Невозможно установить модули perl через cpanm в средах conda

Я могу попытаться ответить на первую часть вопроса: как использовать правильный perl при установке пакетов в среде conda. Я на Ubuntu 20.04:

• Сначала я установил Anaconda в /home/hakon/anaconda3
• Затем я создал тестовую среду:

$ conda create --name perl_test
$ conda activate perl_test

• Установил perl 5.26.2 в окружение:

$ conda install -c anaconda perl

• Инициализировал cpan (это предполагает, что у меня не было предыдущей конфигурации cpan (~/.cpan/) и локальной библиотеки (~/perl5/) в моем домашнем каталоге). Выберите вариант local::lib ниже:

$ cpan
Loading internal null logger. Install Log::Log4perl for logging messages
Sorry, we have to rerun the configuration dialog for CPAN.pm due to
some missing parameters. Configuration will be written to
 <</home/hakon/.cpan/CPAN/MyConfig.pm>>


CPAN.pm requires configuration, but most of it can be done automatically.
If you answer 'no' below, you will enter an interactive dialog for each
configuration option instead.

Would you like to configure as much as possible automatically? [yes] 

 <install_help>

Warning: You do not have write permission for Perl library directories.

To install modules, you need to configure a local Perl library directory or
escalate your privileges.  CPAN can help you by bootstrapping the local::lib
module or by configuring itself to use 'sudo' (if available).  You may also
resolve this problem manually if you need to customize your setup.

What approach do you want?  (Choose 'local::lib', 'sudo' or 'manual')
 [local::lib]           


Autoconfiguration complete.

Attempting to bootstrap local::lib...

Writing /home/hakon/.cpan/CPAN/MyConfig.pm for bootstrap...
commit: wrote '/home/hakon/.cpan/CPAN/MyConfig.pm'
Fetching with HTTP::Tiny:
http://www.cpan.org/authors/01mailrc.txt.gz
Reading '/home/hakon/.cpan/sources/authors/01mailrc.txt.gz'
............................................................................DONE
Fetching with HTTP::Tiny:
http://www.cpan.org/modules/02packages.details.txt.gz
Reading '/home/hakon/.cpan/sources/modules/02packages.details.txt.gz'
  Database was generated on Thu, 14 Jan 2021 19:17:03 GMT
  HTTP::Date not available
.............
  New CPAN.pm version (v2.28) available.
  [Currently running version is v2.18]
  You might want to try
    install CPAN
    reload cpan
  to both upgrade CPAN.pm and run the new version without leaving
  the current session.


...............................................................DONE
Fetching with HTTP::Tiny:
http://www.cpan.org/modules/03modlist.data.gz
Reading '/home/hakon/.cpan/sources/modules/03modlist.data.gz'
DONE
Writing /home/hakon/.cpan/Metadata
Fetching with HTTP::Tiny:
http://www.cpan.org/authors/id/H/HA/HAARG/local-lib-2.000024.tar.gz
Fetching with HTTP::Tiny:
http://www.cpan.org/authors/id/H/HA/HAARG/CHECKSUMS
Checksum for /home/hakon/.cpan/sources/authors/id/H/HA/HAARG/local-lib-2.000024.tar.gz ok
'YAML' not installed, will not store persistent state
Configuring H/HA/HAARG/local-lib-2.000024.tar.gz with Makefile.PL
Attempting to create directory /home/hakon/perl5

Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for local::lib
Writing MYMETA.yml and MYMETA.json
  HAARG/local-lib-2.000024.tar.gz
  /home/hakon/anaconda3/envs/perl_test/bin/perl Makefile.PL --bootstrap -- OK
Running make for H/HA/HAARG/local-lib-2.000024.tar.gz
cp lib/POD2/DE/local/lib.pod blib/lib/POD2/DE/local/lib.pod
cp lib/local/lib.pm blib/lib/local/lib.pm
cp lib/lib/core/only.pm blib/lib/lib/core/only.pm
cp lib/POD2/PT_BR/local/lib.pod blib/lib/POD2/PT_BR/local/lib.pod
Manifying 4 pod documents
  HAARG/local-lib-2.000024.tar.gz
  /bin/make -- OK
Running make test
PERL_DL_NONLAZY=1 "/home/hakon/anaconda3/envs/perl_test/bin/perl" "-I/home/hakon/perl5/lib/perl5" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/bad_variables.t ...... ok   
t/carp-mismatch.t ...... ok   
t/classmethod.t ........ ok   
t/de-dup.t ............. ok   
t/lib-core-only.t ...... ok   
t/pipeline.t ........... ok   
t/shell.t .............. ok       
t/stackable.t .......... ok     
t/subroutine-in-inc.t .. ok   
t/taint-mode.t ......... ok   
All tests successful.
Files=10, Tests=196,  1 wallclock secs ( 0.04 usr  0.01 sys +  0.93 cusr  0.28 csys =  1.26 CPU)
Result: PASS
  HAARG/local-lib-2.000024.tar.gz
  /bin/make test -- OK
Running make install
Manifying 4 pod documents
Installing /home/hakon/perl5/lib/perl5/POD2/PT_BR/local/lib.pod
Installing /home/hakon/perl5/lib/perl5/POD2/DE/local/lib.pod
Installing /home/hakon/perl5/lib/perl5/local/lib.pm
Installing /home/hakon/perl5/lib/perl5/lib/core/only.pm
Installing /home/hakon/perl5/man/man3/lib::core::only.3
Installing /home/hakon/perl5/man/man3/local::lib.3
Installing /home/hakon/perl5/man/man3/POD2::PT_BR::local::lib.3
Installing /home/hakon/perl5/man/man3/POD2::DE::local::lib.3
Appending installation info to /home/hakon/perl5/lib/perl5/x86_64-linux-thread-multi/perllocal.pod
  HAARG/local-lib-2.000024.tar.gz
  /bin/make install  -- OK

local::lib is installed. You must now add the following environment variables
to your shell configuration files (or registry, if you are on Windows) and
then restart your command line shell and CPAN before installing modules:

PATH="/home/hakon/perl5/bin${PATH:+:${PATH}}"; export PATH;
PERL5LIB="/home/hakon/perl5/lib/perl5${PERL5LIB:+:${PERL5LIB}}"; export PERL5LIB;
PERL_LOCAL_LIB_ROOT="/home/hakon/perl5${PERL_LOCAL_LIB_ROOT:+:${PERL_LOCAL_LIB_ROOT}}"; export PERL_LOCAL_LIB_ROOT;
PERL_MB_OPT="--install_base \"/home/hakon/perl5\""; export PERL_MB_OPT;
PERL_MM_OPT="INSTALL_BASE=/home/hakon/perl5"; export PERL_MM_OPT;

Would you like me to append that to /home/hakon/.bashrc now? [yes] no

Обратите внимание, что на предыдущий вопрос я ответил отрицательно.

commit: wrote '/home/hakon/.cpan/CPAN/MyConfig.pm'

You can re-run configuration any time with 'o conf init' in the CPAN shell
Terminal does not support AddHistory.

cpan shell -- CPAN exploration and modules installation (v2.18)
Enter 'h' for help.

cpan[1]> q
Terminal does not support GetHistory.
Lockfile removed.

*** Remember to add these environment variables to your shell config
    and restart your shell before running cpan again ***

PATH="/home/hakon/perl5/bin${PATH:+:${PATH}}"; export PATH;
PERL5LIB="/home/hakon/perl5/lib/perl5${PERL5LIB:+:${PERL5LIB}}"; export PERL5LIB;
PERL_LOCAL_LIB_ROOT="/home/hakon/perl5${PERL_LOCAL_LIB_ROOT:+:${PERL_LOCAL_LIB_ROOT}}"; export PERL_LOCAL_LIB_ROOT;
PERL_MB_OPT="--install_base \"/home/hakon/perl5\""; export PERL_MB_OPT;
PERL_MM_OPT="INSTALL_BASE=/home/hakon/perl5"; export PERL_MM_OPT;

• Теперь я скопировал сгенерированную локальную библиотеку в среду conda:

$ echo $CONDA_PREFIX
/home/hakon/anaconda3/envs/perl_test
$ mv ~/perl5 /home/hakon/anaconda3/envs/perl_test

• Затем настройте среду conda так, чтобы локальная библиотека активировалась при активации среды:

$ mkdir -p $CONDA_PREFIX/etc/conda/activate.d
$ vim $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh

• Добавьте следующее содержимое в предыдущий файл env_vars.sh:

export PATH="$CONDA_PREFIX/perl5/bin${PATH:+:${PATH}}"
export PERL5LIB="$CONDA_PREFIX/perl5/lib/perl5${PERL5LIB:+:${PERL5LIB}}";
export PERL_LOCAL_LIB_ROOT="$CONDA_PREFIX/perl5${PERL_LOCAL_LIB_ROOT:+:${PERL_LOCAL_LIB_ROOT}}";
export PERL_MB_OPT="--install_base \"$CONDA_PREFIX/perl5\""
export PERL_MM_OPT="INSTALL_BASE=$CONDA_PREFIX/perl5"

• Перезапустите среду conda, чтобы загрузить указанные выше переменные среды:

$ conda deactivate
$ conda activate perl_test

• Установить cpanm

$ cpan App::cpanminus

• Установите модуль:

$ which cpanm
/home/hakon/anaconda3/envs/perl_test/perl5/bin/cpanm
$ cpanm forks
--> Working on forks
Fetching http://www.cpan.org/authors/id/R/RY/RYBSKEJ/forks-0.36.tar.gz ... OK
Configuring forks-0.36 ... OK
==> Found dependencies: Devel::Symdump, Acme::Damn, Sys::SigAction, List::MoreUtils
--> Working on Devel::Symdump
Fetching http://www.cpan.org/authors/id/A/AN/ANDK/Devel-Symdump-2.18.tar.gz ... OK
Configuring Devel-Symdump-2.18 ... OK
Building and testing Devel-Symdump-2.18 ... OK
Successfully installed Devel-Symdump-2.18
--> Working on Acme::Damn
Fetching http://www.cpan.org/authors/id/I/IB/IBB/Acme-Damn-0.08.tar.gz ... OK
Configuring Acme-Damn-0.08 ... OK
==> Found dependencies: Test::Exception
--> Working on Test::Exception
Fetching http://www.cpan.org/authors/id/E/EX/EXODIST/Test-Exception-0.43.tar.gz ... OK
Configuring Test-Exception-0.43 ... OK
==> Found dependencies: Sub::Uplevel
--> Working on Sub::Uplevel
Fetching http://www.cpan.org/authors/id/D/DA/DAGOLDEN/Sub-Uplevel-0.2800.tar.gz ... OK
Configuring Sub-Uplevel-0.2800 ... OK
Building and testing Sub-Uplevel-0.2800 ... OK
Successfully installed Sub-Uplevel-0.2800
Building and testing Test-Exception-0.43 ... OK
Successfully installed Test-Exception-0.43
Building and testing Acme-Damn-0.08 ... FAIL
! Installing Acme::Damn failed. See /home/hakon/.cpanm/work/1610661561.1411986/build.log for details. Retry with --force to force install it.
--> Working on Sys::SigAction
Fetching http://www.cpan.org/authors/id/L/LB/LBAXTER/Sys-SigAction-0.23.tar.gz ... OK
Configuring Sys-SigAction-0.23 ... OK
Building and testing Sys-SigAction-0.23 ... OK
Successfully installed Sys-SigAction-0.23
--> Working on List::MoreUtils
Fetching http://www.cpan.org/authors/id/R/RE/REHSACK/List-MoreUtils-0.430.tar.gz ... OK
Configuring List-MoreUtils-0.430 ... OK
==> Found dependencies: Exporter::Tiny, Test::LeakTrace
--> Working on Exporter::Tiny
Fetching http://www.cpan.org/authors/id/T/TO/TOBYINK/Exporter-Tiny-1.002002.tar.gz ... OK
Configuring Exporter-Tiny-1.002002 ... OK
Building and testing Exporter-Tiny-1.002002 ... OK
Successfully installed Exporter-Tiny-1.002002
--> Working on Test::LeakTrace
Fetching http://www.cpan.org/authors/id/L/LE/LEEJO/Test-LeakTrace-0.17.tar.gz ... OK
Configuring Test-LeakTrace-0.17 ... OK
Building and testing Test-LeakTrace-0.17 ... FAIL
! Installing Test::LeakTrace failed. See /home/hakon/.cpanm/work/1610661561.1411986/build.log for details. Retry with --force to force install it.
! Installing the dependencies failed: Module 'Test::LeakTrace' is not installed
! Bailing out the installation for List-MoreUtils-0.430.
! Installing the dependencies failed: Module 'List::MoreUtils' is not installed, Module 'Acme::Damn' is not installed
! Bailing out the installation for forks-0.36.
5 distributions installed

Так что это не удается. Если я попытаюсь установить неисправный модуль Acme::Damn вручную:

$ wget https://cpan.metacpan.org/authors/id/I/IB/IBB/Acme-Damn-0.08.tar.gz
$ tar zxvf Acme-Damn-0.08.tar.gz
$ cd Acme-Damn-0.08
$ perl Makefile.PL
Checking if your kit is complete...
Looks good
Warning: prerequisite Test::Exception 0 not found.
Generating a Unix-style Makefile
Writing Makefile for Acme::Damn
Writing MYMETA.yml and MYMETA.json
$ make
cp Damn.pm blib/lib/Acme/Damn.pm
Running Mkbootstrap for Damn ()
chmod 644 "Damn.bs"
"/home/hakon/anaconda3/envs/perl_test/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- Damn.bs blib/arch/auto/Acme/Damn/Damn.bs 644
"/home/hakon/anaconda3/envs/perl_test/bin/perl" "/home/hakon/anaconda3/envs/perl_test/lib/5.26.2/ExtUtils/xsubpp"  -typemap '/home/hakon/anaconda3/envs/perl_test/lib/5.26.2/ExtUtils/typemap'  Damn.xs > Damn.xsc
mv Damn.xsc Damn.c
/tmp/build/80754af9/perl_1527832170752/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc -c  -I. -D_REENTRANT -D_GNU_SOURCE --sysroot=/tmp/build/80754af9/perl_1527832170752/_build_env/x86_64-conda_cos6-linux-gnu/sysroot -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -O2   -DVERSION=\"0.08\" -DXS_VERSION=\"0.08\" -fPIC --sysroot=/tmp/build/80754af9/perl_1527832170752/_build_env/x86_64-conda_cos6-linux-gnu/sysroot "-I/home/hakon/anaconda3/envs/perl_test/lib/5.26.2/x86_64-linux-thread-multi/CORE"   Damn.c
/bin/sh: 1: /tmp/build/80754af9/perl_1527832170752/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc: not found
make: *** [Makefile:337: Damn.o] Error 127

Это показывает, что make пытается использовать несуществующий компилятор C:

 /tmp/build/80754af9/perl_1527832170752/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc

Подсказку, почему это происходит, дают данные конфигурации Perl для cc:

$ perl -V | grep cc=./
    cc='/tmp/build/80754af9/perl_1527832170752/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc'

Я думаю, что когда perl пытается скомпилировать модуль XS, он использует тот же компилятор C, который использовался для компиляции perl. Но в этом случае этого компилятора больше не существует, поскольку conda установила (загрузила) предварительно скомпилированный Perl (поэтому переменная cc относится к компилятору на другой машине, машине, которая использовалась для компиляции perl)

Вероятно, это означает, что вы не можете (не должны) устанавливать модули XS со скачанным предварительно скомпилированным Perl. Я бы порекомендовал вместо этого собрать Perl из исходников на той же машине.

Изменить

Плохо, на самом деле можно установить тот же компилятор, который использовался для сборки Perl, выполнив:

$ conda install -c anaconda gcc_linux-64
$ which  x86_64-conda_cos6-linux-gnu-gcc
/home/hakon/anaconda3/envs/perl_test/bin/x86_64-conda_cos6-linux-gnu-gcc

Но я пока не могу заставить perl Makefile.PL использовать эту версию..

Изменить 2

Добавлен дополнительный вопрос.

Изменить 3

После применения исправления в дополнительном вопросе мне удалось установить модуль:

$ cpanm forks
--> Working on forks
Fetching http://www.cpan.org/authors/id/R/RY/RYBSKEJ/forks-0.36.tar.gz ... OK
Configuring forks-0.36 ... OK
==> Found dependencies: Acme::Damn, List::MoreUtils
--> Working on Acme::Damn
Fetching http://www.cpan.org/authors/id/I/IB/IBB/Acme-Damn-0.08.tar.gz ... OK
Configuring Acme-Damn-0.08 ... OK
Building and testing Acme-Damn-0.08 ... OK
Successfully installed Acme-Damn-0.08
--> Working on List::MoreUtils
Fetching http://www.cpan.org/authors/id/R/RE/REHSACK/List-MoreUtils-0.430.tar.gz ... OK
Configuring List-MoreUtils-0.430 ... OK
==> Found dependencies: Test::LeakTrace
--> Working on Test::LeakTrace
Fetching http://www.cpan.org/authors/id/L/LE/LEEJO/Test-LeakTrace-0.17.tar.gz ... OK
Configuring Test-LeakTrace-0.17 ... OK
Building and testing Test-LeakTrace-0.17 ... OK
Successfully installed Test-LeakTrace-0.17
Building and testing List-MoreUtils-0.430 ... OK
Successfully installed List-MoreUtils-0.430
Building and testing forks-0.36 ... OK
Successfully installed forks-0.36
4 distributions installed