detected) steps to +## extract, patch, configure/setup, build and install the software. +## Make sure the mee_install function does install everything to the +## image directory "${D}" + +#mee_extract() { +# bee_extract "${@}" +#} + +#mee_patch() { +# bee_patch "${@}" +#} + +#mee_configure() { +# bee_configure +#} + +mee_build() { + echo -e '#! /bin/bash\nprun perl $(basename "$0") "$@"' >wrapper + chmod +x wrapper +} + +mee_install() { + mkdir -p "$D$BINDIR" + + # list generated by + # for cmd in $(cd /pkg/perl-5.28.1-0/bin;ls); do test -e /usr/bin/$cmd || echo $cmd;done | fmt -w 80| sed 's/.*/ & \\/' + # + for cmd in \ + ansi2html bdf2gdfont.pl bp_aacomp.pl bp_biofetch_genbank_proxy.pl \ + bp_bioflat_index.pl bp_biogetseq.pl bp_blast2tree.pl bp_bulk_load_gff.pl \ + bp_chaos_plot.pl bp_classify_hits_kingdom.pl bp_composite_LD.pl \ + bp_das_server.pl bp_dbsplit.pl bp_download_query_genbank.pl bp_einfo \ + bp_extract_feature_seq.pl bp_fast_load_gff.pl bp_fastam9_to_table.pl \ + bp_fetch.pl bp_filter_search.pl bp_find-blast-matches.pl bp_flanks.pl \ + bp_gccalc.pl bp_genbank2gff.pl bp_genbank2gff3.pl bp_genbank_ref_extractor \ + bp_generate_histogram.pl bp_heterogeneity_test.pl bp_hivq.pl \ + bp_hmmer_to_table.pl bp_index.pl bp_load_gff.pl bp_local_taxonomydb_query.pl \ + bp_make_mrna_protein.pl bp_mask_by_search.pl bp_meta_gff.pl bp_mrtrans.pl \ + bp_mutate.pl bp_netinstall.pl bp_nexus2nh.pl bp_nrdb.pl bp_oligo_count.pl \ + bp_parse_hmmsearch.pl bp_process_gadfly.pl bp_process_sgd.pl \ + bp_process_wormbase.pl bp_query_entrez_taxa.pl bp_remote_blast.pl \ + bp_revtrans-motif.pl bp_search2alnblocks.pl bp_search2gff.pl bp_search2table.pl \ + bp_search2tribe.pl bp_seq_length.pl bp_seqconvert.pl bp_seqcut.pl \ + bp_seqfeature_delete.pl bp_seqfeature_gff3.pl bp_seqfeature_load.pl \ + bp_seqpart.pl bp_seqret.pl bp_seqretsplit.pl bp_split_seq.pl bp_sreformat.pl \ + bp_taxid4species.pl bp_taxonomy2tree.pl bp_translate_seq.pl bp_tree2pag.pl \ + bp_unflatten_seq.pl combig-script.sh combig.pl config_data corelist count.pl \ + count2huge.pl cpan cpan-mirrors cpan2dist cpanel_json_xs cpanfile-dump \ + cpanp cpanp-run-perl crc32 dave dbilogstrip dbiprof dbiproxy dm_date \ + dm_zdump enc2xs encguess extract_vba find-compounds.pl findrule gedi h2ph \ + h2xs htmltree huge-count.pl huge-delete.pl huge-merge.pl huge-sort.pl \ + huge-split.pl hypnotoad instmodsh iperl json_pp json_xs kocos-script.sh \ + kocos.pl kwalitee-metrics l4p-tmpl leo libnetcfg lwp-download lwp-dump \ + lwp-mirror lwp-request markdent-html markdown2pod mech-dump mo-inline \ + modemtest mojo moose-outdated morbo msgconvert mymeta-cpanfile net-server \ + odf2pod odf_set_fields odf_set_title odfbuild odfextract odffilesearch \ + odffindbasic odfhighlight odfmetadoc odfsearch oodoc_test oodoc_version \ + package-stash-conflicts pause-permissions pdl pdl2 pdldoc perl perl5.28.1 \ + perlbug perlcritic perldl perldoc perlivp perlsh perlthanks perltidy \ + piconv pl2pm plackup pod2html pod2latex pod2man pod2text pod2usage \ + pod_cover podchecker podselect podspell pptemplate prove ptar ptardiff \ + ptargrep ptked ptksh puudecode puuencode rank-script.sh rank.pl re.pl \ + readline_usb reply scan-perl-prereqs-nqlite schwartzmon shasum snmpkey \ + splain stag-autoschema.pl stag-db.pl stag-diff.pl stag-drawtree.pl \ + stag-filter.pl stag-findsubtree.pl stag-flatten.pl stag-grep.pl stag-handle.pl \ + stag-itext2simple.pl stag-itext2sxpr.pl stag-itext2xml.pl stag-join.pl \ + stag-merge.pl stag-mogrify.pl stag-parse.pl stag-query.pl stag-splitter.pl \ + stag-view.pl stag-xml2itext.pl statistic.pl test-yaml text2odf text2table \ + tkjpeg tpage ttree ucalc use-devel-checklib widget xpath xsubpp zipdetails \ + ; do + ln "$B/wrapper" "$D$BINDIR/$cmd" + done +} +## by default this may be 'make install DESTDIR="${D}"' + +############################################################################### +## +## Additional hints: +## +## The name of this bee-file should follow the following naming convention: +## pkgname-pkgversion-pkgrevision.bee +## +## You may remove all comments as long as SRCURL[0] is set. +## +## Everything in this file will be executed in a bash environment. +## +## Build the package by executing +## './pkg-version-N.bee' or +## 'beesh ./pkg-version-N.bee' +## +## see http://beezinga.org/ +## From 091d5a44cbe52a6b1be3055fde9f4445b6f4eb90 Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Mon, 27 Apr 2020 18:23:24 +0200 Subject: [PATCH 4/7] perl-wrapper: Use perl-5.12.1-0 We want to take small steps. When we replace the perl installed into /usr/local/ this time, we don't want to make an implicit upgrade but use the package with the same perl version number instead. Let the package wrpper use the package "perl-5.12.1-0" instead of "perl" which is the recommended version. Rebuild list of commands to supply in /usr/bin. --- perl-wrapper.be0 | 70 ++++++++++++++++++++++-------------------------- 1 file changed, 32 insertions(+), 38 deletions(-) diff --git a/perl-wrapper.be0 b/perl-wrapper.be0 index dc9434e91..6fd115768 100755 --- a/perl-wrapper.be0 +++ b/perl-wrapper.be0 @@ -58,7 +58,7 @@ SRCURL[0]="" #} mee_build() { - echo -e '#! /bin/bash\nprun perl $(basename "$0") "$@"' >wrapper + echo -e '#! /bin/bash\nprun perl-5.12.1-0 $(basename "$0") "$@"' >wrapper chmod +x wrapper } @@ -66,50 +66,44 @@ mee_install() { mkdir -p "$D$BINDIR" # list generated by - # for cmd in $(cd /pkg/perl-5.28.1-0/bin;ls); do test -e /usr/bin/$cmd || echo $cmd;done | fmt -w 80| sed 's/.*/ & \\/' + # for cmd in $(cd /pkg/perl-5.12.1-0/bin;ls); do test -e /usr/bin/$cmd || echo $cmd;done | fmt -w 80| sed 's/.*/ & \\/' # for cmd in \ - ansi2html bdf2gdfont.pl bp_aacomp.pl bp_biofetch_genbank_proxy.pl \ - bp_bioflat_index.pl bp_biogetseq.pl bp_blast2tree.pl bp_bulk_load_gff.pl \ - bp_chaos_plot.pl bp_classify_hits_kingdom.pl bp_composite_LD.pl \ - bp_das_server.pl bp_dbsplit.pl bp_download_query_genbank.pl bp_einfo \ - bp_extract_feature_seq.pl bp_fast_load_gff.pl bp_fastam9_to_table.pl \ - bp_fetch.pl bp_filter_search.pl bp_find-blast-matches.pl bp_flanks.pl \ - bp_gccalc.pl bp_genbank2gff.pl bp_genbank2gff3.pl bp_genbank_ref_extractor \ - bp_generate_histogram.pl bp_heterogeneity_test.pl bp_hivq.pl \ - bp_hmmer_to_table.pl bp_index.pl bp_load_gff.pl bp_local_taxonomydb_query.pl \ - bp_make_mrna_protein.pl bp_mask_by_search.pl bp_meta_gff.pl bp_mrtrans.pl \ - bp_mutate.pl bp_netinstall.pl bp_nexus2nh.pl bp_nrdb.pl bp_oligo_count.pl \ - bp_parse_hmmsearch.pl bp_process_gadfly.pl bp_process_sgd.pl \ - bp_process_wormbase.pl bp_query_entrez_taxa.pl bp_remote_blast.pl \ - bp_revtrans-motif.pl bp_search2alnblocks.pl bp_search2gff.pl bp_search2table.pl \ - bp_search2tribe.pl bp_seq_length.pl bp_seqconvert.pl bp_seqcut.pl \ - bp_seqfeature_delete.pl bp_seqfeature_gff3.pl bp_seqfeature_load.pl \ - bp_seqpart.pl bp_seqret.pl bp_seqretsplit.pl bp_split_seq.pl bp_sreformat.pl \ - bp_taxid4species.pl bp_taxonomy2tree.pl bp_translate_seq.pl bp_tree2pag.pl \ - bp_unflatten_seq.pl combig-script.sh combig.pl config_data corelist count.pl \ - count2huge.pl cpan cpan-mirrors cpan2dist cpanel_json_xs cpanfile-dump \ - cpanp cpanp-run-perl crc32 dave dbilogstrip dbiprof dbiproxy dm_date \ - dm_zdump enc2xs encguess extract_vba find-compounds.pl findrule gedi h2ph \ - h2xs htmltree huge-count.pl huge-delete.pl huge-merge.pl huge-sort.pl \ - huge-split.pl hypnotoad instmodsh iperl json_pp json_xs kocos-script.sh \ - kocos.pl kwalitee-metrics l4p-tmpl leo libnetcfg lwp-download lwp-dump \ - lwp-mirror lwp-request markdent-html markdown2pod mech-dump mo-inline \ - modemtest mojo moose-outdated morbo msgconvert mymeta-cpanfile net-server \ + a2p bdf2gdfont.pl bp_aacomp bp_biofetch_genbank_proxy bp_bioflat_index \ + bp_biogetseq bp_dbsplit bp_download_query_genbank bp_einfo \ + bp_extract_feature_seq bp_fastam9_to_table bp_fetch bp_filter_search \ + bp_find-blast-matches bp_flanks bp_gccalc bp_genbank2gff3 \ + bp_genbank_ref_extractor bp_index bp_local_taxonomydb_query \ + bp_make_mrna_protein bp_mask_by_search bp_mrtrans bp_mutate bp_nexus2nh \ + bp_nrdb bp_oligo_count bp_process_gadfly bp_process_sgd bp_query_entrez_taxa \ + bp_remote_blast.pl bp_revtrans-motif bp_search2alnblocks bp_search2gff \ + bp_search2table bp_search2tribe bp_seq_length bp_seqconvert bp_seqcut \ + bp_seqpart bp_seqret bp_seqretsplit bp_split_seq bp_sreformat bp_taxid4species \ + bp_taxonomy2tree bp_translate_seq bp_tree2pag bp_unflatten_seq c2ph \ + combig-script.sh combig.pl config_data corelist count.pl count2huge.pl cpan \ + cpan-mirrors cpan2dist cpanel_json_xs cpanp cpanp-run-perl crc32 db_archive \ + db_checkpoint db_deadlock db_dump db_hotbackup db_load db_printlog db_recover \ + db_sql db_stat db_upgrade db_verify dbilogstrip dbiprof dbiproxy dm_date \ + dm_zdump dprofpp enc2xs encguess extract_vba find-compounds.pl find2perl \ + findrule gedi h2ph h2xs htmltree huge-count.pl huge-delete.pl huge-merge.pl \ + huge-sort.pl huge-split.pl hypnotoad instmodsh json_pp json_xs kocos-script.sh \ + kocos.pl l4p-tmpl leo libnetcfg lwp-download lwp-dump lwp-mirror lwp-request \ + mech-dump mo-inline modemtest mojo moose-outdated morbo msgconvert net-server \ odf2pod odf_set_fields odf_set_title odfbuild odfextract odffilesearch \ odffindbasic odfhighlight odfmetadoc odfsearch oodoc_test oodoc_version \ - package-stash-conflicts pause-permissions pdl pdl2 pdldoc perl perl5.28.1 \ - perlbug perlcritic perldl perldoc perlivp perlsh perlthanks perltidy \ - piconv pl2pm plackup pod2html pod2latex pod2man pod2text pod2usage \ - pod_cover podchecker podselect podspell pptemplate prove ptar ptardiff \ - ptargrep ptked ptksh puudecode puuencode rank-script.sh rank.pl re.pl \ - readline_usb reply scan-perl-prereqs-nqlite schwartzmon shasum snmpkey \ - splain stag-autoschema.pl stag-db.pl stag-diff.pl stag-drawtree.pl \ + package-stash-conflicts pdl pdl2 pdldoc perl5.12.1 perlbug perlcritic perldl \ + perldoc perlivp perlsh perlthanks perltidy piconv pl2pm plackup pod2html \ + pod2latex pod2man pod2text pod2usage pod_cover podchecker podselect podspell \ + pptemplate prove psed pstruct ptar ptardiff ptargrep ptked ptksh puudecode \ + puuencode rank-script.sh rank.pl readline_usb s2p schwartzmon shasum \ + snmpkey splain stag-autoschema.pl stag-db.pl stag-diff.pl stag-drawtree.pl \ stag-filter.pl stag-findsubtree.pl stag-flatten.pl stag-grep.pl stag-handle.pl \ stag-itext2simple.pl stag-itext2sxpr.pl stag-itext2xml.pl stag-join.pl \ stag-merge.pl stag-mogrify.pl stag-parse.pl stag-query.pl stag-splitter.pl \ - stag-view.pl stag-xml2itext.pl statistic.pl test-yaml text2odf text2table \ - tkjpeg tpage ttree ucalc use-devel-checklib widget xpath xsubpp zipdetails \ + stag-view.pl stag-xml2itext.pl statistic.pl streamzip test-yaml text2odf \ + text2table tkjpeg tpage ttree ucalc use-devel-checklib widget xpath \ + xsubpp yamlpp5-events yamlpp5-highlight yamlpp5-load yamlpp5-load-dump \ + yamlpp5-parse-emit zipdetails \ ; do ln "$B/wrapper" "$D$BINDIR/$cmd" done From 451ee0ee0d1409d8f30ee90db8a66dbcbec4a8a2 Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Mon, 27 Apr 2020 18:32:46 +0200 Subject: [PATCH 5/7] perl-wrapper: Create /usr/local/bin/perl symlink As noted in [#1419], several scripts still use `/usr/local/bin/perl` as a shebang so provide a symlink. [#1419]: https://github.molgen.mpg.de/mariux64/bee-files/issues/1419 --- perl-wrapper.be0 | 2 ++ 1 file changed, 2 insertions(+) diff --git a/perl-wrapper.be0 b/perl-wrapper.be0 index 6fd115768..96fee891a 100755 --- a/perl-wrapper.be0 +++ b/perl-wrapper.be0 @@ -107,6 +107,8 @@ mee_install() { ; do ln "$B/wrapper" "$D$BINDIR/$cmd" done + mkdir -p "$D$PREFIX/local/bin" + ln -s "$BINDIR/perl" "$D$PREFIX/local/bin/perl" } ## by default this may be 'make install DESTDIR="${D}"' From de977a36112b1cc2f9753cca66f53a2103a10009 Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Mon, 27 Apr 2020 18:45:06 +0200 Subject: [PATCH 6/7] perl-wrapper: Increment build number --- perl-wrapper.be0 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/perl-wrapper.be0 b/perl-wrapper.be0 index 96fee891a..e57c0debb 100755 --- a/perl-wrapper.be0 +++ b/perl-wrapper.be0 @@ -1,6 +1,6 @@ #!/usr/bin/env beesh -# BEE_VERSION perl-wrapper-1.1-0 +# BEE_VERSION perl-wrapper-1.1-1 ## this file was created by bee init and should be executed to build a ## bee-package. (Additional hints are located at the end of this file.) From 1ea4670d07ab774116b4b5ca8e100cad92bd581f Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Mon, 27 Apr 2020 19:16:54 +0200 Subject: [PATCH 7/7] perl-wrapper: Make sure, /usr/bin/perl is generated /usr/bin/perl might not be included in the list generated by the command quoted in the script if perl-5.12.1-2.x86_64 is still installed, because this packages includes a symlink /usr/bin/perl -> /usr/local/bin/perl. --- perl-wrapper.be0 | 1 + 1 file changed, 1 insertion(+) diff --git a/perl-wrapper.be0 b/perl-wrapper.be0 index e57c0debb..068fd386e 100755 --- a/perl-wrapper.be0 +++ b/perl-wrapper.be0 @@ -107,6 +107,7 @@ mee_install() { ; do ln "$B/wrapper" "$D$BINDIR/$cmd" done + ln "$B/wrapper" "$D$BINDIR/perl" mkdir -p "$D$PREFIX/local/bin" ln -s "$BINDIR/perl" "$D$PREFIX/local/bin/perl" }