Dear Roland,
Thanks for your reply,
If you are unable to reproduce the issue, could you please provide me with some information to help me understand the source of the problem?
Firstly, could you outline your steps for upgrading the system packages? I'm concerned that I might have done something incorrectly or that I'm missing a step.
Additionally, could you please verify if your /etc/spack/defaults/packages.yaml file on the login node has the definition for the "zlib-api" virtual library? It should look something like this: "zlib-api": ["zlib", "zlib-ng+compat"] or "zlib-api": ["zlib-ng+compat", "zlib"]
Furthermore, what is the output of your "spack providers" command on the login node when run as softadm? Mine is the following:
$ spack providers Virtual packages: D daal flame glu iconv jpeg libllvm luajit mpe onedal pil scalapack tbb xxd awk elf fuse go-or-gccgo-bootstrap ipp lapack libosmesa mariadb-client mpi opencl pkgconfig sycl unwind yacc blas fftw-api gl golang java libglx lua-lang mkl mysql-client pbs rpc szip uuid ziglang
Although I added "zlib-api": ["zlib-ng+compat", "zlib"] to the /etc/spack/defaults/packages.yaml file, the zlib-api does not appear in the virtual packages list in my output.
Also, could you please show me the beginning of your /var/lib/spack/repos/builtin/packages/r/package.py file, also on the login node? For instance, this is mine:
--------------------------------- $ cat /var/lib/spack/repos/builtin/packages/r/package.py # Copyright 2013-2024 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
from spack.package import *
class R(AutotoolsPackage): """R is 'GNU S', a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc. Please consult the R project homepage for further information."""
homepage = "https://www.r-project.org" url = "https://cloud.r-project.org/src/base/R-4/R-4.4.0.tar.gz"
extendable = True
license("GPL-2.0-or-later")
version("4.4.0", sha256="ace4125f9b976d2c53bcc5fca30c75e30d4edc401584859cbadb080e72b5f030") version("4.3.3", sha256="80851231393b85bf3877ee9e39b282e750ed864c5ec60cbd68e6e139f0520330") version("4.3.2", sha256="b3f5760ac2eee8026a3f0eefcb25b47723d978038eee8e844762094c860c452a") version("4.3.1", sha256="8dd0bf24f1023c6f618c3b317383d291b4a494f40d73b983ac22ffea99e4ba99") version("4.3.0", sha256="45dcc48b6cf27d361020f77fde1a39209e997b81402b3663ca1c010056a6a609") version("4.2.3", sha256="55e4a9a6d43be314e2c03d0266a6fa5444afdce50b303bfc3b82b3979516e074") version("4.2.2", sha256="0ff62b42ec51afa5713caee7c4fde7a0c45940ba39bef8c5c9487fef0c953df5") version("4.2.1", sha256="4d52db486d27848e54613d4ee977ad952ec08ce17807e1b525b10cd4436c643f") version("4.2.0", sha256="38eab7719b7ad095388f06aa090c5a2b202791945de60d3e2bb0eab1f5097488") version("4.1.3", sha256="15ff5b333c61094060b2a52e9c1d8ec55cc42dd029e39ca22abdaa909526fed6") version("4.1.2", sha256="2036225e9f7207d4ce097e54972aecdaa8b40d7d9911cd26491fac5a0fab38af") version("4.1.1", sha256="515e03265752257d0b7036f380f82e42b46ed8473f54f25c7b67ed25bbbdd364") version("4.1.0", sha256="e8e68959d7282ca147360fc9644ada9bd161bab781bab14d33b8999a95182781") version("4.0.5", sha256="0a3ee079aa772e131fe5435311ab627fcbccb5a50cabc54292e6f62046f1ffef") version("4.0.4", sha256="523f27d69744a08c8f0bd5e1e6c3d89a4db29ed983388ba70963a3cd3a4a802e") version("4.0.3", sha256="09983a8a78d5fb6bc45d27b1c55f9ba5265f78fa54a55c13ae691f87c5bb9e0d") version("4.0.2", sha256="d3bceab364da0876625e4097808b42512395fdf41292f4915ab1fd257c1bbe75") version("4.0.1", sha256="95fe24a4d8d8f8f888460c8f5fe4311cec656e7a1722d233218bc03861bc6f32") version("4.0.0", sha256="06beb0291b569978484eb0dcb5d2339665ec745737bdfb4e873e7a5a75492940") version("3.6.3", sha256="89302990d8e8add536e12125ec591d6951022cf8475861b3690bc8bf1cefaa8f") version("3.6.2", sha256="bd65a45cddfb88f37370fbcee4ac8dd3f1aebeebe47c2f968fd9770ba2bbc954") version("3.6.1", sha256="5baa9ebd3e71acecdcc3da31d9042fb174d55a42829f8315f2457080978b1389") version("3.6.0", sha256="36fcac3e452666158e62459c6fc810adc247c7109ed71c5b6c3ad5fc2bf57509") version("3.5.3", sha256="2bfa37b7bd709f003d6b8a172ddfb6d03ddd2d672d6096439523039f7a8e678c") version("3.5.2", sha256="e53d8c3cf20f2b8d7a9c1631b6f6a22874506fb392034758b3bb341c586c5b62") version("3.5.1", sha256="0463bff5eea0f3d93fa071f79c18d0993878fd4f2e18ae6cf22c1639d11457ed") version("3.5.0", sha256="fd1725535e21797d3d9fea8963d99be0ba4c3aecadcf081b43e261458b416870") version("3.4.4", sha256="b3e97d2fab7256d1c655c4075934725ba1cd7cb9237240a11bb22ccdad960337") version("3.4.3", sha256="7a3cb831de5b4151e1f890113ed207527b7d4b16df9ec6b35e0964170007f426") version("3.4.2", sha256="971e30c2436cf645f58552905105d75788bd9733bddbcb7c4fbff4c1a6d80c64") version("3.4.1", sha256="02b1135d15ea969a3582caeb95594a05e830a6debcdb5b85ed2d5836a6a3fc78") version("3.4.0", sha256="288e9ed42457c47720780433b3d5c3c20983048b789291cc6a7baa11f9428b91") version("3.3.3", sha256="5ab768053a275084618fb669b4fbaadcc39158998a87e8465323829590bcfc6c") version("3.3.2", sha256="d294ad21e9f574fb4828ebb3a94b8cb34f4f304a41687a994be00dd41a4e514c") version("3.3.1", sha256="3dc59ae5831f5380f83c169bac2103ad052efe0ecec4ffa74bde4d85a0fda9e2") version("3.3.0", sha256="9256b154b1a5993d844bee7b1955cd49c99ad72cef03cce3cd1bdca1310311e4") version("3.2.5", sha256="60745672dce5ddc201806fa59f6d4e0ba6554d8ed78d0f9f0d79a629978f80b5") version("3.2.3", sha256="b93b7d878138279234160f007cb9b7f81b8a72c012a15566e9ec5395cfd9b6c1") version("3.2.2", sha256="9c9152e74134b68b0f3a1c7083764adc1cb56fd8336bec003fd0ca550cd2461d") version("3.2.1", sha256="d59dbc3f04f4604a5cf0fb210b8ea703ef2438b3ee65fd5ab536ec5234f4c982") version("3.2.0", sha256="f5ae953f18ba6f3d55b46556bbbf73441350f9fd22625402b723a2b81ff64f35") version("3.1.3", sha256="07e98323935baa38079204bfb9414a029704bb9c0ca5ab317020ae521a377312") version("3.1.2", sha256="bcd150afcae0e02f6efb5f35a6ab72432be82e849ec52ce0bb89d8c342a8fa7a")
variant("X", default=False, description="Enable X11 support (TCLTK, PNG, JPEG, TIFF, CAIRO)") variant("memory_profiling", default=False, description="Enable memory profiling") variant("rmath", default=False, description="Build standalone Rmath library")
depends_on("blas") depends_on("lapack")
depends_on("bzip2") depends_on("curl+libidn2") # R didn't anticipate the celebratory non-breaking major version bump of curl 8. depends_on("curl@:7", when="@:4.2") depends_on("icu4c") depends_on("java") depends_on("libtirpc") depends_on("ncurses") depends_on("pcre", when="@:3.6.3") depends_on("pcre2", when="@4:") depends_on("readline") depends_on("xz") depends_on("which", type=("build", "run")) depends_on("zlib-api") depends_on("zlib@1.2.5:", when="^[virtuals=zlib-api] zlib") depends_on("texinfo", type="build") --------------------- CUT the output
As you can see, my most recent version is 4.4.0 and it depends_on("zlib-api"), which for some reason is not being recognized in my system.
Best regards, Tiago Almeida