ERROR: sys-libs/pam-1.7.2::gentoo failed (compile phase):

[northfrisia]

Hi,

sys-libs/pam-1.7.2. failed to compile.

Here are the logs:
The emerge info -> https://bpa.st/2R4BW
The output of emerge -pqv -> https://bpa.st/HJFGG
The build log -> https://bpa.st/CQ5T6
The environment -> (wget paste failed here "400 Bad request" ???)
Will see whether I will be able to add this file later...

My Gentoo is updated daily, I am running multilib.
This error is an older one, since I hoped that is would be a temporary...
...which is not unfortunately.

How can I fix this?

Cheers!
NorthFrisia

[netfab]

Hi,

Same as https://forums.gentoo.org/viewtopic-t-1176001.html

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[...]x86_64-pc-linux-gnu/bin/ld: /usr/lib/libcrypt.so: error adding symbols: file in wrong format
collect2: error: ld returned 1 exit status 

No solution but it seems you are not alone in this case.

[netfab]

Can you please post the outputs of following commands :

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$ ls -l /usr/lib*/libcrypt.so*

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$ pkgconf --path libcrypt

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$ qfile /usr/lib*/pkgconfig/libcrypt.pc

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$ qfile /usr/lib*/libcrypt.so*

The qfile utility is from app-portage/portage-utils.

Your emerge --info and build.log shows that portage is building the package only for 64-bit.
But, on this command :

[122/525] x86_64-pc-linux-gnu-gcc -o modules/pam_pwhistory/pam_pwhistory.so modules/pam_pwhistory/pam_pwhistory.so.p/pam_pwhistory.c.o modules/pam_pwhistory/pam_pwhistory.so.p/opasswd.c.o modules/pam_pwhistory/pam_pwhistory.so.p/pwhistory_config.c.o -Wl,--as-needed -Wl,--allow-shlib-undefined -shared -fPIC -Wl,--fatal-warnings -Wl,--no-undefined-version -Wl,-O1 -O2 -pipe -march=znver2 -mtune=znver2 -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,--undefined-version '-Wl,-rpath,$ORIGIN/../../libpam' -Wl,--start-group libpam_internal/libpam_internal.a libpam/libpam.so.0.85.1 -Wl,--version-script=/var/tmp/portage/sys-libs/pam-1.7.2/work/Linux-PAM-1.7.2/modules/pam_pwhistory/module.map /usr/lib/libcrypt.so -Wl,--end-group
[...]
/usr/x86_64-pc-linux-gnu/binutils-bin/2.46.0/ld: /usr/lib/libcrypt.so: error adding symbols: file in wrong format
collect2: error: ld returned 1 exit status

/usr/lib/libcrypt.so is a 32bit path.
Maybe this file (and others) is an orphan file on your filesystem.

[grknight]

The source of the issue is this:

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    build.pkg_config_path: /usr/lib/pkgconfig:/usr/share/pkgconfig
    pkg_config_path      : /usr/lib/pkgconfig:/usr/share/pkgconfig

Those paths should be /usr/lib64 and not /usr/lib.

How are you running emerge? from a root prompt? Feels a lot like environment bleed or some other way of overriding pkgconfig path.

[grknight]

To be clear, this is what I get for the configure stage of sys-libs/pam-1.7.2 for those variables:

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    build.pkg_config_path: /usr/share/pkgconfig
    pkg_config_path      : /usr/share/pkgconfig

The meson code in an ebuild looks for PKG_CONFIG_LIBDIR or BUILD_PKG_CONFIG_LIBDIR to be set in the environment.
This is normally supplied by other eclasses.

I believe this is a case where emerge --info --verbose may be of some help

[northfrisia]

Can you please post the outputs of following commands :

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$ ls -l /usr/lib*/libcrypt.so*

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$ pkgconf --path libcrypt

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$ qfile /usr/lib*/pkgconfig/libcrypt.pc

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$ qfile /usr/lib*/libcrypt.so*

The qfile utility is from app-portage/portage-utils.

Your emerge --info and build.log shows that portage is building the package only for 64-bit.
But, on this command :

[122/525] x86_64-pc-linux-gnu-gcc -o modules/pam_pwhistory/pam_pwhistory.so modules/pam_pwhistory/pam_pwhistory.so.p/pam_pwhistory.c.o modules/pam_pwhistory/pam_pwhistory.so.p/opasswd.c.o modules/pam_pwhistory/pam_pwhistory.so.p/pwhistory_config.c.o -Wl,--as-needed -Wl,--allow-shlib-undefined -shared -fPIC -Wl,--fatal-warnings -Wl,--no-undefined-version -Wl,-O1 -O2 -pipe -march=znver2 -mtune=znver2 -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,--undefined-version '-Wl,-rpath,$ORIGIN/../../libpam' -Wl,--start-group libpam_internal/libpam_internal.a libpam/libpam.so.0.85.1 -Wl,--version-script=/var/tmp/portage/sys-libs/pam-1.7.2/work/Linux-PAM-1.7.2/modules/pam_pwhistory/module.map /usr/lib/libcrypt.so -Wl,--end-group
[...]
/usr/x86_64-pc-linux-gnu/binutils-bin/2.46.0/ld: /usr/lib/libcrypt.so: error adding symbols: file in wrong format
collect2: error: ld returned 1 exit status

/usr/lib/libcrypt.so is a 32bit path.
Maybe this file (and others) is an orphan file on your filesystem.

I am multilib (32/64 bit) by the way (see initial post)

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$ ls -l /usr/lib*/libcrypt.so*

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lrwxrwxrwx 1 root root     17 2025-11-10 17:42 /usr/lib/libcrypt.so -> libcrypt.so.2.0.0
lrwxrwxrwx 1 root root     17 2025-11-10 17:42 /usr/lib/libcrypt.so.1 -> libcrypt.so.1.1.0
-rwxr-xr-x 1 root root 214320 2025-11-10 17:42 /usr/lib/libcrypt.so.1.1.0
lrwxrwxrwx 1 root root     17 2025-11-10 17:42 /usr/lib/libcrypt.so.2 -> libcrypt.so.2.0.0
-rwxr-xr-x 1 root root 214320 2025-11-10 17:42 /usr/lib/libcrypt.so.2.0.0
lrwxrwxrwx 1 root root     17 2025-11-10 17:42 /usr/lib64/libcrypt.so -> libcrypt.so.2.0.0
lrwxrwxrwx 1 root root     17 2025-11-10 17:42 /usr/lib64/libcrypt.so.1 -> libcrypt.so.1.1.0
-rwxr-xr-x 1 root root 206712 2025-11-10 17:42 /usr/lib64/libcrypt.so.1.1.0
lrwxrwxrwx 1 root root     17 2025-11-10 17:42 /usr/lib64/libcrypt.so.2 -> libcrypt.so.2.0.0
-rwxr-xr-x 1 root root 202616 2025-11-10 17:42 /usr/lib64/libcrypt.so.2.0.0

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pkgconf --path libcrypt 

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/usr/lib/pkgconfig/libcrypt.pc

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qfile /usr/lib*/pkgconfig/libcrypt.pc 

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sys-libs/libxcrypt: /usr/lib/pkgconfig/libcrypt.pc
sys-libs/libxcrypt: /usr/lib64/pkgconfig/libcrypt.pc

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qfile /usr/lib*/libcrypt.so* 

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sys-libs/libxcrypt: /usr/lib/libcrypt.so.2
sys-libs/libxcrypt: /usr/lib/libcrypt.so.2.0.0
sys-libs/libxcrypt: /usr/lib/libcrypt.so
sys-libs/libxcrypt: /usr/lib/libcrypt.so.1
sys-libs/libxcrypt: /usr/lib/libcrypt.so.1.1.0
sys-libs/libxcrypt: /usr/lib64/libcrypt.so.2
sys-libs/libxcrypt: /usr/lib64/libcrypt.so.2.0.0
sys-libs/libxcrypt: /usr/lib64/libcrypt.so
sys-libs/libxcrypt: /usr/lib64/libcrypt.so.1
sys-libs/libxcrypt: /usr/lib64/libcrypt.so.1.1.0

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How are you running emerge? from a root prompt? 

Yes

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emerge --info --verbose 

https://bpa.st/EFRQ


By the way
sys-apps/systemd-utils-259.3:0/0::gentoo
now fails at the same ninja-step seemingly (looking at the error after compilation failed...
no deeper analysis, though)

[netfab]

Please post the outputs of :

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$ ls -l /usr/lib*/pkgconfig/libcrypt.pc

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$ emerge -pv sys-libs/libxcrypt

Can you try to reinstall sys-libs/libxcrypt to see if it makes any difference :

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# emerge -av1 sys-libs/libxcrypt

[northfrisia]

Please post the outputs of :

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$ ls -l /usr/lib*/pkgconfig/libcrypt.pc

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$ emerge -pv sys-libs/libxcrypt

Can you try to reinstall sys-libs/libxcrypt to see if it makes any difference :

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# emerge -av1 sys-libs/libxcrypt

First I reinstalled sys-libs/libxcrypt

the compilation of libxcrypt was painless, the following compilation of pam failed.

Here are the outputs of the mentioned commands:

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#> ls -l /usr/lib*/pkgconfig/libcrypt.pc
lrwxrwxrwx 1 root root 12 2026-03-22 11:29 /usr/lib/pkgconfig/libcrypt.pc -> libxcrypt.pc
lrwxrwxrwx 1 root root 12 2026-03-22 11:29 /usr/lib64/pkgconfig/libcrypt.pc -> libxcrypt.pc

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#> emerge -pv sys-libs/libxcrypt
These are the packages that would be merged, in order:

Calculating dependencies  ... done!
Dependency resolution took 2.90 s (backtrack: 0/20).

[ebuild   R    ] sys-libs/libxcrypt-4.4.38:0/1::gentoo  USE="(compat) (system) (-headers-only) -static-libs -test" ABI_X86="32 (64) (-x32)" 0 KiB

Total: 1 package (1 reinstall), Size of downloads: 0 KiB

[netfab]

Please post outputs of :

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# pkg-config --variable pc_path pkg-config

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$ env | grep PATH

[grknight]

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PKG_CONFIG_PATH="/usr/lib/pkgconfig"

This should not be set anywhere and is causing you problems. Find out where it coming from and remove it. Often an environment file somewhere in /etc or a shell configuration.

If found in /etc/env.d, then don't forget to execute env-update ; source /etc/profile. A new login or reboot may be required to apply the environment change beyond that.

[northfrisia]

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PKG_CONFIG_PATH="/usr/lib/pkgconfig"

This should not be set anywhere and is causing you problems. Find out where it coming from and remove it. Often an environment file somewhere in /etc or a shell configuration.

If found in /etc/env.d, then don't forget to execute env-update ; source /etc/profile. A new login or reboot may be required to apply the environment change beyond that.

That fixed it! Oh YEAH! Thanks a lot too all, which contributed and helped to pin point this...

ATTENTION! For all reading this...
After pam is recompiled successfully you need to recompile your login manager (sddm in my case)
BEFORE you logout or reboot otherwise you are locked out.

PKG_CONFIG_PATH is set bei nvidia and vpl via scripts copied to /etc.
In my case I found a leftover in my .zshrc, which seemed to be the culprit here.

May be "This should not be set anywhere " is a little too broad...? (guessing, since official sources set it in scripts below /etc/. ...)

[Hu]

PKG_CONFIG_PATH must be set only to paths which contain pkg-config files that are correct for the build being run. In the general case of running emerge on arbitrary packages, it seems dangerous to have it set because of the variety of packages that might consume it. Exactly what official sources are setting it, where are they writing it, and to what value are they setting it?

[northfrisia]

I found the following place, where PKG_CONFIG_PTH gets set:

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/etc>grep -r PKG_CONFIG_PATH
env.d/99cuda879098:PKG_CONFIG_PATH=/opt/cuda/pkgconfig
environment.d/10-gentoo-env.conf:PKG_CONFIG_PATH=/opt/cuda/pkgconfig
csh.env:setenv PKG_CONFIG_PATH '/opt/cuda/pkgconfig'
profile.env:export PKG_CONFIG_PATH='/opt/cuda/pkgconfig'
vpl/vars.sh:PKG_CONFIG_PATH=$(prepend_path "$vpl_pkgconfig" "${PKG_CONFIG_PATH:-}")
vpl/vars.sh:export PKG_CONFIG_PATH

I could identify some of the packages:

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dev-util/nvidia-cuda-toolkit
env-update
???
???
media-libs/libvpl