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marf007
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PostPosted: Wed Oct 07, 2015 5:27 pm    Post subject: Gentoo bootstrap on mac os x failed during stage 3 Reply with quote

As the title says, got the following error during bootstrapping stage 3, when compiling perl.

ld: library not found for -lgcc_s.10.4
x86_64-apple-darwin14-clang-3.5.2: error: linker command failed with exit code 1
GNUmakefile:354: recipe for target 'libperl.5.22.0.dylib' failed

System is mac os x 10.10.5
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kikko
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PostPosted: Thu Oct 08, 2015 5:46 pm    Post subject: Reply with quote

Hi marf007
are you following "Prefix" to do this? Which steps have you followed so far?
Anyway, a problem similar to yours has been reported to GCC's bugzilla: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=42825
Regards
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marf007
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PostPosted: Thu Oct 08, 2015 6:18 pm    Post subject: Reply with quote

I was following the General bootstrap process and run
Code:
./bootstrap-prefix.sh

The error came during stage3 of the bootstrap, when compiling perl. I can provide any logs (stage*.log and perl-5.22.0/temp/build.log) if needed. Meanwhile, I will create this link to that library, as described in that bug report and run it once more...

kikko wrote:
Hi marf007
are you following "Prefix" to do this? Which steps have you followed so far?
Anyway, a problem similar to yours has been reported to GCC's bugzilla: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=42825
Regards
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marf007
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PostPosted: Thu Oct 08, 2015 7:49 pm    Post subject: Reply with quote

Hi kikko,

this time it compiled perl, but I run into another problem:
Code:
[blocks B      ] <dev-libs/openssl-1.0.2d-r1:0 ("<dev-libs/openssl-1.0.2d-r1:0" is blocking app-misc/c_rehash-1.7-r1)

I could unblock it with
Code:
=app-misc/c_rehash-1.7-r1 **

but I assumed that the bootstrap should run smoothly out of box.
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kikko
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PostPosted: Fri Oct 09, 2015 11:16 am    Post subject: Reply with quote

Hi marf007
can you please post the whole output?

Thanks :)
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marf007
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PostPosted: Fri Oct 09, 2015 2:20 pm    Post subject: Reply with quote

Hi kikko,

that's the output, before that it performed a sync.
I guess it's happened pretty much at the end of stage3.

Code:
>>> Checking server timestamp ...
Calculating dependencies  .... done!
[ebuild  NS    ] sys-libs/ncurses-5.9-r101 [5.9-r4] USE="cxx unicode (-ada) -debug -doc (-gpm) -minimal -profile -static-libs -tinfo -trace"
[ebuild     U  ] app-arch/xz-utils-5.2.2 [5.2.1-r1] USE="nls*"
[ebuild     U  ] sys-devel/gnuconfig-20150727 [20150308]
[ebuild  N    *] app-misc/c_rehash-1.7-r1
[ebuild  N     ] app-misc/editor-wrapper-4
[ebuild  N     ] virtual/shadow-0
[ebuild  N     ] sys-process/pidof-bsd-20050501-r4
[ebuild  N     ] sys-apps/which-2.21
[ebuild  N     ] sys-process/pkill-darwin-1.0
[ebuild  N     ] app-arch/gzip-1.6  USE="-pic -static"
[ebuild  N     ] sys-apps/darwin-miscutils-10
[ebuild     U  ] sys-apps/file-5.24 [5.22] PYTHON_TARGETS="(-pypy)"
[ebuild  N     ] sys-apps/less-481  USE="unicode -pcre"
[ebuild  N     ] virtual/service-manager-0  USE="(prefix)"
[ebuild  N     ] virtual/pager-0
[ebuild  N     ] sys-apps/diffutils-3.3  USE="nls -static"
[ebuild     U  ] sys-apps/coreutils-8.24 [8.23-r00.1] USE="nls*"
[ebuild  N     ] app-editors/nano-2.4.2  USE="magic ncurses nls spell unicode -debug -justify -minimal -slang -static"
[ebuild  N     ] virtual/editor-0
[ebuild  N     ] dev-perl/libintl-perl-1.240.0
[ebuild  N     ] virtual/perl-File-Spec-3.560.0
[ebuild  N     ] virtual/perl-ExtUtils-MakeMaker-7.40.100_rc
[ebuild  N     ] dev-perl/Text-Unidecode-1.240.0
[ebuild  N     ] dev-perl/Unicode-EastAsianWidth-1.330.0-r1
[ebuild  N     ] sys-apps/debianutils-4.4  USE="-static"
[ebuild  N     ] sys-apps/texinfo-6.0  USE="nls -static"
[ebuild  N     ] sys-apps/groff-1.22.3  USE="-X -examples"
[ebuild  N     ] sys-apps/man-1.6g-r1  USE="lzma nls (-selinux)"
[ebuild  N     ] virtual/man-0-r1
[ebuild  N     ] app-misc/ca-certificates-20150426.3.20-r1  USE="cacert"
[ebuild  N     ] dev-libs/openssl-1.0.2d  USE="asm tls-heartbeat zlib -bindist -gmp -kerberos -rfc3779 -sctp -static-libs {-test} -vanilla"
[ebuild  N     ] net-misc/openssh-6.9_p1-r2  USE="hpn pie ssl -X -X509 -bindist -debug -kerberos -ldap -ldns -libedit (-pam) -sctp (-selinux) -skey -ssh1 -static"
[ebuild     U  ] net-misc/wget-1.16.3-r2 [1.16.3] USE="nls* ssl* -libressl%"
[ebuild  N     ] virtual/ssh-0  USE="-minimal"
[ebuild  N     ] virtual/package-manager-0
[ebuild     U  ] sys-devel/binutils-apple-6.3 [6.1]
[blocks B      ] <dev-libs/openssl-1.0.2d-r1:0 ("<dev-libs/openssl-1.0.2d-r1:0" is blocking app-misc/c_rehash-1.7-r1)

 * Error: The above package list contains packages which cannot be
 * installed at the same time on the same system.

  (dev-libs/openssl-1.0.2d:0/0::gentoo_prefix, ebuild scheduled for merge) pulled in by
    >=dev-libs/openssl-0.9.6d:0[bindist=] (>=dev-libs/openssl-0.9.6d:0[-bindist]) required by (net-misc/openssh-6.9_p1-r2:0/0::gentoo_prefix, ebuild scheduled for merge)
    dev-libs/openssl:0 required by (net-misc/wget-1.16.3-r2:0/0::gentoo_prefix, ebuild scheduled for merge)
    dev-libs/openssl required by (net-misc/openssh-6.9_p1-r2:0/0::gentoo_prefix, ebuild scheduled for merge)

  (app-misc/c_rehash-1.7-r1:0/0::gentoo_prefix, ebuild scheduled for merge) pulled in by
    >=app-misc/c_rehash-1.7-r1 required by (app-misc/ca-certificates-20150426.3.20-r1:0/0::gentoo_prefix, ebuild scheduled for merge)


For more information about Blocked Packages, please refer to the following
section of the Gentoo Linux x86 Handbook (architecture is irrelevant):

https://wiki.gentoo.org/wiki/Handbook:X86/Working/Portage#Blocked_packages


The following keyword changes are necessary to proceed:
 (see "package.accept_keywords" in the portage(5) man page for more details)
# required by app-misc/ca-certificates-20150426.3.20-r1::gentoo_prefix
# required by dev-libs/openssl-1.0.2d::gentoo_prefix
# required by net-misc/wget-1.16.3-r2::gentoo_prefix[ssl,-libressl,-gnutls,-static]
# required by @system
# required by @world (argument)
=app-misc/c_rehash-1.7-r1 **

NOTE: The --autounmask-keep-masks option will prevent emerge
      from creating package.unmask or ** keyword changes.

Use --autounmask-write to write changes to config files (honoring
CONFIG_PROTECT). Carefully examine the list of proposed changes,
paying special attention to mask or keyword changes that may expose
experimental or unstable packages.
 
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kikko
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PostPosted: Sat Oct 10, 2015 9:13 am    Post subject: Reply with quote

Hi marf007
Your system is trying to emerge OpenSSL v. 1.0.2d, while "app-misc/c_rehash-1.7-r1" requires an higher version, i.e. OpenSSL v. 1.0.2d-r1
marf007 wrote:
Code:
[ebuild  N     ] dev-libs/openssl-1.0.2d  USE="asm tls-heartbeat zlib -bindist -gmp -kerberos -rfc3779 -sctp -static-libs {-test} -vanilla"
   ...
[blocks B      ] <dev-libs/openssl-1.0.2d-r1:0 ("<dev-libs/openssl-1.0.2d-r1:0" is blocking app-misc/c_rehash-1.7-r1)

In my system's tree, that version of "app-misc/c_rehash" is the only one available, so this "reverse dependency" is a constraint for me too (I've tried to downgrade OpenSSL, but I get the same result as yours)
You can try one of the following:
  • see if the version dev-libs/openssl-1.0.2d-r1 for your gentoo prefix
    Code:
    emerge -1va =dev-libs/openssl-1.0.2d

  • try to mask the versions of app-misc/ca-certificates which is causing the c_rehash to be pulled in (you can see the depgraph https://bpaste.net/show/d81a2d30c1b8)
    Code:
    echo ">app-misc/ca-certificates-20141019.3.19" >> /etc/portage/package.mask

Last will solve also the manual unmasking of app-misc/c_rehash on your system, which will no longer be needed.
Watch out, since you are running a gentoo prefix:
  • /etc/portage/ is where your make.conf is also located, not sure where this path is in PREFIX ($EPREFIX/etc/portage maybe?)
  • /etc/portage/package.mask could be a directory, in this case you can redirect that echo to a file in that dir


Regards
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marf007
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PostPosted: Sat Oct 10, 2015 2:12 pm    Post subject: Reply with quote

Thanks, kikko.

It worked, but I run into yet another problem. The installation of ncurses-5.9-r101 ends with an error, due to file
collision. See below, I didn't include a list of all files, since it's far too long, seems like every single file which
would be installed is affected.

Code:
>>> Installing (1 of 35) sys-libs/ncurses-5.9-r101::gentoo_prefix
 * This package will overwrite one or more files that may belong to other
 * packages (see list below). You can use a command such as `portageq
 * owners / <filename>` to identify the installed package that owns a
 * file. If portageq reports that only one package owns a file then do
 * NOT file a bug report. A bug report is only useful if it identifies at
 * least two or more packages that are known to install the same file(s).
 * If a collision occurs and you can not explain where the file came from
 * then you should simply ignore the collision since there is not enough
 * information to determine if a real problem exists. Please do NOT file
 * a bug report at http://bugs.gentoo.org unless you report exactly which
 * two packages install the same file(s). See
 * http://wiki.gentoo.org/wiki/Knowledge_Base:Blockers for tips on how to
 * solve the problem. And once again, please do NOT file a bug report
 * unless you have completely understood the above message.
 *
 * package sys-libs/ncurses-5.9-r101 NOT merged
 *
 * Detected file collision(s):
...
 * Searching all installed packages for file collisions...
 *
 * Press Ctrl-C to Stop
 *
 * sys-libs/ncurses-5.9-r4:0::gentoo_prefix
 *      /etc/env.d/50ncurses
 *      /etc/terminfo/61/ansi
 *      /etc/terminfo/64/dumb
 *      /etc/terminfo/6c/linux
 *      /etc/terminfo/72/rxvt
 *      /etc/terminfo/72/rxvt-unicode
 *      /etc/terminfo/73/screen
 *      /etc/terminfo/73/sun
 *      /etc/terminfo/76/vt100
 *      /etc/terminfo/76/vt102
 *      /etc/terminfo/76/vt220
 *      /etc/terminfo/76/vt52
 *      /etc/terminfo/78/xterm
 *      /etc/terminfo/78/xterm-color
 *      /etc/terminfo/78/xterm-xfree86
 *      /usr/bin/clear
 *      /usr/bin/infocmp
 *      /usr/bin/ncurses5-config
 *      /usr/bin/ncursesw5-config
 *      /usr/bin/tabs
 *
 * Package 'sys-libs/ncurses-5.9-r101' NOT merged due to file collisions.
 * If necessary, refer to your elog messages for the whole content of the
 * above message.
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kikko
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PostPosted: Sat Oct 10, 2015 10:16 pm    Post subject: Reply with quote

Hi marf007
sure you have a real bad luck :? sys-libs/ncurses-5.9-r101 and sys-libs/ncurses-5.9-r4 are from 2 different "slots", this means that they can be side by side since they don't interfere each other (in theory)
Code:

[I] sys-libs/ncurses
     Available versions:
     (0)    5.9-r3 (~)5.9-r4 5.9-r5(0/5) (~)6.0-r1(0/6)
     (5)    5.9-r99(5/5) (~)5.9-r101(5/5) (~)6.0(5/6)
       {ada +cxx debug doc gpm minimal profile static-libs test threads tinfo trace unicode ABI_MIPS="n32 n64 o32" ABI_PPC="32 64" ABI_S390="32 64" ABI_X86="32 64 x32"}
     Installed versions:  6.0-r1(11:40:46 12/09/2015)(cxx gpm unicode -ada -debug -doc -minimal -profile -static-libs -test -threads -tinfo -trace ABI_MIPS="-n32 -n64 -o32" ABI_PPC="-32 -64" ABI_S390="-32 -64" ABI_X86="64 -32 -x32")
     Homepage:            https://www.gnu.org/software/ncurses/ http://dickey.his.com/ncurses/
     Description:         console display library

In your case, the "r101" package is trying to overwrite files belonging to the "r4". Having a conflict is very rare, you should file a bug for that IMHO
Anyway, I've tried emerging 6.0 on the side of 6.0-r1 and it doesn't conflicts, you could try unmask those packages and see if you can get over this point

Regards
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marf007
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PostPosted: Sun Oct 11, 2015 12:03 pm    Post subject: Reply with quote

Hi Kikko,

thank you so much for your support. What you suggest worked. But, guess what... I run into another problem, see below.
I thinking of giving up...

Happened after stage3, when I did a
Code:
emerge -e system

as suggest by the guide

Code:
 
 * QA Notice: Found .so dynamic libraries on Darwin:
 *     Users/marek/Gentoo-2015-10-10/usr/lib/help2man/bindtextdomain.so
 * QA Notice: invalid self-reference install_name bindtextdomain.so in /Users/marek/Gentoo-2015-10-10/usr/lib/help2man/bindtextdomain.so
 * ERROR: sys-apps/help2man-1.47.2::gentoo_prefix failed:
 *   invalid install_name found, your application or library will crash at runtime
 *
 * Call stack:
 *   misc-functions.sh, line 1225:  Called install_qa_check
 *   misc-functions.sh, line  241:  Called install_qa_check_macho
 *   misc-functions.sh, line  422:  Called die
 * The specific snippet of code:
 *         has allow_broken_install_names ${FEATURES} || \
 *            die "invalid install_name found, your application or library will crash at runtime"
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kikko
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PostPosted: Sun Oct 11, 2015 11:33 pm    Post subject: Reply with quote

Hi marf007
sure this installation is hard, thus make it to work will be very satisfying :twisted:
Code:
emerge --emptytree (-e)
    Reinstalls target atoms and their entire deep dependency tree, as though no packages are currently installed. You should run this with --pretend first to make sure the result is what you expect.

so you are called to recompile everything, in order to be sure that every piece is in place and works properly
There is a similar issue to yours (related to coreutils, but the message is the same): see this bug for details
You can try to emerge -ep system, and see the package list. You can manually emerge the packages (for example), in order to see if "help2man" is the only one not working

Regards
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marf007
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PostPosted: Mon Oct 12, 2015 7:28 pm    Post subject: Reply with quote

Hi Kikko, thanks again.

Since I wanted to update OS X to El Capitan (from Yosemite) anyway, I think I will do an update first, and will wait till a prefix installation for El Capitan is available. Hopefully, it will work better. :wink:
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