Script for updating openssl, zlib, glibc in software.eessi.io version 2023.06

[bedroge]

This addresses some Gentoo GLSAs and a openssl CVE. I'll upload the new tarballs manually.

output of glsa check script

>>> The following updates will be performed for this GLSA:
>>> No upgrade path exists for these packages:
     dev-libs/openssl-1.1.1u


Checking GLSA 202401-18
>>> The following updates will be performed for this GLSA:
>>> Updates that will be performed:
     sys-libs/zlib-1.3-r2 (vulnerable: sys-libs/zlib-1.2.13-r1)


Checking GLSA 202402-01
>>> The following updates will be performed for this GLSA:
>>> Updates that will be performed:
     sys-libs/glibc-2.38-r10 (vulnerable: sys-libs/glibc-2.37-r7)

OpenSSL 1.1.x is EOL, and we masked 3.x, which is probably why it doesn't show an upgrade path.

diff for x86_64

 app-text/po4a-0.69::gentoo
 app-text/sgml-common-0.6.3-r7::gentoo
 app-text/xmlto-0.0.28-r10::gentoo
+dev-build/autoconf-2.71-r6::gentoo
+dev-build/autoconf-archive-2023.02.20::gentoo
+dev-build/autoconf-wrapper-20221207-r1::gentoo
+dev-build/automake-1.16.5-r1::gentoo
+dev-build/automake-wrapper-20221207::gentoo
+dev-build/gtk-doc-am-1.33.2::gentoo
+dev-build/libtool-2.4.7-r1::gentoo
+dev-build/make-4.4.1-r1::gentoo
+dev-build/meson-1.1.1::gentoo
+dev-build/meson-format-array-0::gentoo
 dev-db/sqlite-3.42.0::gentoo
 dev-lang/lua-5.1.5-r200::gentoo
 dev-lang/luajit-2.1.0_beta3_p20220613::gentoo
@@ -102,7 +112,7 @@
 dev-libs/mpfr-4.2.0_p9::gentoo
 dev-libs/nettle-3.9.1::gentoo
 dev-libs/npth-1.6-r1::gentoo
-dev-libs/openssl-1.1.1u::gentoo
+dev-libs/openssl-1.1.1w::gentoo
 dev-libs/popt-1.19::gentoo
 dev-lua/lpeg-1.0.2-r101::gentoo
 dev-lua/lua-bit32-5.3.5.1-r1::gentoo
@@ -215,10 +225,7 @@
 dev-python/zipp-3.15.0::gentoo
 dev-util/direnv-2.32.2::eessi
 dev-util/gperf-3.1-r1::gentoo
-dev-util/gtk-doc-am-1.33.2::gentoo
 dev-util/hermes-2.9::gentoo
-dev-util/meson-1.1.1::gentoo
-dev-util/meson-format-array-0::gentoo
 dev-util/patchelf-0.18.0::gentoo
 dev-util/pkgconf-1.8.1::gentoo
 dev-util/re2c-2.2::gentoo
@@ -271,11 +278,6 @@
 sys-auth/passwdqc-2.0.2-r1::gentoo
 sys-cluster/lmod-8.7.23::gentoo
 sys-cluster/rdma-core-45.0::gentoo
-sys-devel/autoconf-2.71-r6::gentoo
-sys-devel/autoconf-archive-2023.02.20::gentoo
-sys-devel/autoconf-wrapper-20221207-r1::gentoo
-sys-devel/automake-1.16.5-r1::gentoo
-sys-devel/automake-wrapper-20221207::gentoo
 sys-devel/bc-1.07.1-r6::gentoo
 sys-devel/binutils-2.40-r5::gentoo
 sys-devel/binutils-config-5.5::gentoo
@@ -285,17 +287,15 @@
 sys-devel/gcc-config-2.11::gentoo
 sys-devel/gettext-0.21.1::gentoo
 sys-devel/gnuconfig-20230121::gentoo
-sys-devel/libtool-2.4.7-r1::gentoo
 sys-devel/m4-1.4.19-r2::gentoo
-sys-devel/make-4.4.1-r1::gentoo
 sys-devel/patch-2.7.6-r5::gentoo
 sys-fabric/opa-psm2-11.2.205::eessi
 sys-fs/e2fsprogs-1.47.0-r1::gentoo
 sys-fs/udev-init-scripts-35::gentoo
-sys-kernel/installkernel-gentoo-7::gentoo
+sys-kernel/installkernel-7::gentoo
 sys-kernel/linux-headers-6.3::gentoo
 sys-libs/gdbm-1.23::gentoo
-sys-libs/glibc-2.37-r7::gentoo
+sys-libs/glibc-2.37-r10::gentoo
 sys-libs/libcap-2.69::gentoo
 sys-libs/libseccomp-2.5.4::gentoo
 sys-libs/libxcrypt-4.4.35::gentoo
@@ -303,7 +303,7 @@
 sys-libs/pam-1.5.3::gentoo
 sys-libs/readline-8.2_p1::gentoo
 sys-libs/timezone-data-2023c::gentoo
-sys-libs/zlib-1.2.13-r1::gentoo
+sys-libs/zlib-1.3-r2::gentoo
 sys-process/numactl-2.0.16::gentoo
 sys-process/procps-3.3.17-r1::gentoo
 sys-process/psmisc-23.6::gentoo

diff for aarch64

 app-text/po4a-0.69::gentoo
 app-text/sgml-common-0.6.3-r7::gentoo
 app-text/xmlto-0.0.28-r10::gentoo
+dev-build/autoconf-2.71-r6::gentoo
+dev-build/autoconf-archive-2023.02.20::gentoo
+dev-build/autoconf-wrapper-20221207-r1::gentoo
+dev-build/automake-1.16.5-r1::gentoo
+dev-build/automake-wrapper-20221207::gentoo
+dev-build/gtk-doc-am-1.33.2::gentoo
+dev-build/libtool-2.4.7-r1::gentoo
+dev-build/make-4.4.1-r1::gentoo
+dev-build/meson-1.1.1::gentoo
+dev-build/meson-format-array-0::gentoo
 dev-db/sqlite-3.42.0::gentoo
 dev-lang/lua-5.1.5-r200::gentoo
 dev-lang/luajit-2.1.0_beta3_p20220613::gentoo
@@ -102,7 +112,7 @@
 dev-libs/mpfr-4.2.0_p9::gentoo
 dev-libs/nettle-3.9.1::gentoo
 dev-libs/npth-1.6-r1::gentoo
-dev-libs/openssl-1.1.1u::gentoo
+dev-libs/openssl-1.1.1w::gentoo
 dev-libs/popt-1.19::gentoo
 dev-lua/lpeg-1.0.2-r101::gentoo
 dev-lua/lua-bit32-5.3.5.1-r1::gentoo
@@ -215,10 +225,7 @@
 dev-python/zipp-3.15.0::gentoo
 dev-util/direnv-2.32.2::eessi
 dev-util/gperf-3.1-r1::gentoo
-dev-util/gtk-doc-am-1.33.2::gentoo
 dev-util/hermes-2.9::gentoo
-dev-util/meson-1.1.1::gentoo
-dev-util/meson-format-array-0::gentoo
 dev-util/patchelf-0.18.0::gentoo
 dev-util/pkgconf-1.8.1::gentoo
 dev-util/re2c-2.2::gentoo
@@ -271,11 +278,6 @@
 sys-auth/passwdqc-2.0.2-r1::gentoo
 sys-cluster/lmod-8.7.23::gentoo
 sys-cluster/rdma-core-45.0::gentoo
-sys-devel/autoconf-2.71-r6::gentoo
-sys-devel/autoconf-archive-2023.02.20::gentoo
-sys-devel/autoconf-wrapper-20221207-r1::gentoo
-sys-devel/automake-1.16.5-r1::gentoo
-sys-devel/automake-wrapper-20221207::gentoo
 sys-devel/bc-1.07.1-r6::gentoo
 sys-devel/binutils-2.40-r5::gentoo
 sys-devel/binutils-config-5.5::gentoo
@@ -285,16 +287,14 @@
 sys-devel/gcc-config-2.11::gentoo
 sys-devel/gettext-0.21.1::gentoo
 sys-devel/gnuconfig-20230121::gentoo
-sys-devel/libtool-2.4.7-r1::gentoo
 sys-devel/m4-1.4.19-r2::gentoo
-sys-devel/make-4.4.1-r1::gentoo
 sys-devel/patch-2.7.6-r5::gentoo
 sys-fs/e2fsprogs-1.47.0-r1::gentoo
 sys-fs/udev-init-scripts-35::gentoo
-sys-kernel/installkernel-gentoo-7::gentoo
+sys-kernel/installkernel-7::gentoo
 sys-kernel/linux-headers-6.3::gentoo
 sys-libs/gdbm-1.23::gentoo
-sys-libs/glibc-2.37-r7::gentoo
+sys-libs/glibc-2.37-r10::gentoo
 sys-libs/libcap-2.69::gentoo
 sys-libs/libseccomp-2.5.4::gentoo
 sys-libs/libxcrypt-4.4.35::gentoo
@@ -302,7 +302,7 @@
 sys-libs/pam-1.5.3::gentoo
 sys-libs/readline-8.2_p1::gentoo
 sys-libs/timezone-data-2023c::gentoo
-sys-libs/zlib-1.2.13-r1::gentoo
+sys-libs/zlib-1.3-r2::gentoo
 sys-process/numactl-2.0.16::gentoo
 sys-process/procps-3.3.17-r1::gentoo
 sys-process/psmisc-23.6::gentoo

Looks like some packages were renamed, which is why the diff shows some more packages than expected.

[eessi-bot]

Instance eessi-bot-mc-aws is configured to build:

• arch x86_64/generic for repo eessi-hpc.org-2023.06-compat
• arch x86_64/generic for repo eessi-hpc.org-2023.06-software
• arch x86_64/generic for repo eessi.io-2023.06-compat
• arch x86_64/generic for repo eessi.io-2023.06-software
• arch x86_64/intel/haswell for repo eessi-hpc.org-2023.06-compat
• arch x86_64/intel/haswell for repo eessi-hpc.org-2023.06-software
• arch x86_64/intel/haswell for repo eessi.io-2023.06-compat
• arch x86_64/intel/haswell for repo eessi.io-2023.06-software
• arch x86_64/intel/skylake_avx512 for repo eessi-hpc.org-2023.06-compat
• arch x86_64/intel/skylake_avx512 for repo eessi-hpc.org-2023.06-software
• arch x86_64/intel/skylake_avx512 for repo eessi.io-2023.06-compat
• arch x86_64/intel/skylake_avx512 for repo eessi.io-2023.06-software
• arch x86_64/amd/zen2 for repo eessi-hpc.org-2023.06-compat
• arch x86_64/amd/zen2 for repo eessi-hpc.org-2023.06-software
• arch x86_64/amd/zen2 for repo eessi.io-2023.06-compat
• arch x86_64/amd/zen2 for repo eessi.io-2023.06-software
• arch x86_64/amd/zen3 for repo eessi-hpc.org-2023.06-compat
• arch x86_64/amd/zen3 for repo eessi-hpc.org-2023.06-software
• arch x86_64/amd/zen3 for repo eessi.io-2023.06-compat
• arch x86_64/amd/zen3 for repo eessi.io-2023.06-software
• arch aarch64/generic for repo eessi-hpc.org-2023.06-compat
• arch aarch64/generic for repo eessi-hpc.org-2023.06-software
• arch aarch64/generic for repo eessi.io-2023.06-compat
• arch aarch64/generic for repo eessi.io-2023.06-software
• arch aarch64/neoverse_n1 for repo eessi-hpc.org-2023.06-compat
• arch aarch64/neoverse_n1 for repo eessi-hpc.org-2023.06-software
• arch aarch64/neoverse_n1 for repo eessi.io-2023.06-compat
• arch aarch64/neoverse_n1 for repo eessi.io-2023.06-software
• arch aarch64/neoverse_v1 for repo eessi-hpc.org-2023.06-compat
• arch aarch64/neoverse_v1 for repo eessi-hpc.org-2023.06-software
• arch aarch64/neoverse_v1 for repo eessi.io-2023.06-compat
• arch aarch64/neoverse_v1 for repo eessi.io-2023.06-software

[boegel]

-sys-libs/zlib-1.2.13-r1::gentoo
+sys-libs/zlib-1.3-r2::gentoo

I'm a bit worried about this part...

This implies removing libz.so.1.2.13 and installing libz.so.1.3 instead.
I suspect that may break some things that link to libz.so.1.2.3 (or even libz.so)

[bedroge]

Updated version of the diffs with the latest version of the script:

diff for x86_64

diff in installed packages:
--- /tmp/tmp.dE6K4maS7D/installed-pkgs-pre-update.txt	2024-02-08 15:35:45.035993854 +0000
+++ /tmp/tmp.dE6K4maS7D/installed-pkgs-post-update.txt	2024-02-08 15:47:52.767865818 +0000
@@ -71,6 +71,16 @@
 app-text/po4a-0.69::gentoo
 app-text/sgml-common-0.6.3-r7::gentoo
 app-text/xmlto-0.0.28-r10::gentoo
+dev-build/autoconf-2.71-r6::gentoo
+dev-build/autoconf-archive-2023.02.20::gentoo
+dev-build/autoconf-wrapper-20221207-r1::gentoo
+dev-build/automake-1.16.5-r1::gentoo
+dev-build/automake-wrapper-20221207::gentoo
+dev-build/gtk-doc-am-1.33.2::gentoo
+dev-build/libtool-2.4.7-r1::gentoo
+dev-build/make-4.4.1-r1::gentoo
+dev-build/meson-1.1.1::gentoo
+dev-build/meson-format-array-0::gentoo
 dev-db/sqlite-3.42.0::gentoo
 dev-lang/lua-5.1.5-r200::gentoo
 dev-lang/luajit-2.1.0_beta3_p20220613::gentoo
@@ -102,7 +112,7 @@
 dev-libs/mpfr-4.2.0_p9::gentoo
 dev-libs/nettle-3.9.1::gentoo
 dev-libs/npth-1.6-r1::gentoo
-dev-libs/openssl-1.1.1u::gentoo
+dev-libs/openssl-1.1.1w::gentoo
 dev-libs/popt-1.19::gentoo
 dev-lua/lpeg-1.0.2-r101::gentoo
 dev-lua/lua-bit32-5.3.5.1-r1::gentoo
@@ -215,10 +225,7 @@
 dev-python/zipp-3.15.0::gentoo
 dev-util/direnv-2.32.2::eessi
 dev-util/gperf-3.1-r1::gentoo
-dev-util/gtk-doc-am-1.33.2::gentoo
 dev-util/hermes-2.9::gentoo
-dev-util/meson-1.1.1::gentoo
-dev-util/meson-format-array-0::gentoo
 dev-util/patchelf-0.18.0::gentoo
 dev-util/pkgconf-1.8.1::gentoo
 dev-util/re2c-2.2::gentoo
@@ -271,11 +278,6 @@
 sys-auth/passwdqc-2.0.2-r1::gentoo
 sys-cluster/lmod-8.7.23::gentoo
 sys-cluster/rdma-core-45.0::gentoo
-sys-devel/autoconf-2.71-r6::gentoo
-sys-devel/autoconf-archive-2023.02.20::gentoo
-sys-devel/autoconf-wrapper-20221207-r1::gentoo
-sys-devel/automake-1.16.5-r1::gentoo
-sys-devel/automake-wrapper-20221207::gentoo
 sys-devel/bc-1.07.1-r6::gentoo
 sys-devel/binutils-2.40-r5::gentoo
 sys-devel/binutils-config-5.5::gentoo
@@ -285,16 +287,14 @@
 sys-devel/gcc-config-2.11::gentoo
 sys-devel/gettext-0.21.1::gentoo
 sys-devel/gnuconfig-20230121::gentoo
-sys-devel/libtool-2.4.7-r1::gentoo
 sys-devel/m4-1.4.19-r2::gentoo
-sys-devel/make-4.4.1-r1::gentoo
 sys-devel/patch-2.7.6-r5::gentoo
 sys-fs/e2fsprogs-1.47.0-r1::gentoo
 sys-fs/udev-init-scripts-35::gentoo
-sys-kernel/installkernel-gentoo-7::gentoo
+sys-kernel/installkernel-7::gentoo
 sys-kernel/linux-headers-6.3::gentoo
 sys-libs/gdbm-1.23::gentoo
-sys-libs/glibc-2.37-r7::gentoo
+sys-libs/glibc-2.37-r10::gentoo
 sys-libs/libcap-2.69::gentoo
 sys-libs/libseccomp-2.5.4::gentoo
 sys-libs/libxcrypt-4.4.35::gentoo
@@ -302,7 +302,7 @@
 sys-libs/pam-1.5.3::gentoo
 sys-libs/readline-8.2_p1::gentoo
 sys-libs/timezone-data-2023c::gentoo
-sys-libs/zlib-1.2.13-r1::gentoo
+sys-libs/zlib-1.2.13-r2::gentoo
 sys-process/numactl-2.0.16::gentoo
 sys-process/procps-3.3.17-r1::gentoo
 sys-process/psmisc-23.6::gentoo

diff for aarch64

diff in installed packages:
--- /tmp/tmp.qGJcbJ7pCs/installed-pkgs-pre-update.txt	2024-02-08 15:35:57.772342598 +0000
+++ /tmp/tmp.qGJcbJ7pCs/installed-pkgs-post-update.txt	2024-02-08 15:52:50.518865486 +0000
@@ -71,6 +71,16 @@
 app-text/po4a-0.69::gentoo
 app-text/sgml-common-0.6.3-r7::gentoo
 app-text/xmlto-0.0.28-r10::gentoo
+dev-build/autoconf-2.71-r6::gentoo
+dev-build/autoconf-archive-2023.02.20::gentoo
+dev-build/autoconf-wrapper-20221207-r1::gentoo
+dev-build/automake-1.16.5-r1::gentoo
+dev-build/automake-wrapper-20221207::gentoo
+dev-build/gtk-doc-am-1.33.2::gentoo
+dev-build/libtool-2.4.7-r1::gentoo
+dev-build/make-4.4.1-r1::gentoo
+dev-build/meson-1.1.1::gentoo
+dev-build/meson-format-array-0::gentoo
 dev-db/sqlite-3.42.0::gentoo
 dev-lang/lua-5.1.5-r200::gentoo
 dev-lang/luajit-2.1.0_beta3_p20220613::gentoo
@@ -102,7 +112,7 @@
 dev-libs/mpfr-4.2.0_p9::gentoo
 dev-libs/nettle-3.9.1::gentoo
 dev-libs/npth-1.6-r1::gentoo
-dev-libs/openssl-1.1.1u::gentoo
+dev-libs/openssl-1.1.1w::gentoo
 dev-libs/popt-1.19::gentoo
 dev-lua/lpeg-1.0.2-r101::gentoo
 dev-lua/lua-bit32-5.3.5.1-r1::gentoo
@@ -215,10 +225,7 @@
 dev-python/zipp-3.15.0::gentoo
 dev-util/direnv-2.32.2::eessi
 dev-util/gperf-3.1-r1::gentoo
-dev-util/gtk-doc-am-1.33.2::gentoo
 dev-util/hermes-2.9::gentoo
-dev-util/meson-1.1.1::gentoo
-dev-util/meson-format-array-0::gentoo
 dev-util/patchelf-0.18.0::gentoo
 dev-util/pkgconf-1.8.1::gentoo
 dev-util/re2c-2.2::gentoo
@@ -271,11 +278,6 @@
 sys-auth/passwdqc-2.0.2-r1::gentoo
 sys-cluster/lmod-8.7.23::gentoo
 sys-cluster/rdma-core-45.0::gentoo
-sys-devel/autoconf-2.71-r6::gentoo
-sys-devel/autoconf-archive-2023.02.20::gentoo
-sys-devel/autoconf-wrapper-20221207-r1::gentoo
-sys-devel/automake-1.16.5-r1::gentoo
-sys-devel/automake-wrapper-20221207::gentoo
 sys-devel/bc-1.07.1-r6::gentoo
 sys-devel/binutils-2.40-r5::gentoo
 sys-devel/binutils-config-5.5::gentoo
@@ -285,17 +287,15 @@
 sys-devel/gcc-config-2.11::gentoo
 sys-devel/gettext-0.21.1::gentoo
 sys-devel/gnuconfig-20230121::gentoo
-sys-devel/libtool-2.4.7-r1::gentoo
 sys-devel/m4-1.4.19-r2::gentoo
-sys-devel/make-4.4.1-r1::gentoo
 sys-devel/patch-2.7.6-r5::gentoo
 sys-fabric/opa-psm2-11.2.205::eessi
 sys-fs/e2fsprogs-1.47.0-r1::gentoo
 sys-fs/udev-init-scripts-35::gentoo
-sys-kernel/installkernel-gentoo-7::gentoo
+sys-kernel/installkernel-7::gentoo
 sys-kernel/linux-headers-6.3::gentoo
 sys-libs/gdbm-1.23::gentoo
-sys-libs/glibc-2.37-r7::gentoo
+sys-libs/glibc-2.37-r10::gentoo
 sys-libs/libcap-2.69::gentoo
 sys-libs/libseccomp-2.5.4::gentoo
 sys-libs/libxcrypt-4.4.35::gentoo
@@ -303,7 +303,7 @@
 sys-libs/pam-1.5.3::gentoo
 sys-libs/readline-8.2_p1::gentoo
 sys-libs/timezone-data-2023c::gentoo
-sys-libs/zlib-1.2.13-r1::gentoo
+sys-libs/zlib-1.2.13-r2::gentoo
 sys-process/numactl-2.0.16::gentoo
 sys-process/procps-3.3.17-r1::gentoo
 sys-process/psmisc-23.6::gentoo

[boegel]

Problem with CI should be fixed with #198 #196

[boegel]

staging PRs merged