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#84 Patches from PDL Debian package

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2016-09-23
2016-06-18
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The attached patches are included in the Debian package for PDL 2.016, please consider applying them.

  • doc_vendor_install.patch
    Description: Fix doc_vendor_install target by supporting DESTDIR.
    Author: Bas Couwenberg sebastic@debian.org
  • spelling-errors.patch
    Description: Fix spelling errors.
    Author: Bas Couwenberg sebastic@debian.org
  • pdl-cppflags.patch
    Description: Use CPPFLAGS for pdl executable.
    Author: Bas Couwenberg sebastic@debian.org
  • dumper_gnukfreebsd.patch
    Description: Fix Dumper.pm on kFreebsd.
    'gnukfreebsd' was assumed as a bsd userland,
    which disabled/broke calls to 'uuencode' and 'uudecode'.
    Author: Henning Glawe glaweh@debian.org
  • doc_dirlist.patch
    Description: Accept comma-separated directory lists in scantree.pl.
    Used by trigger in postinst.
    Author: Henning Glawe glaweh@debian.org
    Bug-Debian: https://bugs.debian.org/681937
  • slatec_default_integer_8.patch
    Description: Use 64bit integers in Slatec module.
    For the time being, always use 64bit integers in Fortran libs
    slatec and minuit by default, as Debian perl packages switched
    to ivsize=8 on all arches, implying a 64bit index type in PDL.
    Author: Henning Glawe glaweh@debian.org
  • minuit_default_integer_8.patch
    Description: Use 64bit integers in Minuit module.
    For the time being, always use 64bit integers in Fortran libs
    slatec and minuit by default, as Debian perl packages switched
    to ivsize=8 on all arches, implying a 64bit index type in PDL.
    Author: Henning Glawe glaweh@debian.org

Kind Regards,

Bas

7 Attachments

Discussion

  • Bas Couwenberg

    Bas Couwenberg - 2016-06-18

    Here's another patch to fix to the manpages generated for PDL::IFiles.

    • manpage-has-bad-whatis-entry.patch
      Description: Add module description for manpage whatis entry.
      Author: Bas Couwenberg sebastic@debian.org
     
  • Bas Couwenberg

    Bas Couwenberg - 2016-06-24

    The lintian QA tool reported a couple of new spelling errors for the latest build.

     
  • Bas Couwenberg

    Bas Couwenberg - 2016-07-04

    Reiner Herrmann suplied an updated reproducible-build.patch.

     
  • Derek Lamb

    Derek Lamb - 2016-09-16

    Thank you for these patches. Most have been applied, they are currently on the debian_patches branch--there is an open pull request on GitHub . I elected to not change history and keep the erroneous spellings as-is in the Changes* files.

    The slatec_default_integer_8.patch and minuit_default_integer_8.patch are unlikely to be portable: applying them on my Mac causes compilation warnings (where before there were none) and some tests to fail. If you can supply a more portable patch, please do--this might involve $Config{'ivtype'} or the realctype from PDL::Types. If you can not, I will merge the existing changes in to master soon but keep this ticket open pending a more portable version of those patches.

    It would be helpful to have an example perl -V from a Debian system to compare to my Mac, and to know what problem you were trying to solve with these two integer_8.patches: Segfault? Test failure? Compiler error? Compiler warning? Something else?

    Thanks again!

     
  • Bas Couwenberg

    Bas Couwenberg - 2016-09-17

    I'm not the author of those patches, I don't know more about them than what's included in the patch description. Henning Glawe should be able to tell you more about those patches. This seems to be most relevant part of the description: "Debian perl packages switched
    to ivsize=8 on all arches"

    I've only updated the PDL packages in Debian because no one was working on them any more and some of the PDL packages are reverse dependencies of the GIS packages I maintain. See the discussion on the debian-perl list: https://lists.debian.org/debian-perl/2016/06/msg00008.html

    perl -V on Debian unstable:

    $ perl -V
    Summary of my perl5 (revision 5 version 22 subversion 2) configuration:
    
      Platform:
        osname=linux, osvers=3.16.0, archname=x86_64-linux-gnu-thread-multi
        uname='linux localhost 3.16.0 #1 smp debian 3.16.0 x86_64 gnulinux '
        config_args='-Dusethreads -Duselargefiles -Dcc=x86_64-linux-gnu-gcc -Dcpp=x86_64-linux-gnu-cpp -Dld=x86_64-linux-gnu-gcc -Dccflags=-DDEBIAN -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/perl-evYEmQ/perl-5.22.2=. -fstack-protector-strong -Wformat -Werror=format-security -Dldflags= -Wl,-z,relro -Dlddlflags=-shared -Wl,-z,relro -Dcccdlflags=-fPIC -Darchname=x86_64-linux-gnu -Dprefix=/usr -Dprivlib=/usr/share/perl/5.22 -Darchlib=/usr/lib/x86_64-linux-gnu/perl/5.22 -Dvendorprefix=/usr -Dvendorlib=/usr/share/perl5 -Dvendorarch=/usr/lib/x86_64-linux-gnu/perl5/5.22 -Dsiteprefix=/usr/local -Dsitelib=/usr/local/share/perl/5.22.2 -Dsitearch=/usr/local/lib/x86_64-linux-gnu/perl/5.22.2 -Dman1dir=/usr/share/man/man1 -Dman3dir=/usr/share/man/man3 -Dsiteman1dir=/usr/local/man/man1 -Dsiteman3dir=/usr/local/man/man3 -Dusesitecustomize -Duse64bitint -Dman1ext=1 -Dman3ext=3perl -Dpager=/usr/bin/sensible-pager -Uafs -Ud_csh -Ud_ualarm -Uusesfio -Uusenm -Ui_libutil -Uversiononly -DDEBUGGING=-g -Doptimize=-O2 -dEs -Duseshrplib -Dlibperl=libperl.so.5.22.2'
        hint=recommended, useposix=true, d_sigaction=define
        useithreads=define, usemultiplicity=define
        use64bitint=define, use64bitall=define, uselongdouble=undef
        usemymalloc=n, bincompat5005=undef
      Compiler:
        cc='x86_64-linux-gnu-gcc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
        optimize='-O2 -g',
        cppflags='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include'
        ccversion='', gccversion='6.2.0 20160822', gccosandvers=''
        intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678, doublekind=3
        d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16, longdblkind=3
        ivtype='long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
        alignbytes=8, prototype=define
      Linker and Libraries:
        ld='x86_64-linux-gnu-gcc', ldflags =' -fstack-protector-strong -L/usr/local/lib'
        libpth=/usr/local/lib /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed /usr/include/x86_64-linux-gnu /usr/lib /lib/x86_64-linux-gnu /lib/../lib /usr/lib/x86_64-linux-gnu /usr/lib/../lib /lib
        libs=-lgdbm -lgdbm_compat -ldb -ldl -lm -lpthread -lc -lcrypt
        perllibs=-ldl -lm -lpthread -lc -lcrypt
        libc=libc-2.23.so, so=so, useshrplib=true, libperl=libperl.so.5.22
        gnulibc_version='2.23'
      Dynamic Linking:
        dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
        cccdlflags='-fPIC', lddlflags='-shared -L/usr/local/lib -fstack-protector-strong'
    
    Characteristics of this binary (from libperl): 
      Compile-time options: HAS_TIMES MULTIPLICITY PERLIO_LAYERS
                            PERL_DONT_CREATE_GVSV
                            PERL_HASH_FUNC_ONE_AT_A_TIME_HARD
                            PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
                            PERL_NEW_COPY_ON_WRITE PERL_PRESERVE_IVUV
                            USE_64_BIT_ALL USE_64_BIT_INT USE_ITHREADS
                            USE_LARGE_FILES USE_LOCALE USE_LOCALE_COLLATE
                            USE_LOCALE_CTYPE USE_LOCALE_NUMERIC USE_LOCALE_TIME
                            USE_PERLIO USE_PERL_ATOF USE_REENTRANT_API
                            USE_SITECUSTOMIZE
      Locally applied patches:
            DEBPKG:debian/cpan_definstalldirs - Provide a sensible INSTALLDIRS default for modules installed from CPAN.
            DEBPKG:debian/db_file_ver - http://bugs.debian.org/340047 Remove overly restrictive DB_File version check.
            DEBPKG:debian/doc_info - Replace generic man(1) instructions with Debian-specific information.
            DEBPKG:debian/enc2xs_inc - http://bugs.debian.org/290336 Tweak enc2xs to follow symlinks and ignore missing @INC directories.
            DEBPKG:debian/errno_ver - http://bugs.debian.org/343351 Remove Errno version check due to upgrade problems with long-running processes.
            DEBPKG:debian/libperl_embed_doc - http://bugs.debian.org/186778 Note that libperl-dev package is required for embedded linking
            DEBPKG:fixes/respect_umask - Respect umask during installation
            DEBPKG:debian/writable_site_dirs - Set umask approproately for site install directories
            DEBPKG:debian/extutils_set_libperl_path - EU:MM: set location of libperl.a under /usr/lib
            DEBPKG:debian/no_packlist_perllocal - Don't install .packlist or perllocal.pod for perl or vendor
            DEBPKG:debian/fakeroot - Postpone LD_LIBRARY_PATH evaluation to the binary targets.
            DEBPKG:debian/instmodsh_doc - Debian policy doesn't install .packlist files for core or vendor.
            DEBPKG:debian/ld_run_path - Remove standard libs from LD_RUN_PATH as per Debian policy.
            DEBPKG:debian/libnet_config_path - Set location of libnet.cfg to /etc/perl/Net as /usr may not be writable.
            DEBPKG:debian/mod_paths - Tweak @INC ordering for Debian
            DEBPKG:debian/prune_libs - http://bugs.debian.org/128355 Prune the list of libraries wanted to what we actually need.
            DEBPKG:fixes/net_smtp_docs - [rt.cpan.org #36038] http://bugs.debian.org/100195 Document the Net::SMTP 'Port' option
            DEBPKG:debian/perlivp - http://bugs.debian.org/510895 Make perlivp skip include directories in /usr/local
            DEBPKG:debian/deprecate-with-apt - http://bugs.debian.org/747628 Point users to Debian packages of deprecated core modules
            DEBPKG:debian/squelch-locale-warnings - http://bugs.debian.org/508764 Squelch locale warnings in Debian package maintainer scripts
            DEBPKG:debian/skip-upstream-git-tests - Skip tests specific to the upstream Git repository
            DEBPKG:debian/patchlevel - http://bugs.debian.org/567489 List packaged patches for 5.22.2-5 in patchlevel.h
            DEBPKG:debian/skip-kfreebsd-crash - http://bugs.debian.org/628493 [perl #96272] Skip a crashing test case in t/op/threads.t on GNU/kFreeBSD
            DEBPKG:fixes/document_makemaker_ccflags - http://bugs.debian.org/628522 [rt.cpan.org #68613] Document that CCFLAGS should include $Config{ccflags}
            DEBPKG:debian/find_html2text - http://bugs.debian.org/640479 Configure CPAN::Distribution with correct name of html2text
            DEBPKG:debian/perl5db-x-terminal-emulator.patch - http://bugs.debian.org/668490 Invoke x-terminal-emulator rather than xterm in perl5db.pl
            DEBPKG:debian/cpan-missing-site-dirs - http://bugs.debian.org/688842 Fix CPAN::FirstTime defaults with nonexisting site dirs if a parent is writable
            DEBPKG:fixes/memoize_storable_nstore - [rt.cpan.org #77790] http://bugs.debian.org/587650 Memoize::Storable: respect 'nstore' option not respected
            DEBPKG:debian/regen-skip - Skip a regeneration check in unrelated git repositories
            DEBPKG:debian/makemaker-pasthru - http://bugs.debian.org/758471 Pass LD settings through to subdirectories
            DEBPKG:fixes/pod_man_reproducible_date - http://bugs.debian.org/759405 Support POD_MAN_DATE in Pod::Man for the left-hand footer
            DEBPKG:debian/locale-robustness - http://bugs.debian.org/782068 [perl #124310] Make t/run/locale.t survive missing locales masked by LC_ALL
            DEBPKG:fixes/podman-utc - http://bugs.debian.org/780259 Make the embedded date from Pod::Man reproducible
            DEBPKG:fixes/podman-utc-docs - http://bugs.debian.org/780259 Documentation and test suite updates for UTC fix
            DEBPKG:fixes/podman-empty-date - http://bugs.debian.org/780259 Support an empty POD_MAN_DATE environment variable
            DEBPKG:fixes/podman-pipe - http://bugs.debian.org/777405 Better errors for man pages from standard input
            DEBPKG:debian/pod2man-customized - Update porting/customized.dat for pod2man modifications
            DEBPKG:debian/makemaker-manext - http://bugs.debian.org/247370 Make EU::MakeMaker honour MANnEXT settings in generated manpage headers
            DEBPKG:debian/makemaker_customized - Update t/porting/customized.dat for files patched in Debian
            DEBPKG:debian/do-not-record-build-date - [6baa8db] http://bugs.debian.org/774422 [perl #125830] Allow overriding the compile time in "perl -V" output
            DEBPKG:fixes/podman-source-date-epoch - http://bugs.debian.org/801621 Make Pod::Man honor the SOURCE_DATE_EPOCH environment variable
            DEBPKG:fixes/podman-source-date-epoch-cleanups - http://bugs.debian.org/801621 Coding style and documentation for SOURCE_EPOCH_DATE
            DEBPKG:fixes/podman-source-date-epoch-testfix - http://bugs.debian.org/807086 Guard for building with SOURCE_DATE_EPOCH or POD_MAN_DATE set
            DEBPKG:debian/devel-ppport-reproducibility - http://bugs.debian.org/801523 Sort the list of XS code files when generating RealPPPort.xs
            DEBPKG:fixes/encode-unicode-bom - http://bugs.debian.org/798727 [rt.cpan.org #107043] Address https://rt.cpan.org/Public/Bug/Display.html?id=107043
            DEBPKG:debian/encode-unicode-bom-doc - http://bugs.debian.org/798727 Document Debian backport of Encode::Unicode fix
            DEBPKG:debian/kfreebsd-softupdates - http://bugs.debian.org/796798 Work around Debian Bug#796798
            DEBPKG:fixes/autodie-scope - http://bugs.debian.org/798096 Fix a scoping issue with "no autodie" and the "system" sub
            DEBPKG:debian/debugperl-compat-fix - [perl #127212] http://bugs.debian.org/810326 Disable PERL_TRACK_MEMPOOL for debugging builds
            DEBPKG:fixes/crosscompile-no-targethost - [perl #127234] Fix the Configure escape with usecrosscompile but no targethost
            DEBPKG:fixes/podlators-no-encode - [rt.cpan.org #111156] Degrade gracefully if utf8 is requested but Encode is not available
            DEBPKG:debian/cross-time-hires - [rt.cpan.org #111391] Add an environment variable to skip running configuration probes
            DEBPKG:fixes/encode-unicode-pod - Unicode.pm: Fix POD error
            DEBPKG:fixes/memoize-pod - [rt.cpan.org #89441] Fix POD errors in Memoize
            DEBPKG:fixes/ok-pod - Added encoding for pod.
            DEBPKG:debian/hurd-softupdates - http://bugs.debian.org/822735 Fix t/op/stat.t failures on hurd
            DEBPKG:fixes/xsloader-eval - [rt.cpan.org #115808] http://bugs.debian.org/829578 =?UTF-8?q?Don=E2=80=99t=20let=20XSLoader=20load=20relative=20path?= =?UTF-8?q?s?=
            DEBPKG:fixes/extutils-parsexs-reproducibility - [perl #128517] http://bugs.debian.org/829296 Make the output of ExtUtils::ParseXS reproducible
            DEBPKG:fixes/CVE-2016-1238/remove-dot-when-loading - [perl #127834] (perl #127834) remove . from the end of @INC if complex modules are loaded
            DEBPKG:fixes/CVE-2016-1238/remove-dot-in-padwalker - [perl #127834] perl5db.pl: ensure PadWalker is loaded from standard paths
            DEBPKG:fixes/CVE-2016-1238/remove-dot-in-dist - [perl #127834] dist/: remove . from @INC when loading optional modules
            DEBPKG:fixes/CVE-2016-1238/remove-dot-in-cpan - [perl #127834] cpan/: remove . from @INC when loading optional modules
            DEBPKG:debian/CVE-2016-1238/test-suite-without-dot - [perl #127810] Patch unit tests to explicitly insert "." into @INC when needed.
            DEBPKG:debian/CVE-2016-1238/eumm-without-dot - [perl #127810] Add PERL_USE_UNSAFE_INC support to EU::MM for fortify_inc support.
            DEBPKG:debian/CVE-2016-1238/cpan-without-dot - [perl #127810] Set PERL_USE_UNSAFE_INC for cpan usage
            DEBPKG:debian/CVE-2016-1238/sitecustomize-in-etc - Look for sitecustomize.pl in /etc/perl rather than sitelib on Debian systems
            DEBPKG:debian/CVE-2016-1238/customized - Update customized.dat for CVE-2016-1238 changes
            DEBPKG:debian/CVE-2016-1238/remove-inc-test - Remove test for '.' in @INC as it might not be
            DEBPKG:fixes/extutils_makemaker_reproducible - http://bugs.debian.org/835815 http://bugs.debian.org/834190 Make perllocal.pod files reproducible
            DEBPKG:debian/mm_eu_reproducible_customized - Update customized.dat for MakeMaker::ExtUtils reproducibility fixes
            DEBPKG:debian/document_inc_removal - Document in perlvar that we remove '.' from @INC by default
      Built under linux
      Compiled at Sep  3 2016 09:48:53
      @INC:
        /etc/perl
        /usr/local/lib/x86_64-linux-gnu/perl/5.22.2
        /usr/local/share/perl/5.22.2
        /usr/lib/x86_64-linux-gnu/perl5/5.22
        /usr/share/perl5
        /usr/lib/x86_64-linux-gnu/perl/5.22
        /usr/share/perl/5.22
        /usr/local/lib/site_perl
        /usr/lib/x86_64-linux-gnu/perl-base
    

    Please note we'll be transitioning to 5.24 soon, see: https://bugs.debian.org/830200

     
  • Derek Lamb

    Derek Lamb - 2016-09-23

    A developer's release, PDL-2.016_02, which is now on CPAN, contains these patches except for the aforementioned slatec and minuit patches. Please test: PDL-2.017 is slated for code freeze October 3rd, release 1 week later.

     

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