From 6c356e1d532116d6a79d1178f07f09114fc7134e Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Fri, 24 Apr 2020 17:44:52 +0200 Subject: [PATCH 01/19] Add texinfo-4.13a Add package build script from TEMPLATE.sh for a very old version of texinfo. Required to build ancient gcc version. --- texinfo-4.13a-0.build.sh | 44 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100755 texinfo-4.13a-0.build.sh diff --git a/texinfo-4.13a-0.build.sh b/texinfo-4.13a-0.build.sh new file mode 100755 index 0000000..96132fb --- /dev/null +++ b/texinfo-4.13a-0.build.sh @@ -0,0 +1,44 @@ +#! /bin/bash + +PKG=texinfo +VERSION=4.13a +V=4.13 +BUILD=0 + +PREFIX=/pkg/$PKG-$VERSION-$BUILD +if [ -n "$TESTING" ]; then PREFIX=/dev/shm/$PKG-$VERSION-$BUILD ; fi + +set -xe +umask 022 + +BUILD_TMPDIR=/dev/shm/$PKG-$VERSION-$BUILD.build.tmp +test -d $BUILD_TMPDIR && ( chmod -R u+rwx $BUILD_TMPDIR || true ; rm -rf $BUILD_TMPDIR ) +mkdir -p $BUILD_TMPDIR/home +export TMPDIR=$BUILD_TMPDIR +export HOME=$BUILD_TMPDIR/home + +exec $PREFIX/profile <<-EOF + PATH=$PREFIX/bin:\$PATH + if [ -d $PREFIX/.compatlibs ]; then export LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:\$LD_LIBRARY_PATH} ; fi +EOF +. $PREFIX/profile + +export MAKEFLAGS="-j $(nproc)" + +BUILDDIR=$PREFIX/build + +mkdir -p $BUILDDIR +cd $BUILDDIR + +test -e texinfo-$VERSION.tar.xz || wget https://ftp.gnu.org/gnu/texinfo/texinfo-$VERSION.tar.gz +test -d texinfo-$V || tar xvf texinfo-$VERSION.tar.gz +cd texinfo-$V +./configure \ + --prefix=$PREFIX +make +make install + +exit From 8fdcefa09f47c3f502d407300c1bc26916953b6d Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Thu, 23 Apr 2020 15:33:42 +0200 Subject: [PATCH 02/19] Add gcc-4.5.1 Create build script with cp gcc-9.2.0-0.build.sh gcc-4.5.1-0.build.sh and update version number. --- gcc-4.5.1-0.build.sh | 72 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100755 gcc-4.5.1-0.build.sh diff --git a/gcc-4.5.1-0.build.sh b/gcc-4.5.1-0.build.sh new file mode 100755 index 0000000..c35bf84 --- /dev/null +++ b/gcc-4.5.1-0.build.sh @@ -0,0 +1,72 @@ +#! /bin/bash + +# Note: The test suite run address sanitizer tests. In the current mariux64 environment +# this requires +# +# sudo sysctl vm.overcommit_memory=0 + +PKG=gcc +VERSION=4.5.1 +BUILD=0 +URL=http://ftp.gnu.org/gnu/gcc/gcc-${VERSION}/gcc-${VERSION}.tar.gz + +PREFIX=/pkg/$PKG-$VERSION-$BUILD +if [ -n "$TESTING" ]; then PREFIX=/dev/shm/$PKG-$VERSION-$BUILD ; fi + +set -xe +umask 022 + +BUILD_TMPDIR=/dev/shm/$PKG-$VERSION-$BUILD.build.tmp +test -d $BUILD_TMPDIR && ( chmod -R u+rwx $BUILD_TMPDIR || true ; rm -rf $BUILD_TMPDIR ) +mkdir -p $BUILD_TMPDIR/home +export TMPDIR=$BUILD_TMPDIR +export HOME=$BUILD_TMPDIR/home + +exec $PREFIX/profile <<-EOF + PATH=$PREFIX/bin:\$PATH + if [ -d $PREFIX/.compatlibs ]; then export LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:\$LD_LIBRARY_PATH} ; fi +EOF +. $PREFIX/profile + +export MAKEFLAGS="-j $(nproc)" + +BUILDDIR=$PREFIX/build + +mkdir -p $BUILDDIR +cd $BUILDDIR + +test -e gcc-${VERSION}.tar.gz || wget $URL +test -d gcc-$VERSION || tar xvf gcc-${VERSION}.tar.gz +cd gcc-$VERSION +mkdir -p objdir +cd objdir +$BUILDDIR/gcc-$VERSION/configure \ + --prefix=$PREFIX \ + --enable-shared \ + --enable-threads=posix \ + --enable-__cxa_atexit \ + --enable-clocale=gnu \ + --enable-languages=c,fortran,c++,objc,obj-c++ \ + --disable-multilib \ + --with-system-zlib \ + --with-diagnostics-color=auto-if-env + +make +make -k check 2>&1 | tee check.log +make install + +cd $PREFIX +mkdir -vp lib +ln -sfv ${PREFIX}/bin/cpp lib/ +ln -sfv gcc bin/cc + +install -v -dm755 lib/bfd-plugins +ln -sfv ../../libexec/gcc/$(gcc -dumpmachine)/$VERSION/liblto_plugin.so lib/bfd-plugins/ + +# and dump these ... +rm -v lib64/*-gdb.py + +exit From 78c4c7415d5b9ce5adc7346b4929519041b2b0ef Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Thu, 23 Apr 2020 17:11:07 +0200 Subject: [PATCH 03/19] gcc-4.5.1: Use texinfo 4.13 This version of GCC has .texi files that are incompatible with the current version of texinfo. Use older version of texinfo. --- gcc-4.5.1-0.build.sh | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gcc-4.5.1-0.build.sh b/gcc-4.5.1-0.build.sh index c35bf84..ef7fe9e 100755 --- a/gcc-4.5.1-0.build.sh +++ b/gcc-4.5.1-0.build.sh @@ -10,6 +10,8 @@ VERSION=4.5.1 BUILD=0 URL=http://ftp.gnu.org/gnu/gcc/gcc-${VERSION}/gcc-${VERSION}.tar.gz +. /pkg/texinfo-4.13a-0/profile + PREFIX=/pkg/$PKG-$VERSION-$BUILD if [ -n "$TESTING" ]; then PREFIX=/dev/shm/$PKG-$VERSION-$BUILD ; fi From 2a78f60d20389ed83e54be5768ac1f5e3a9f10fe Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Thu, 23 Apr 2020 17:39:34 +0200 Subject: [PATCH 04/19] gcc-4.5.1: Add patch for glibc >=2.26 --- gcc-4.5.1-0.build.sh | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gcc-4.5.1-0.build.sh b/gcc-4.5.1-0.build.sh index ef7fe9e..699801d 100755 --- a/gcc-4.5.1-0.build.sh +++ b/gcc-4.5.1-0.build.sh @@ -43,6 +43,39 @@ cd $BUILDDIR test -e gcc-${VERSION}.tar.gz || wget $URL test -d gcc-$VERSION || tar xvf gcc-${VERSION}.tar.gz cd gcc-$VERSION + +patch -N -p 1 <<__EOF__ +From 146285bd5724fe602df2ea2d171dd3f0cfc425a8 Mon Sep 17 00:00:00 2001 +From: Donald Buczek +Date: Thu, 23 Apr 2020 17:19:31 +0200 +Subject: [PATCH] i386/linux-unwind.h: Remove struct ucontext + +With glibc 2.26, the "struct ucontext" definition was removed [1]. + +Replace with ucontext_t so we can compile with glibc >=2.26. + +[1]: https://sourceware.org/glibc/wiki/Release/2.26#Removal_of_.27struct_ucontext.27 +--- + gcc/config/i386/linux-unwind.h | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/gcc/config/i386/linux-unwind.h b/gcc/config/i386/linux-unwind.h +index 36ee370..061921f 100644 +--- a/gcc/config/i386/linux-unwind.h ++++ b/gcc/config/i386/linux-unwind.h +@@ -47,7 +47,7 @@ x86_64_fallback_frame_state (struct _Unwind_Context *context, + if (*(unsigned char *)(pc+0) == 0x48 + && *(unsigned long *)(pc+1) == 0x050f0000000fc0c7) + { +- struct ucontext *uc_ = context->cfa; ++ ucontext_t *uc_ = context->cfa; + /* The void * cast is necessary to avoid an aliasing warning. + The aliasing warning is correct, but should not be a problem + because it does not alias anything. */ +-- +2.26.2 +__EOF__ + mkdir -p objdir cd objdir $BUILDDIR/gcc-$VERSION/configure \ From 302551dab1a1f99b1be295f24188cd5a498b7e07 Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Thu, 23 Apr 2020 18:00:19 +0200 Subject: [PATCH 05/19] gcc-4.5.1: Disable all languages but C --- gcc-4.5.1-0.build.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gcc-4.5.1-0.build.sh b/gcc-4.5.1-0.build.sh index 699801d..0d93291 100755 --- a/gcc-4.5.1-0.build.sh +++ b/gcc-4.5.1-0.build.sh @@ -44,7 +44,7 @@ test -e gcc-${VERSION}.tar.gz || wget $URL test -d gcc-$VERSION || tar xvf gcc-${VERSION}.tar.gz cd gcc-$VERSION -patch -N -p 1 <<__EOF__ +patch -N -p 1 <<__EOF__ || true From 146285bd5724fe602df2ea2d171dd3f0cfc425a8 Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Thu, 23 Apr 2020 17:19:31 +0200 @@ -84,7 +84,7 @@ $BUILDDIR/gcc-$VERSION/configure \ --enable-threads=posix \ --enable-__cxa_atexit \ --enable-clocale=gnu \ - --enable-languages=c,fortran,c++,objc,obj-c++ \ + --enable-languages=c \ --disable-multilib \ --with-system-zlib \ --with-diagnostics-color=auto-if-env From 0584006189e48e92f2ff33414e7938a142e290b4 Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Thu, 23 Apr 2020 19:33:01 +0200 Subject: [PATCH 06/19] gcc-4.5.1: Disable libmudflap We have unclear compile errors with libmudflap. This is only needed for certain instrumentation options. Disabled. --- gcc-4.5.1-0.build.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gcc-4.5.1-0.build.sh b/gcc-4.5.1-0.build.sh index 0d93291..2d7dd72 100755 --- a/gcc-4.5.1-0.build.sh +++ b/gcc-4.5.1-0.build.sh @@ -87,7 +87,8 @@ $BUILDDIR/gcc-$VERSION/configure \ --enable-languages=c \ --disable-multilib \ --with-system-zlib \ - --with-diagnostics-color=auto-if-env + --with-diagnostics-color=auto-if-env \ + --disable-libmudflap make make -k check 2>&1 | tee check.log From b553404afa086635cac31cab5a2ab890e90aede6 Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Thu, 23 Apr 2020 19:16:15 +0200 Subject: [PATCH 07/19] gcc-4.5.1: Continue after check failures We have two failing checks remaining: FAIL: gcc.c-torture/compile/limits-exprparen.c FAIL: gcc.dg/cpp/trad/include.c The first one is a construct with excessive brackets: #define LBR1 ( ( ( ( ( ( ( ( ( ( #define LBR2 LBR1 LBR1 LBR1 LBR1 LBR1 LBR1 LBR1 LBR1 LBR1 LBR1 #define LBR3 LBR2 LBR2 LBR2 LBR2 LBR2 LBR2 LBR2 LBR2 LBR2 LBR2 #define LBR4 LBR3 LBR3 LBR3 LBR3 LBR3 LBR3 LBR3 LBR3 LBR3 LBR3 ... This is not something we'd expect in the real world. The other one probably has an issue with the current glibc: #define __STDC__ 1 /* Stop complaints about non-ISO compilers. */ #define stdlib 1 #include /* { dg-bogus "o such file or directory" } */ The test is about whether macros inside '#include <' and '>' are expanded. This is also something we don't really care about. So we decided not to track these down. Ignore the failing tests instead. --- gcc-4.5.1-0.build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gcc-4.5.1-0.build.sh b/gcc-4.5.1-0.build.sh index 2d7dd72..77824db 100755 --- a/gcc-4.5.1-0.build.sh +++ b/gcc-4.5.1-0.build.sh @@ -91,7 +91,7 @@ $BUILDDIR/gcc-$VERSION/configure \ --disable-libmudflap make -make -k check 2>&1 | tee check.log +(make -k check 2>&1 || true) | tee check.log make install cd $PREFIX From 8c0449b5fd25a2bbd90c1308e5f9ff0a552affb8 Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Thu, 23 Apr 2020 22:05:11 +0200 Subject: [PATCH 08/19] gcc-4.5.1: Do not use -j on make install Parallel install seems to mess to. Disable MAKEFLAGS="-j .." for make install. --- gcc-4.5.1-0.build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gcc-4.5.1-0.build.sh b/gcc-4.5.1-0.build.sh index 77824db..7cb8b4c 100755 --- a/gcc-4.5.1-0.build.sh +++ b/gcc-4.5.1-0.build.sh @@ -92,7 +92,7 @@ $BUILDDIR/gcc-$VERSION/configure \ make (make -k check 2>&1 || true) | tee check.log -make install +MAKEFLAGS= make install cd $PREFIX mkdir -vp lib From 21746cffa07dedb2d7f8ccf2a3a6c762dd4fc2a3 Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Thu, 23 Apr 2020 22:07:21 +0200 Subject: [PATCH 09/19] gcc-4.5.1: remove extra commands Remove post-install commands, which we don't need for this version to avoid + rm -v 'lib64/*-gdb.py' rm: cannot remove 'lib64/*-gdb.py': No such file or directory --- gcc-4.5.1-0.build.sh | 3 --- 1 file changed, 3 deletions(-) diff --git a/gcc-4.5.1-0.build.sh b/gcc-4.5.1-0.build.sh index 7cb8b4c..e04ba16 100755 --- a/gcc-4.5.1-0.build.sh +++ b/gcc-4.5.1-0.build.sh @@ -102,7 +102,4 @@ ln -sfv gcc bin/cc install -v -dm755 lib/bfd-plugins ln -sfv ../../libexec/gcc/$(gcc -dumpmachine)/$VERSION/liblto_plugin.so lib/bfd-plugins/ -# and dump these ... -rm -v lib64/*-gdb.py - exit From e5ddcebb2a613bf4d10ed24a800869d04af15480 Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Thu, 23 Apr 2020 11:21:23 +0200 Subject: [PATCH 10/19] Add perl-5.12.1 We want a perl version in /pkg which is identically to the /usr/local/bin perl version we are going to remove. Create file with cp perl-5.28.1-0.build.sh perl-5.12.1-0.build.sh and update versions. --- perl-5.12.1-0.build.sh | 578 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 578 insertions(+) create mode 100755 perl-5.12.1-0.build.sh diff --git a/perl-5.12.1-0.build.sh b/perl-5.12.1-0.build.sh new file mode 100755 index 0000000..e0341b3 --- /dev/null +++ b/perl-5.12.1-0.build.sh @@ -0,0 +1,578 @@ +#! /bin/bash + +PKG=perl +VERSION=5.12.1 +BUILD=0 + +PREFIX=/pkg/$PKG-$VERSION-$BUILD +if [ -n "$TESTING" ]; then PREFIX=/dev/shm/$PKG-$VERSION-$BUILD ; fi + +set -xe +umask 022 + +BUILD_TMPDIR=/dev/shm/$PKG-$VERSION-$BUILD.build.tmp +test -d $BUILD_TMPDIR && rm -rf $BUILD_TMPDIR +mkdir -p $BUILD_TMPDIR/home +export TMPDIR=$BUILD_TMPDIR +export HOME=$BUILD_TMPDIR/home + +exec $PREFIX/profile <<-EOF + PATH=$PREFIX/bin:\$PATH + if [ -d $PREFIX/.compatlibs ]; then export LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:\$LD_LIBRARY_PATH} ; fi +EOF +. $PREFIX/profile + +# Tk test needs display +# +if [ -z "$DISPLAY" ]; then + echo "DISPLAY not set. Required for Tk tests." >&2 + exit 1 +fi + +# If you hit errors and want to rerun from where you failed, +# use "if false","fi" to avoid rebuilding everything before +# the error. +# +# A good point to place the "if false" is here. +# +# Just uncomment and move the "fi" line to where +# you want to restart. +# +#if false; then ######################################################### DEBUG +#fi ######################################################### DEBUG + +export MAKEFLAGS="-j $(nproc)" + +BUILDDIR=$PREFIX/build + +mkdir -p $BUILDDIR +cd $BUILDDIR + +# The problem with a git checkout is, that the perl build system does many things +# differentily when is sees .git - e.g. run additional developer checks. +#test -d perl || git clone https://perl5.git.perl.org/perl.git +#cd perl +#git checkout "v$VERSION" ; git reset --hard + +test -e perl-$VERSION.tar.gz || wget http://www.cpan.org/src/5.0/perl-$VERSION.tar.gz +test -d perl-$VERSION || tar xf perl-$VERSION.tar.gz +cd perl-$VERSION + +# -d : use defaults for all answers. +# -e : go on without questioning past the production of config.sh. +# -s : silent mode, only echoes questions and essential information. +# -Dusedevel : allow devel (uneven minor) versions. Prevents bin/perl->bin/perlVERSION symlink +# -Duseshrplib : build shared perl library (required when perl is to be included in a shared library) +# -DEBUGGING : add debugging code (perl -D) +# +./Configure -des -Duseshrplib -Dprefix=$PREFIX + +make -j$(nproc) + +# Note: If you get a failure in porting/utils test here, it might be, that we are +# running cpan somewhere else which leads to an extra and unexpected "\n" being +# emitted by CPAN.pm BEGIN and a failure of the test (which does "perl -c CPAN.pm") +# +make test +make install + +cd $PREFIX; + +test -e $HOME/.cpan/CPAN/MyConfig.pm && rm $HOME/.cpan/CPAN/MyConfig.pm +cpanload(); + CPAN::Shell->o('conf','recommends_policy',0); + CPAN::Shell->o('conf','commit'); +_EOF_ + +cpan -u # update everything we already have + +# After the update we have a new ExtUtils::MakeMaker. +# Patch this version to avoid stomping on a perl bug +# We've got this when building net-snmp (down below). +# Errors: +# "panic: attempt to copy freed scalar" +# "Bizarre copy of HASH in list assignment# +# this is from perl bug: +# https://rt.perl.org/Public/Bug/Display.html?id=77706 +# triggered by ExtUtils::MakeMaker. +# This patch prevents this +# + +(cd lib/site_perl/$VERSION/ExtUtils; patch -N -p1 < /src/mariux/patches/MakeMaker-0001-MakeMaker.pm-Avoid-triggering-perl-bug.patch) || true + +# These two with -T (without test), because the tests are interactive and access /dev/tty +# Do these first, because they are required by Bundle::CPAN +# +cpan -T Term::ReadLine::Perl +cpan -T Term::ReadLine::Gnu + +# Now the rest of Bundle::CPAN first, so that we use latest code for the following +# installations +# +cpan Bundle::CPAN + +# mod_perl (Apache::*, Bundle::Apache, mod_perl, modPerl_hooks) is broken. +# Usually it wants Apache httpd source to compile and keeps asking for it forever if it +# doesn't find it. +# we could install it without Access to sources +# perl -MCPAN <<'_EOF_' +# CPAN::HandleConfig->load; +# $CPAN::Config->{'makepl_arg'}='NO_HTTPD=1'; +# CPAN::Shell->install('Apache'); +# _EOF_ +# but its broken anyway (needs a patch to compile against +# current perl) and the version 1.* branch has not been updated +# for a long time. leave it out and everything which depends on it +#cpan Bundle::Apache + +# Tests for GD fail +# The seventh image in den GD.t test looks slightly +# different. Maybe small difference in TrueType font. +# +# Do it first, otherwise we are pulled by Chart::Base +# +cpan -T GD + +cpan Log::Log4perl # many module tests request this. + +# Now modules (from autobundle of /usr/local/ installation and manual cleanup and some deduplication) +# +cpan AE +cpan Algorithm::Diff +cpan Algorithm::DiffOld +cpan AnyEvent +cpan AppConfig +cpan Archive::Extract +cpan Archive::Zip +cpan Attribute::Params::Validate +cpan Authen::SASL +cpan B::Keywords +cpan BerkeleyDB +cpan Bit::Vector +cpan CGI +cpan CGI::Fast +cpan CPAN::Admin +cpan CPANPLUS + +# Cache::Memcached has some strange timing tests which fail from time to time +# +cpan -T Cache::Memcached +cpan Capture::Tiny +cpan Carp::Clan +cpan Chart::Base +cpan Class::Accessor +cpan Class::Data::Inheritable +cpan Class::ISA +cpan Class::Inspector +cpan Class::Load +cpan Class::Singleton +cpan Class::Tiny +PERL5LIB=".${PERL5LIB:+:$PERL5LIB}" cpan Class::Trigger +cpan Clone +cpan Config::General +cpan Config::Tiny +cpan Crypt::OpenSSL::RSA +cpan Crypt::OpenSSL::Random +cpan Crypt::RC4 +PERL5LIB=".${PERL5LIB:+:$PERL5LIB}" cpan -T Crypt::SSLeay +cpan DBD::SQLite +cpan DBD::mysql +cpan DBI +cpan File::Flock # required by Daemon::Generic +cpan Daemon::Generic +cpan Data::ObjectDriver +cpan Data::OptList +cpan Data::Stag +cpan Date::Calendar +cpan Date::Parse +PERL5LIB=".${PERL5LIB:+:$PERL5LIB}" cpan Test::utf8 # required by Test::File::ShareDir::Dist +cpan Test::File::ShareDir::Dist # required by DateTime::Locale +cpan DateTime::Locale # required by DateTime +cpan DateTime +cpan DateTime::Locale +cpan DateTime::TimeZone +cpan Devel::CheckLib +cpan Devel::GlobalDestruction +cpan Devel::InnerPackage +cpan Devel::SelfStubber +cpan Devel::StackTrace +cpan Devel::StackTrace::AsHTML +cpan Devel::Symdump +cpan Device::SerialPort +cpan Digest::HMAC +cpan Digest::Perl::MD5 +cpan Digest::SHA1 +cpan Dist::CheckConflicts +cpan Email::Abstract +cpan Email::Address +cpan Email::Date::Format +cpan Email::FolderType +cpan Email::LocalDelivery +cpan Email::MIME +cpan Email::MIME::Attachment::Stripper +cpan Email::MIME::ContentType +cpan Email::MIME::Encodings +cpan Email::MessageID +cpan Email::Outlook::Message +cpan Email::Reply +cpan Email::Send +cpan Email::Simple +cpan Encode::Detect +cpan Encode::Locale +cpan Eval::LineNumbers +cpan Event +cpan Exception::Class +cpan ExtUtils::PkgConfig +cpan FCGI +cpan File::CheckTree +cpan File::Copy::Recursive +cpan -f IO::Event # for File::Flock +cpan File::Flock +cpan File::FnMatch +cpan File::HomeDir +cpan File::Listing +cpan File::Path::Expand +cpan File::Remove +cpan File::ShareDir +cpan File::Slurp +cpan File::Which +cpan Filesys::Notify::Simple +cpan Filter::Util::Exec +cpan Font::AFM +cpan Font::TTF +cpan GD::Graph +cpan GD::Graph::histogram +cpan GD::SVG +cpan GD::Text +cpan Glib +cpan Graph +cpan Graphics::ColorNames +cpan Graphics::ColorNames::HTML +cpan Graphics::ColorNames::Windows +cpan Graphics::ColorNames::Netscape +cpan Graphics::ColorObject +cpan HTML::Tree +cpan HTML::Parser +cpan HTML::Form +cpan HTML::Formatter +cpan HTML::Scrubber +cpan HTML::TableParser +cpan HTML::Tagset +cpan HTML::TreeBuilder +cpan HTTP::Body +cpan HTTP::Cookies +cpan HTTP::DAV # note: tests fail if cpan build dir is on nfs +cpan HTTP::Daemon +cpan HTTP::Date +cpan HTTP::Negotiate +cpan HTTP::Server::Simple +cpan Hash::MultiValue +cpan Hook::LexWrap +cpan IO::All +cpan IO::CaptureOutput +cpan IO::Multiplex +cpan IO::Pty +cpan IO::Socket::SSL +cpan IO::String +cpan IO::Stringy +cpan IPC::Run +cpan IPC::Run3 +cpan Inline +cpan Inline::C + +# HTTP::Headers::Fast t/lazy_load_for_storable.t want to verify that +# Storable is not loaded right away, but it is pulled in from Test::More +# +cpan -T HTTP::Headers::Fast; # required by JSON::RPC +cpan JSON +cpan JSON::PP::Compat5006 +PERL5LIB=".${PERL5LIB:+:$PERL5LIB}" cpan Class::Accessor::Lite # required by JSON::RPC +cpan JSON::RPC +cpan JSON::XS +cpan LWP +cpan Lingua::EN::Inflect +cpan Linux::Inotify2 +PERL5LIB=".${PERL5LIB:+:$PERL5LIB}" cpan Linux::USBKeyboard +cpan List::MoreUtils +cpan Log::Message +cpan Log::Log4perl +cpan MIME::Tools +cpan MRO::Compat +cpan Mail::Box +cpan Mail::Box::IMAP4 +cpan Mail::Box::POP3 +cpan Mail::DKIM +cpan Mail::Util +cpan Mail::IMAPClient +cpan Mail::Identity +cpan Mail::Message +cpan Mail::Transport +cpan Math::Bezier +cpan Math::Calc::Units +cpan Math::Interpolate +cpan Math::IntervalSearch +cpan Math::Random::ISAAC +cpan Math::Random::ISAAC::PP +cpan Math::Round +cpan Math::VecStat +cpan Module::Build +cpan Module::Implementation +cpan Module::Pluggable +cpan Module::Runtime +cpan Mojo +cpan Mozilla::CA +cpan Net::DNS +cpan Net::HTTP +cpan Net::IMAP::Client +cpan Net::IMAP::Simple +cpan Net::SNMP +cpan Net::SSL +cpan Net::SSLeay +cpan Net::Server +cpan NetAddr::IP +cpan OLE::Storage_Lite +cpan Object::Accessor +cpan Object::Realize::Later +cpan PDF::API2 + +# +# seems to fail (sometimes) with parallel builds during install: +# can't write to symdb /dev/shm/perl-5.28.1-0/lib/site_perl/5.28.1/x86_64-linux/PDL/pdldoc.db at blib/lib/PDL/Doc.pm line 497. +# +MAKEFLAGS= cpan PDL +cpan PPITerm::UI +PERL5LIB=".${PERL5LIB:+:$PERL5LIB}" cpan PPI::Document # required by PPIx::Regexp +PERL5LIB=".${PERL5LIB:+:$PERL5LIB}" cpan Task::Weaken # required by PPIx::Regexp +cpan PPIx::Regexp +cpan Package::Constants +cpan Package::DeprecationManager +cpan Package::Stash +cpan Package::Stash::XS +cpan Params::Util +cpan Params::Validate +cpan Parse::RecDescent +cpan PatchReader +cpan Path::FindDev +cpan Path::FindDev::Object +cpan Path::IsDev +cpan Path::Tiny +cpan Pegex +cpan Perl::Critic +cpan Perl::Tidy +cpan Plack +cpan Pod::Coverage +cpan Pod::LaTeX +cpan Pod::Plainer +cpan Pod::Spell +cpan Probe::Perl +cpan Readonly +cpan Regexp::Common +cpan Return::Value +cpan Role::Tiny +cpan Router::Simple +cpan SVG +cpan Set::IntSpan +cpan Shell +cpan Spreadsheet::ParseExcel +cpan Starlink::AST +cpan Statistics::Descriptive +cpan Statistics::Distributions +cpan Stream::Buffered +cpan String::CRC32 +cpan String::Format +cpan Sub::Exporter +cpan Sub::Exporter::Progressive +cpan Sub::Install +cpan Sub::Uplevel +cpan Switch +cpan Task::Weaken +cpan Template +cpan Template::Plugin::GD +cpan Term::UI +cpan Test::Deep +cpan Test::Differences +cpan Test::Exception +cpan Test::Fatal +cpan Test::Inter +cpan Test::Most +cpan Test::NoWarnings +cpan Test::Number::Delta +cpan Test::Object +cpan Test::Output +cpan Test::Pod +cpan Test::Pod::Coverage +cpan Test::Requires +cpan Test::Script +cpan Test::SharedFork +cpan Test::SubCalls +cpan Test::TCP +cpan -f Test::Taint # test sometimes fail, because Test::More sets untainted environment variable TEST_ACTIVE +cpan Test::Warn +cpan Test::YAML +cpan Text::CSV +cpan Text::Diff +cpan Text::Format +cpan Text::Soundex +cpan TheSchwartz +cpan Tie::DBI +cpan Tie::RDBM +cpan Time::Date +cpan Time::Period +cpan Tk +cpan Tie::Watch +cpan Tree::DAG_Node +cpan Try::Tiny +cpan URI +cpan Unix::Syslog +cpan User::Identity +cpan Version::Requirements +cpan WWW::Dict::Leo::Org +cpan WWW::Mechanize +cpan WWW::RobotRules +cpan XML::DOM +cpan XML::LibXML +cpan XML::LibXSLT +cpan XML::NamespaceSupport +cpan XML::Parser +cpan XML::Parser::Lite +cpan XML::Quote +cpan XML::RegExp +cpan XML::SAX +cpan XML::SAX::Base +cpan XML::SAX::Expat +cpan XML::Simple +cpan XML::Twig +cpan XML::XPath +cpan YAML +cpan YAML::LibYAML + +cpan common::sense +cpan inc::latest +cpan install +cpan local::lib + +cpan Date::Manip +( + cd $PREFIX/build + test -e Donald-1.05.tar.gz || wget https://github.molgen.mpg.de/donald/Donald/archive/1.05.tar.gz -O Donald-1.05.tar.gz + test -d Donald-1.05 || tar xf Donald-1.05.tar.gz + cd Donald-1.05 + cpan . +) +cpan PDL::Stats +( + cd $PREFIX/build + test -e Pcap-0.02.tar.gz || cp /home/buczek/build/Pcap/Pcap-0.02.tar.gz . + test -d Pcap-0.02 || tar xf Pcap-0.02.tar.gz + cd Pcap-0.02 + cpan . +) + +( + cd $PREFIX/build + test -e rrdtool-1.6.0.tar.gz || wget https://oss.oetiker.ch/rrdtool/pub/rrdtool-1.6.0.tar.gz + test -d rrdtool-1.6.0 || tar xf rrdtool-1.6.0.tar.gz + cd rrdtool-1.6.0 + ./configure --prefix $PREFIX + make -j $(nproc) + cd bindings/perl-shared/ + cpan . + cd ../perl-piped + cpan . +) + +( + cd $PREFIX/build + test -e net-snmp-5.8.tar.gz || wget https://downloads.sourceforge.net/project/net-snmp/net-snmp/5.8/net-snmp-5.8.tar.gz + test -d net-snmp-5.8 || tar xvf net-snmp-5.8.tar.gz + cd net-snmp-5.8 + patch -N -p1 < /src/mariux/patches/net-snmp-0001-Fix-incompatible-definitions-of-U64-type.patch || true + ./configure --prefix $PREFIX + # make -j sometimes fails "ranlib: .libs/libnetsnmpmibs.a: Malformed archive" + make + make install +) + +# Do bioperl last, because it doesn't declare all dependencies correctly +# +cpan Bio::Perl +# cpan -T Bio::Biblio # "ERROR 11 Unable to connect to database [medline" instead of xml file from net +cpan Bio::Coordinate +#cpan Bio::Graphics::Browser2 # GBrowse - requires Bio::DB::Sam +#cpan Bio::DB::Sam # Bio-SamTools 'Please enter the location of the bam.h and compiled libbam.a files' + +cpan -f XML::DOM::XPath # test fails , install anyway for Bio::FeatureIO + +cpan Bio::FeatureIO +cpan Bio::Tools::EUtilities +#cpan Bio::Tools::Run::StandAloneBlast # several tests fail - tools not available in required version +#cpan Bio::Network::IO # tests fail (whatever) + +#still missing (found by: /home/buczek/libcheck/perlcompare.pl) +# +#Alien::SVN # Alien-SVN: wants SVN install, assumed obsolete +#Apache::XMLRPC::Lite # SOAP-Lite-1.01 : obsolete +#B::Lint* # B-Lint-1.20-0 : I dont think we need this +#CGI::Apache # mod_perl - requires Apache source and asks for it endlessly +#UDDI::Lite # 17 years old junk +#XMLRPC* # XMLRPC-Lite: dont think we still need that +#Apache::SOAP # depends on Apache + + +# Devel::IPerl -> Markdown::Pod -> Markdent +# Markdown::Pod (0.006) does not work with Markdent 0.27 or 0.28 because of this change: +# https://github.com/houseabsolute/Markdent/commit/b570af7820aa2358263b5eaf403ec96674edfe58 +# +PERL5LIB=".${PERL5LIB:+:$PERL5LIB}" cpan ZMQ::Constants # for Devel::IPerl +PERL5LIB=".${PERL5LIB:+:$PERL5LIB}" cpan ZMQ::LibZMQ3 # for Devel::IPerl +cpan DROLSKY/Markdent-0.26.tar.gz # required by Devel::IPerl - Markdown::Pod -> Markdent. + +cpan ZMUGHAL/Devel-IPerl-0.008.tar.gz # Devel::IPerl 0.009 requires ZMUGHAL/Net-Async-ZMQ which blocks during test +#cpan Devel::IPerl + +cpan Text::NSP # galonska 29.01.2018 -> helpdesk + +cpan Excel::Writer::XLSX # klages 20.03.2018, helpdesk + +# defeat "Can't locate Makefile.PL in @INC", when Build.PL is used +PERL5LIB=".${PERL5LIB:+:$PERL5LIB}" cpan Convert::Morse # serious fun, kreitler + +cpan Math::Amoeba # Multidimensional Function Minimisation (oldie but goldie:), kreitler + +cpan Crypt::OpenSSL::PBKDF2 # some more crypto stuff, kreitler +cpan Crypt::OpenSSL::AES +cpan Crypt::Blowfish +cpan Crypt::Blowfish_PP +cpan Crypt::CAST5 +cpan Crypt::DES +cpan Crypt::TripleDES +cpan Crypt::TripleDES::CBC +cpan Crypt::IDEA +cpan Crypt::Rijndael +cpan Crypt::CBC +cpan Crypt::MCrypt + +cpan OpenOffice::OODoc # The Open OpenDocument Connector + +cpan Digest::MD4 +cpan Data::Grove # from xml-perl. Has some dependency issues, put at end + +# exit 1 # the final stop before closing +exit From 2ef95f03629beea4e919a71cbc66bf13e6e1780e Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Thu, 23 Apr 2020 11:37:25 +0200 Subject: [PATCH 11/19] perl-5.12.1: Add errno fix from perl-5.18.2 Avoid error ext/Errno/t/Errno..............................................FAILED--Further testing stopped: No errno's are exported make: *** [makefile:874: test] Error 29 by adding a fix from perl-5.18.2. --- perl-5.12.1-0.build.sh | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/perl-5.12.1-0.build.sh b/perl-5.12.1-0.build.sh index e0341b3..da6d565 100755 --- a/perl-5.12.1-0.build.sh +++ b/perl-5.12.1-0.build.sh @@ -70,6 +70,14 @@ test -e perl-$VERSION.tar.gz || wget http://www.cpan.org/src/5.0/perl-$VERSION.t test -d perl-$VERSION || tar xf perl-$VERSION.tar.gz cd perl-$VERSION +# Note: make test below would fail with: +# ext/Errno/t/Errno ........... FAILED--Further testing stopped: No errno's are exported +# Cure: +# https://rt.perl.org/Public/Bug/Display.html?id=123784 +# ... caused by a change in GCC 5.0's preprocesor +# ... Simple work-around is to call the preprocessor with -P option +sed -i -e '/"$cppstdin $Config/ s/cppstdin/cppstdin -P/' ext/Errno/Errno_pm.PL + # -d : use defaults for all answers. # -e : go on without questioning past the production of config.sh. # -s : silent mode, only echoes questions and essential information. From 426acd4b3978746a30c3cbc8c8eebd58aa437eff Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Thu, 23 Apr 2020 13:16:11 +0200 Subject: [PATCH 12/19] perl-5.12.1: Add -Dusethreads Add -Dusethreads to make configuration similar to the configuration of /usr/local/bin/perl. --- perl-5.12.1-0.build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/perl-5.12.1-0.build.sh b/perl-5.12.1-0.build.sh index da6d565..ddcd87a 100755 --- a/perl-5.12.1-0.build.sh +++ b/perl-5.12.1-0.build.sh @@ -85,7 +85,7 @@ sed -i -e '/"$cppstdin $Config/ s/cppstdin/cppstdin -P/' ext/Errno/Errno_pm.PL # -Duseshrplib : build shared perl library (required when perl is to be included in a shared library) # -DEBUGGING : add debugging code (perl -D) # -./Configure -des -Duseshrplib -Dprefix=$PREFIX +./Configure -des -Duseshrplib -Dusethreads -Dprefix=$PREFIX make -j$(nproc) From f3cb1748e821ce83c99cdba2838f45d2476d8bcb Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Thu, 23 Apr 2020 19:31:16 +0200 Subject: [PATCH 13/19] perl-5.12.1: Use gcc-4.5.1 Compiling perl-5.12.1 with gcc-7.5.0 and -O2 fails for some tests: +op/range.t ........................................................ # Failed at op/range.t line 289 +op/numconvert.t ................................................... Failed 12/1440 subtests Theses test don't fail, however, with -O0. So it is assumed that the perl code contains undefined behaviour which a more recent compiler uses for optimizations. The tests also succeed when perl is compiled with gcc 4.5.1 which was used to create the perl installation in /usr/local. We want best performance and maximal compatibility with the perl version from /usr/local. Use the old gcc compiler. We use the old gcc compiler only for perl itself, not for cpan modules. Some of these required c++. Also the cpan modules are kept up to date and bugs which surfaced by changes in the compiler are fixed. --- perl-5.12.1-0.build.sh | 3 +++ 1 file changed, 3 insertions(+) diff --git a/perl-5.12.1-0.build.sh b/perl-5.12.1-0.build.sh index ddcd87a..55039a3 100755 --- a/perl-5.12.1-0.build.sh +++ b/perl-5.12.1-0.build.sh @@ -78,6 +78,8 @@ cd perl-$VERSION # ... Simple work-around is to call the preprocessor with -P option sed -i -e '/"$cppstdin $Config/ s/cppstdin/cppstdin -P/' ext/Errno/Errno_pm.PL +( . /pkg/gcc-4.5.1-0/profile + # -d : use defaults for all answers. # -e : go on without questioning past the production of config.sh. # -s : silent mode, only echoes questions and essential information. @@ -95,6 +97,7 @@ make -j$(nproc) # make test make install +) cd $PREFIX; From cd4b4f0cc18c9fab19f3da3c510b76c63753421b Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Fri, 24 Apr 2020 19:41:55 +0200 Subject: [PATCH 14/19] perl-5.12.1: Remove ext/Time-Local test This test fails: ok 1 - timelocal second for 1970 1 2 0 0 0 ok 2 - timelocal minute for 1970 1 2 0 0 0 ok 3 - timelocal hour for 1970 1 2 0 0 0 ok 4 - timelocal day for 1970 1 2 0 0 0 ok 5 - timelocal month for 1970 1 2 0 0 0 not ok 6 - timelocal year for 1970 1 2 0 0 0 # Failed test 'timelocal year for 1970 1 2 0 0 0' # at ext/Time-Local/t/Local.t line 97. # got: '170' # expected: '70' which is probably caused by a Y2K fix in localtime() of glibc. The test fails with the perlversion installed into /usr/local as well, which is the version we want to be compatible with. So just remove this test. --- perl-5.12.1-0.build.sh | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/perl-5.12.1-0.build.sh b/perl-5.12.1-0.build.sh index 55039a3..0b376e8 100755 --- a/perl-5.12.1-0.build.sh +++ b/perl-5.12.1-0.build.sh @@ -70,6 +70,22 @@ test -e perl-$VERSION.tar.gz || wget http://www.cpan.org/src/5.0/perl-$VERSION.t test -d perl-$VERSION || tar xf perl-$VERSION.tar.gz cd perl-$VERSION +# Remove ext/Time-Local/t/Local.t test. +# +# probably some Y2K required change in glibc localtime() makes this fail: +# ok 1 - timelocal second for 1970 1 2 0 0 0 +# ok 2 - timelocal minute for 1970 1 2 0 0 0 +# ok 3 - timelocal hour for 1970 1 2 0 0 0 +# ok 4 - timelocal day for 1970 1 2 0 0 0 +# ok 5 - timelocal month for 1970 1 2 0 0 0 +# not ok 6 - timelocal year for 1970 1 2 0 0 0 +# Failed test 'timelocal year for 1970 1 2 0 0 0' +# at ext/Time-Local/t/Local.t line 97. +# got: '170' +# expected: '70' +# +sed -i '/Local\.t/d' MANIFEST + # Note: make test below would fail with: # ext/Errno/t/Errno ........... FAILED--Further testing stopped: No errno's are exported # Cure: From 65ed6613435c681ec1e323cd987298bd5eae40f7 Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Fri, 24 Apr 2020 21:53:13 +0200 Subject: [PATCH 15/19] perl-5.12.1: Add Berkely DB We removed Berekely DB from the system, but it is required here for the BerkeleyDB perl module which is required for DB_File which is required for bioperl. Install Berekeley DB into the package. --- perl-5.12.1-0.build.sh | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/perl-5.12.1-0.build.sh b/perl-5.12.1-0.build.sh index 0b376e8..79e481e 100755 --- a/perl-5.12.1-0.build.sh +++ b/perl-5.12.1-0.build.sh @@ -191,7 +191,22 @@ cpan Archive::Zip cpan Attribute::Params::Validate cpan Authen::SASL cpan B::Keywords -cpan BerkeleyDB + +( + cd $PREFIX/build + # https://ftp6.gwdg.de/pub/linux/slackware/slackware-14.0/source/l/db48/db-4.8.30.tar.xz + test -e db-4.8.30.tar.xz || cp /src/mariux/md5repo/de18e52d5ec52489621cbab083858484/db-4.8.30.tar.xz . + test -d db-4.8.30 || tar xf db-4.8.30.tar.xz + cd db-4.8.30 + # for unknown reason, the "docs" directory is missing in the distribution + sed -i 's/install_docs//' dist/Makefile.in + cd build_unix + CFLAGS="-O2 -fPIC" CXXFLAGS=${CFLAGS} ../dist/configure --prefix=${PREFIX} --enable-compat185 --enable-cxx --disable-test --enable-shared + make + make install +) + +BERKELEYDB_INCLUDE=$PREFIX/include BERKELEYDB_LIB=$PREFIX/lib cpan BerkeleyDB cpan Bit::Vector cpan CGI cpan CGI::Fast From f2c009ad04872936b9e41084a0359188d8867568 Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Sat, 25 Apr 2020 11:22:45 +0200 Subject: [PATCH 16/19] perl-5.12.1: Disable tests for PDL We have a single failed test for PDL because of missing "pngtopnm". Disable tests for this module. --- perl-5.12.1-0.build.sh | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/perl-5.12.1-0.build.sh b/perl-5.12.1-0.build.sh index 79e481e..db8d2b5 100755 --- a/perl-5.12.1-0.build.sh +++ b/perl-5.12.1-0.build.sh @@ -394,11 +394,26 @@ cpan Object::Accessor cpan Object::Realize::Later cpan PDF::API2 +# PDL # # seems to fail (sometimes) with parallel builds during install: # can't write to symdb /dev/shm/perl-5.28.1-0/lib/site_perl/5.28.1/x86_64-linux/PDL/pdldoc.db at blib/lib/PDL/Doc.pm line 497. +# disabled parallel build # -MAKEFLAGS= cpan PDL +# Also one test fails: +# Oops, this is not a PNM fileconverter error: sh: pngtopnm: command not found +# at /dev/shm/perl-5.12.1-0.build.tmp/home/.cpan/build/PDL-2.021-0/blib/lib/PDL/IO/Pnm.pm line 79. +# PDL::IO::Pnm::rbarf("/dev/shm/perl-5.12.1-0.build.tmp/xx7fgrpX1_", "Oops, this is not a PNM file") called at /dev/shm/perl-5.12.1-0.build.tmp/home/.cpan/build/PDL-2.021-0/blib/lib/PDL/IO/Pnm.pm line 274 +# PDL::rpnm("PDL", PDL=SCALAR(0x9115a0), "pngtopnm \"/dev/shm/perl-5.12.1-0.build.tmp/o1iV1Ham33/t byte"...) called at /dev/shm/perl-5.12.1-0.build.tmp/home/.cpan/build/PDL-2 .021-0/blib/lib/PDL/IO/Pnm.pm line 248 +# PDL::IO::Pnm::rpnm(PDL=SCALAR(0x9115a0), "pngtopnm \"/dev/shm/perl-5.12.1-0.build.tmp/o1iV1Ham33/t byte"...) called at /dev/shm/perl-5.12.1-0.build.tmp/home/.cpan/build/PDL -2.021-0/blib/lib/PDL/IO/Pic.pm line 322 +# PDL::rpic("PDL", "/dev/shm/perl-5.12.1-0.build.tmp/o1iV1Ham33/t byte_a.png") called at /dev/shm/perl-5.12.1-0.build.tmp/home/.cpan/build/PDL-2.021-0/blib/lib/PDL/IO/Pic.pm line 277 +# PDL::IO::Pic::rpic("/dev/shm/perl-5.12.1-0.build.tmp/o1iV1Ham33/t byte_a.png") called at t/pic_16bit.t line 51 +# # Looks like your test exited with 255 just after 2. +# t/pic_16bit.t ................... +# +# disable tests +# +MAKEFLAGS= cpan -f PDL cpan PPITerm::UI PERL5LIB=".${PERL5LIB:+:$PERL5LIB}" cpan PPI::Document # required by PPIx::Regexp PERL5LIB=".${PERL5LIB:+:$PERL5LIB}" cpan Task::Weaken # required by PPIx::Regexp From 46e280b2b4e91c489d95ff1127942a06815360d1 Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Sat, 25 Apr 2020 18:22:43 +0200 Subject: [PATCH 17/19] perl-5.12.1: Add DB_File for Bio::Perl --- perl-5.12.1-0.build.sh | 2 ++ 1 file changed, 2 insertions(+) diff --git a/perl-5.12.1-0.build.sh b/perl-5.12.1-0.build.sh index db8d2b5..004ecf2 100755 --- a/perl-5.12.1-0.build.sh +++ b/perl-5.12.1-0.build.sh @@ -567,6 +567,8 @@ cpan PDL::Stats make install ) +DB_FILE_INCLUDE=$PREFIX/include DB_FILE_LIB=$PREFIX/lib cpan DB_File # for Bio::Perl + # Do bioperl last, because it doesn't declare all dependencies correctly # cpan Bio::Perl From 1cefaf10a69368fef7f6299613f500e5b448efdd Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Sat, 25 Apr 2020 16:16:58 +0200 Subject: [PATCH 18/19] perl-5.12-1: Remove Devel::IPerl Avoid ZMUGHAL/Devel-IPerl-0.008.tar.gz requires perl '5.013002'; you have only 5.012001; giving up --- perl-5.12.1-0.build.sh | 24 ------------------------ 1 file changed, 24 deletions(-) diff --git a/perl-5.12.1-0.build.sh b/perl-5.12.1-0.build.sh index 004ecf2..d16be9b 100755 --- a/perl-5.12.1-0.build.sh +++ b/perl-5.12.1-0.build.sh @@ -581,30 +581,6 @@ cpan -f XML::DOM::XPath # test fails , install anyway for Bio::FeatureIO cpan Bio::FeatureIO cpan Bio::Tools::EUtilities -#cpan Bio::Tools::Run::StandAloneBlast # several tests fail - tools not available in required version -#cpan Bio::Network::IO # tests fail (whatever) - -#still missing (found by: /home/buczek/libcheck/perlcompare.pl) -# -#Alien::SVN # Alien-SVN: wants SVN install, assumed obsolete -#Apache::XMLRPC::Lite # SOAP-Lite-1.01 : obsolete -#B::Lint* # B-Lint-1.20-0 : I dont think we need this -#CGI::Apache # mod_perl - requires Apache source and asks for it endlessly -#UDDI::Lite # 17 years old junk -#XMLRPC* # XMLRPC-Lite: dont think we still need that -#Apache::SOAP # depends on Apache - - -# Devel::IPerl -> Markdown::Pod -> Markdent -# Markdown::Pod (0.006) does not work with Markdent 0.27 or 0.28 because of this change: -# https://github.com/houseabsolute/Markdent/commit/b570af7820aa2358263b5eaf403ec96674edfe58 -# -PERL5LIB=".${PERL5LIB:+:$PERL5LIB}" cpan ZMQ::Constants # for Devel::IPerl -PERL5LIB=".${PERL5LIB:+:$PERL5LIB}" cpan ZMQ::LibZMQ3 # for Devel::IPerl -cpan DROLSKY/Markdent-0.26.tar.gz # required by Devel::IPerl - Markdown::Pod -> Markdent. - -cpan ZMUGHAL/Devel-IPerl-0.008.tar.gz # Devel::IPerl 0.009 requires ZMUGHAL/Net-Async-ZMQ which blocks during test -#cpan Devel::IPerl cpan Text::NSP # galonska 29.01.2018 -> helpdesk From ec2690d4579db8df37bbbd0e04df258df06ba026 Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Sun, 26 Apr 2020 10:48:55 +0200 Subject: [PATCH 19/19] perl-5.12.1: Add Net::SNMP::SSL This perl package should be a replacement for the perl installation in /usr/local. We've compared the list of packages from /usr/local with those installed into this package so far. Ignoring the huge amount of packages in the Bio:: namespace, which are the result of chaotic maintenance, ridiculous fragmentation and continuous reorganization the following packages are missing: DateTime::TimeZone::Local::Win32 File::ShareDir::ProjectDistDir LWP::Protocol::GHTTP LWP::Protocol::http10 Net::SMTP::SSL Apache::SOAP Apache::XMLRPC::Lite DBI::FAQ DateTime::TimeZone::America::Godthab Mojolicious::Command::test Mojolicious::Plugin::PODRenderer PDL::Graphics::PGPLOT PDL::Graphics::PGPLOT::Window PDL::Graphics::PGPLOTOptions PPI::Exception::ParserTimeout Perl::Critic::Policy::Documentation::RequirePodLinksIncludeText Plack::Handler::HTTP::Server::Simple From this list only Net::SMTP::SSL seems relevant, so add this package. --- perl-5.12.1-0.build.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/perl-5.12.1-0.build.sh b/perl-5.12.1-0.build.sh index d16be9b..c6d4fdb 100755 --- a/perl-5.12.1-0.build.sh +++ b/perl-5.12.1-0.build.sh @@ -608,6 +608,7 @@ cpan OpenOffice::OODoc # The Open OpenDocument Connector cpan Digest::MD4 cpan Data::Grove # from xml-perl. Has some dependency issues, put at end +cpan Net::SMTP::SSL # recently installed into /usr/local perl after # exit 1 # the final stop before closing exit