Perl broken on El Capitan

Your perl -V output matches mine. I have not installed additional CPAN modules. What do you see for the following:

Was perl ok prior to adding those two CPAN modules, and can you fully uninstall them to see if proper functionality is restored?

At some point, and depending on how critical perl is to your day, you may find it more practical from a time investment to backup your machine, and in order, depending on whether your normal perl behavior is restored:

1. Apply the 10.11.6 Combo Updater to your existing installation.
2. Full reinstall of 10.11.6

In either case, apply all subsequent El Capitan updates.

No issues with perl 5.18.2 here.

or

Of course, if you tried to install a newer Perl over the top of the Apple default distribution, that could cause unlimited mayhem. Or, installed a newer version via a package manager, and the relevant module locations are getting mixed up.

I don't believe you ever answered my question if perl was working properly before installing those additional CPAN modules?

You have too many barriers that will stand in the way of determining why your system perl is not working properly:

1. Time Machine backup is not working
2. Unwilling to:
   1. El Capitan Combo Update
   2. Clean install El Capitan
   3. Install perlbrew

      Entire perl distribution inside a hidden folder in your home directory, and scripts that allow you to enable/disable/update/run that specific perl version.

3. Ability to catalog any potentially wrong ownership/permissions in the entire System perl installation, or repair it without 2a/2b.
4. No means to selectively reinstall System perl distribution without 2a, or 2b.

You will notice that all your errors point to permissions problems. In Ye Olde Days, Disk Utility used to have an explicit "repair disk permissions" feature, but alas no more. So, start up in Recovery Mode, run Disk Utility from there and do a First Aid on the startup volume. Hopefully that will tackle the problem.

If not, can try downloading the corresponding OnyX version for the OS and in the Maintenance tab run a Permissions verification and repair.

Nope:

mac:~ macjuan$ uname -a

Darwin mac.local 15.6.0 Darwin Kernel Version 15.6.0: Mon Jan 9 23:07:29 PST 2017; root:xnu-3248.60.11.2.1~1/RELEASE_X86_64 x86_64

mac:~ macjuan$ which perl

/usr/bin/perl

mac:~ macjuan$ perl --version

This is perl 5, version 18, subversion 2 (v5.18.2) built for darwin-thread-multi-2level

(with 2 registered patches, see perl -V for more detail)

Copyright 1987-2013, Larry Wall

Perl may be copied only under the terms of either the Artistic License or the

GNU General Public License, which may be found in the Perl 5 source kit.

Complete documentation for Perl, including FAQ lists, should be found on

this system using "man perl" or "perldoc perl". If you have access to the

Internet, point your browser at http://www.perl.org/, the Perl Home Page.

mac:~ macjuan$ perl -e '$_="krJhruaesrltre c a cnP,ohet";$_.=$1,print$2while s/(..)(.)//;'

Just another Perl hacker,mac:~ macjuan$

Have you tried with an Admin-enabled user account?

This might also help in diagnosis. Note this is on a Mid-2015 rMBP running the stock-standard 10.11.6 ElCap that came installed with it, fully patched and up to date. I also have Fink and some extra stuff installed.

mac:~ macjuan$ perl -V

Summary of my perl5 (revision 5 version 18 subversion 2) configuration:

Platform:

osname=darwin, osvers=15.0, archname=darwin-thread-multi-2level

uname='darwin osx219.apple.com 15.0 darwin kernel version 15.0.0: fri may 22 22:03:51 pdt 2015; root:xnu-3216.0.0.1.11~1development_x86_64 x86_64 '

config_args='-ds -e -Dprefix=/usr -Dccflags=-g -pipe -Dldflags= -Dman3ext=3pm -Duseithreads -Duseshrplib -Dinc_version_list=none -Dcc=cc'

hint=recommended, useposix=true, d_sigaction=define

useithreads=define, usemultiplicity=define

useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef

use64bitint=define, use64bitall=define, uselongdouble=undef

usemymalloc=n, bincompat5005=undef

Compiler:

cc='cc', ccflags ='-arch i386 -arch x86_64 -g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -fstack-protector',

optimize='-Os',

cppflags='-g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -fstack-protector'

ccversion='', gccversion='4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.1)', gccosandvers=''

intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678

d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16

ivtype='long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8

alignbytes=8, prototype=define

Linker and Libraries:

ld='cc -mmacosx-version-min=10.11.3', ldflags ='-arch i386 -arch x86_64 -fstack-protector'

libpth=/usr/lib /usr/local/lib

libs=

perllibs=

libc=, so=dylib, useshrplib=true, libperl=libperl.dylib

gnulibc_version=''

Dynamic Linking:

dlsrc=dl_dlopen.xs, dlext=bundle, d_dlsymun=undef, ccdlflags=' '

cccdlflags=' ', lddlflags='-arch i386 -arch x86_64 -bundle -undefined dynamic_lookup -fstack-protector'

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_PRESERVE_IVUV PERL_SAWAMPERSAND 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_PERLIO USE_PERL_ATOF

USE_REENTRANT_API

Locally applied patches:

/Library/Perl/Updates/<version> comes before system perl directories

installprivlib and installarchlib points to the Updates directory

Built under darwin

Compiled at Aug 11 2015 04:22:26

%ENV:

PERL5LIB="/sw/lib/perl5:/sw/lib/perl5/darwin"

@INC:

/sw/lib/perl5/5.18.2/darwin-thread-multi-2level

/sw/lib/perl5/5.18.2

/sw/lib/perl5/darwin-thread-multi-2level

/sw/lib/perl5

/sw/lib/perl5/darwin

/Library/Perl/5.18/darwin-thread-multi-2level

/Library/Perl/5.18

/Network/Library/Perl/5.18/darwin-thread-multi-2level

/Network/Library/Perl/5.18

/Library/Perl/Updates/5.18.2

/System/Library/Perl/5.18/darwin-thread-multi-2level

/System/Library/Perl/5.18

/System/Library/Perl/Extras/5.18/darwin-thread-multi-2level

/System/Library/Perl/Extras/5.18

.

mac:~ macjuan$

There is of course, perlbrew, that lets you install an entire perl distribution, including CPAN in your home directory, and allows you to switch between it and the system perl.

More on perlbrew.

I use a patched version of the discontinued pythonbrew in the same manner, but do not personally use perlbrew myself.

The El Capitan perl is installed by the operating system, and you cannot specifically reinstall it without reinstalling the operating system — hence the perlbrew suggestion.

Your Time Capsule may be gasping its last, and it may be time to bail to a new external backup drive.

There is a buried tool named repair_packages in /usr/libexec. It has a man page by that name. It will allow you to verify, and repair an entire OS X package's permissions.

Before you can run it, you need to temporarily disable the System Integrity protection (SIP) that is protecting the System locations.

See this article if you don't already know how.

When you have rebooted from disabling SIP, then do the following (one contiguous command, no intentional wrap):

sudo /usr/libexec/repair_packages --verify --pkg com.apple.pkg.Essentials >& ~/Desktop/verify.txt

It runs through the entire package in about 2 minutes, and will report any permissions issues it encounters. Eventually, it will come to the Perl installation hierarchy. I redirected to a text file so that you could search for the verify results in that hierarchy.

If there are permissions that need fixing, then the following should do the job:

sudo /usr/libexec/repair_packages --repair --pkg com.apple.pkg.Essentials >& ~/Desktop/repair.txt

When this is done, check if perl is now behaving for you. Then, reboot into Recovery, re-enable SIP, and then reboot normally. If this repair_packages doesn't get the job done, then I am out of ideas.