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HenrikBengtsson / CBI-software

A Scientific Software Stack for HPC (CentOS oriented)
https://wynton.ucsf.edu/hpc/software/software-repositories.html
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CentOS 7 -> Rocky 8 compatibility #93

Open HenrikBengtsson opened 1 year ago

HenrikBengtsson commented 1 year ago

Modules to be tested

Modules that cannot be tested

Modules only available on CentOS 7

Modules working on both CentOS 7 and Rocky 8

The following modules have been validated using make check/<name>:

The following have been validate via real-world use

Modules not working in Rocky 8

cutadapt

$ cutadapt --version
-bash: /wynton/home/cbi/shared/software/CBI/cutadapt-4.4/bin/cutadapt: /wynton/home/cbi/shared/software/CBI/cutadapt-4.4/venv/bin/python: bad interpreter: No such file or directory

emacs

$ emacs --version
emacs: error while loading shared libraries: libpng15.so.15:
cannot open shared object file: No such file or directory

expect

$ expect -version
expect: error while loading shared libraries: libtcl8.5.so: cannot open shared object file: No such file or directory

gdal

$ gdalinfo --version
gdalinfo: error while loading shared libraries: libwebp.so.4: cannot open shared object file: No such file or directory

htop

$ htop --version
htop: error while loading shared libraries: libncursesw.so.5: cannot open shared object file: No such file or directory

markdown-lint

$ markdownlint --version
/usr/bin/env: ‘node’: No such file or directory

mc

$ mc --version
mc: error while loading shared libraries: libncursesw.so.5: cannot open shared object file: No such file or directory

qtop

$ qtop --version
/wynton/home/cbi/shared/software/CBI/qtop-0.9.20161222/qtop: line 3: python: command not found

r

$ R --version
/wynton/home/cbi/shared/software/CBI/R-4.3.1-gcc10/lib64/R/bin/exec/R: error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory

samtools

$ samtools --version
   samtools: error while loading shared libraries: libncursesw.so.5: cannot open shared object file: No such file or directory

sqlite

$ sqlite --version
sqlite3: error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory

tmux and byobu

$ tmux --version
   tmux: error while loading shared libraries: libtinfo.so.5: cannot open shared object file: No such file or directory

tophat

$ tophat --version
/usr/bin/env: ‘python’: No such file or directory
HenrikBengtsson commented 1 year ago

We could automate the validation that are no broken library dependencies by using ldd. For example, Emacs was installed on CentOS 7, but is broken on Rocky 8, because:

[rocky8]$ ldd /wynton/home/cbi/shared/software/CBI/emacs-28.2/bin/emacs | grep "not found"
        libpng15.so.15 => not found
        libtinfo.so.5 => not found

This tells us that this binary is not compatible with the Rocky 8 installation.

Details:

[centos7]$ ldd /wynton/home/cbi/shared/software/CBI/emacs-28.2/bin/emacs
        linux-vdso.so.1 =>  (0x00007f9414ef6000)
        libtiff.so.5 => /lib64/libtiff.so.5 (0x00007f9414a63000)
        libjpeg.so.62 => /lib64/libjpeg.so.62 (0x00007f941480e000)
        libpng15.so.15 => /lib64/libpng15.so.15 (0x00007f94145e3000)
        libgtk-x11-2.0.so.0 => /lib64/libgtk-x11-2.0.so.0 (0x00007f9413f61000)
        libgdk-x11-2.0.so.0 => /lib64/libgdk-x11-2.0.so.0 (0x00007f9413ca0000)
        libatk-1.0.so.0 => /lib64/libatk-1.0.so.0 (0x00007f9413a7a000)
        libgio-2.0.so.0 => /lib64/libgio-2.0.so.0 (0x00007f94136da000)
        libpangoft2-1.0.so.0 => /lib64/libpangoft2-1.0.so.0 (0x00007f94134c4000)
        libpangocairo-1.0.so.0 => /lib64/libpangocairo-1.0.so.0 (0x00007f94132b6000)
        libgdk_pixbuf-2.0.so.0 => /lib64/libgdk_pixbuf-2.0.so.0 (0x00007f941308e000)
        libcairo.so.2 => /lib64/libcairo.so.2 (0x00007f9412d57000)
        libpango-1.0.so.0 => /lib64/libpango-1.0.so.0 (0x00007f9412b11000)
        libfontconfig.so.1 => /lib64/libfontconfig.so.1 (0x00007f94128cf000)
        libgobject-2.0.so.0 => /lib64/libgobject-2.0.so.0 (0x00007f941267e000)
        libfreetype.so.6 => /lib64/libfreetype.so.6 (0x00007f94123bf000)
        libglib-2.0.so.0 => /lib64/libglib-2.0.so.0 (0x00007f94120a9000)
        libSM.so.6 => /lib64/libSM.so.6 (0x00007f9411ea1000)
        libICE.so.6 => /lib64/libICE.so.6 (0x00007f9411c85000)
        libX11.so.6 => /lib64/libX11.so.6 (0x00007f9411947000)
        libX11-xcb.so.1 => /lib64/libX11-xcb.so.1 (0x00007f9411745000)
        libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f941151d000)
        libXrender.so.1 => /lib64/libXrender.so.1 (0x00007f9411312000)
        librsvg-2.so.2 => /lib64/librsvg-2.so.2 (0x00007f94110dc000)
        libm.so.6 => /lib64/libm.so.6 (0x00007f9410dda000)
        librt.so.1 => /lib64/librt.so.1 (0x00007f9410bd2000)
        libXrandr.so.2 => /lib64/libXrandr.so.2 (0x00007f94109c7000)
        libXinerama.so.1 => /lib64/libXinerama.so.1 (0x00007f94107c4000)
        libXfixes.so.3 => /lib64/libXfixes.so.3 (0x00007f94105be000)
        libXext.so.6 => /lib64/libXext.so.6 (0x00007f94103ac000)
        libxml2.so.2 => /lib64/libxml2.so.2 (0x00007f9410042000)
        libgpm.so.2 => /lib64/libgpm.so.2 (0x00007f940fe3b000)
        libtinfo.so.5 => /lib64/libtinfo.so.5 (0x00007f940fc11000)
        libselinux.so.1 => /lib64/libselinux.so.1 (0x00007f940f9ea000)
        libharfbuzz.so.0 => /lib64/libharfbuzz.so.0 (0x00007f940f74d000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f940f531000)
        libanl.so.1 => /lib64/libanl.so.1 (0x00007f940f32d000)
        libz.so.1 => /lib64/libz.so.1 (0x00007f940f117000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00007f940ef13000)
        libgmp.so.10 => /lib64/libgmp.so.10 (0x00007f940ec9b000)
        libc.so.6 => /lib64/libc.so.6 (0x00007f940e8cd000)
        libjbig.so.2.0 => /lib64/libjbig.so.2.0 (0x00007f940e6c1000)
        libgmodule-2.0.so.0 => /lib64/libgmodule-2.0.so.0 (0x00007f940e4bd000)
        libXi.so.6 => /lib64/libXi.so.6 (0x00007f940e2ad000)
        libXcursor.so.1 => /lib64/libXcursor.so.1 (0x00007f940e0a2000)
        libXcomposite.so.1 => /lib64/libXcomposite.so.1 (0x00007f940de9f000)
        libXdamage.so.1 => /lib64/libXdamage.so.1 (0x00007f940dc9c000)
        libffi.so.6 => /lib64/libffi.so.6 (0x00007f940da94000)
        libpcre.so.1 => /lib64/libpcre.so.1 (0x00007f940d832000)
        libresolv.so.2 => /lib64/libresolv.so.2 (0x00007f940d618000)
        libmount.so.1 => /lib64/libmount.so.1 (0x00007f940d3d5000)
        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f940d1bf000)
        libpixman-1.so.0 => /lib64/libpixman-1.so.0 (0x00007f940cf16000)
        libEGL.so.1 => /lib64/libEGL.so.1 (0x00007f940cd02000)
        libxcb-shm.so.0 => /lib64/libxcb-shm.so.0 (0x00007f940cafe000)
        libxcb-render.so.0 => /lib64/libxcb-render.so.0 (0x00007f940c8f0000)
        libGL.so.1 => /lib64/libGL.so.1 (0x00007f940c664000)
        libthai.so.0 => /lib64/libthai.so.0 (0x00007f940c458000)
        libfribidi.so.0 => /lib64/libfribidi.so.0 (0x00007f940c23c000)
        libexpat.so.1 => /lib64/libexpat.so.1 (0x00007f940c011000)
        libuuid.so.1 => /lib64/libuuid.so.1 (0x00007f940be0c000)
        libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f940bbfc000)
        libXau.so.6 => /lib64/libXau.so.6 (0x00007f940b9f8000)
        libcroco-0.6.so.3 => /lib64/libcroco-0.6.so.3 (0x00007f940b7bc000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f9414cd7000)
        liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f940b596000)
        libgraphite2.so.3 => /lib64/libgraphite2.so.3 (0x00007f940b368000)
        libblkid.so.1 => /lib64/libblkid.so.1 (0x00007f940b128000)
        libGLdispatch.so.0 => /lib64/libGLdispatch.so.0 (0x00007f940ae72000)
        libGLX.so.0 => /lib64/libGLX.so.0 (0x00007f940ac40000)
[rocky8]$ ldd /wynton/home/cbi/shared/software/CBI/emacs-28.2/bin/emacs
        linux-vdso.so.1 (0x00007fff7ebdc000)
        libtiff.so.5 => /lib64/libtiff.so.5 (0x00007f87b184e000)
        libjpeg.so.62 => /lib64/libjpeg.so.62 (0x00007f87b15e5000)
        libpng15.so.15 => not found
        libgtk-x11-2.0.so.0 => /lib64/libgtk-x11-2.0.so.0 (0x00007f87b0f4f000)
        libgdk-x11-2.0.so.0 => /lib64/libgdk-x11-2.0.so.0 (0x00007f87b0c88000)
        libatk-1.0.so.0 => /lib64/libatk-1.0.so.0 (0x00007f87b0a60000)
        libgio-2.0.so.0 => /lib64/libgio-2.0.so.0 (0x00007f87b06b6000)
        libpangoft2-1.0.so.0 => /lib64/libpangoft2-1.0.so.0 (0x00007f87b049f000)
        libpangocairo-1.0.so.0 => /lib64/libpangocairo-1.0.so.0 (0x00007f87b0290000)
        libgdk_pixbuf-2.0.so.0 => /lib64/libgdk_pixbuf-2.0.so.0 (0x00007f87b0067000)
        libcairo.so.2 => /lib64/libcairo.so.2 (0x00007f87afd47000)
        libpango-1.0.so.0 => /lib64/libpango-1.0.so.0 (0x00007f87afaff000)
        libfontconfig.so.1 => /lib64/libfontconfig.so.1 (0x00007f87af8ba000)
        libgobject-2.0.so.0 => /lib64/libgobject-2.0.so.0 (0x00007f87af667000)
        libfreetype.so.6 => /lib64/libfreetype.so.6 (0x00007f87af3ab000)
        libglib-2.0.so.0 => /lib64/libglib-2.0.so.0 (0x00007f87af091000)
        libSM.so.6 => /lib64/libSM.so.6 (0x00007f87aee88000)
        libICE.so.6 => /lib64/libICE.so.6 (0x00007f87aec6c000)
        libX11.so.6 => /lib64/libX11.so.6 (0x00007f87ae929000)
        libX11-xcb.so.1 => /lib64/libX11-xcb.so.1 (0x00007f87ae727000)
        libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f87ae4fe000)
        libXrender.so.1 => /lib64/libXrender.so.1 (0x00007f87ae2f3000)
        librsvg-2.so.2 => /lib64/librsvg-2.so.2 (0x00007f87adf66000)
        libm.so.6 => /lib64/libm.so.6 (0x00007f87adbe4000)
        librt.so.1 => /lib64/librt.so.1 (0x00007f87ad9dc000)
        libXrandr.so.2 => /lib64/libXrandr.so.2 (0x00007f87ad7d1000)
        libXinerama.so.1 => /lib64/libXinerama.so.1 (0x00007f87ad5ce000)
        libXfixes.so.3 => /lib64/libXfixes.so.3 (0x00007f87ad3c8000)
        libXext.so.6 => /lib64/libXext.so.6 (0x00007f87ad1b5000)
        libxml2.so.2 => /lib64/libxml2.so.2 (0x00007f87ace4d000)
        libgpm.so.2 => /lib64/libgpm.so.2 (0x00007f87acc46000)
        libtinfo.so.5 => not found
        libselinux.so.1 => /lib64/libselinux.so.1 (0x00007f87aca1b000)
        libharfbuzz.so.0 => /lib64/libharfbuzz.so.0 (0x00007f87ac776000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f87ac556000)
        libanl.so.1 => /lib64/libanl.so.1 (0x00007f87ac352000)
        libz.so.1 => /lib64/libz.so.1 (0x00007f87ac13a000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00007f87abf36000)
        libgmp.so.10 => /lib64/libgmp.so.10 (0x00007f87abc9e000)
        libc.so.6 => /lib64/libc.so.6 (0x00007f87ab8d9000)
        libjbig.so.2.1 => /lib64/libjbig.so.2.1 (0x00007f87ab6cd000)
        libgmodule-2.0.so.0 => /lib64/libgmodule-2.0.so.0 (0x00007f87ab4c9000)
        libXi.so.6 => /lib64/libXi.so.6 (0x00007f87ab2b8000)
        libXcursor.so.1 => /lib64/libXcursor.so.1 (0x00007f87ab0ad000)
        libXcomposite.so.1 => /lib64/libXcomposite.so.1 (0x00007f87aaeaa000)
        libXdamage.so.1 => /lib64/libXdamage.so.1 (0x00007f87aaca7000)
        libffi.so.6 => /lib64/libffi.so.6 (0x00007f87aaa9e000)
        libgnutls.so.30 => /lib64/libgnutls.so.30 (0x00007f87aa6ad000)
        libpcre.so.1 => /lib64/libpcre.so.1 (0x00007f87aa43c000)
        libresolv.so.2 => /lib64/libresolv.so.2 (0x00007f87aa224000)
        libmount.so.1 => /lib64/libmount.so.1 (0x00007f87a9fca000)
        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f87a9db2000)
        libpng16.so.16 => /lib64/libpng16.so.16 (0x00007f87a9b7d000)
        libpixman-1.so.0 => /lib64/libpixman-1.so.0 (0x00007f87a98d5000)
        libxcb-shm.so.0 => /lib64/libxcb-shm.so.0 (0x00007f87a96d1000)
        libxcb-render.so.0 => /lib64/libxcb-render.so.0 (0x00007f87a94c3000)
        libthai.so.0 => /lib64/libthai.so.0 (0x00007f87a92b9000)
        libfribidi.so.0 => /lib64/libfribidi.so.0 (0x00007f87a909d000)
        libexpat.so.1 => /lib64/libexpat.so.1 (0x00007f87a8e61000)
        libuuid.so.1 => /lib64/libuuid.so.1 (0x00007f87a8c59000)
        libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f87a8a48000)
        libXau.so.6 => /lib64/libXau.so.6 (0x00007f87a8844000)
        libcroco-0.6.so.3 => /lib64/libcroco-0.6.so.3 (0x00007f87a8608000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f87b1ac7000)
        liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f87a83e1000)
        libpcre2-8.so.0 => /lib64/libpcre2-8.so.0 (0x00007f87a815d000)
        libgraphite2.so.3 => /lib64/libgraphite2.so.3 (0x00007f87a7f31000)
        libp11-kit.so.0 => /lib64/libp11-kit.so.0 (0x00007f87a7c07000)
        libidn2.so.0 => /lib64/libidn2.so.0 (0x00007f87a79e9000)
        libunistring.so.2 => /lib64/libunistring.so.2 (0x00007f87a7668000)
        libtasn1.so.6 => /lib64/libtasn1.so.6 (0x00007f87a7455000)
        libnettle.so.6 => /lib64/libnettle.so.6 (0x00007f87a721b000)
        libhogweed.so.4 => /lib64/libhogweed.so.4 (0x00007f87a6feb000)
        libblkid.so.1 => /lib64/libblkid.so.1 (0x00007f87a6d98000)
        libdatrie.so.1 => /lib64/libdatrie.so.1 (0x00007f87a6b90000)
HenrikBengtsson commented 1 year ago

Gist of automating the library scan:

home=$(dirname "$(dirname "$(command -v R)")")
mapfile -t files < <(find "$home" -type f -executable)
echo "Scanning ${#files[@]} executable files under $home"
ldd "${files[@]}" | grep -F "not found" | sort -u

outputs:

Scanning 44 executable files under /wynton/home/cbi/shared/software/CBI/R-4.3.1-gcc10
        libicui18n.so.50 => not found
        libicuuc.so.50 => not found
        libpng15.so.15 => not found
        libRblas.so => not found
        libreadline.so.6 => not found
        libRlapack.so => not found
        libtcl8.5.so => not found
        libtk8.5.so => not found

when run on Rocky 8.

HenrikBengtsson commented 1 year ago

Added generic test for this to make check, e.g.

$ ~/repositories/CBI-software/CBI/r
$ make check
...
040.missing-libraries.bats
 ✗ No missing library dependencies
   (from function `fail' in file /wynton/home/cbi/shared/software/CBI/bats-support-0.3.0/src/error.bash, line 40,
    in test file /wynton/home/cbi/hb/repositories/CBI-software/CBI/.incl/tests/040.missing-libraries.bats, line 13)
     `[[ "${#missing[@]}" == 0 ]] || fail "Detected missing library dependencies: ${missing[*]}"' failed
   Scanning 44 executable files under
   Detected missing library dependencies: libicui18n.so.50 libicuuc.so.50 libpng15.so.15 libreadline.so.6 libtcl8.5.so libtk8.5.so

12 tests, 2 failures, 3 skipped
HenrikBengtsson commented 1 year ago

Another example:

[dev3]$ ~/repositories/CBI-software/CBI/miniconda3
$ make check
...
040.missing-libraries.bats
 ✗ No missing library dependencies
   (from function `fail' in file /wynton/home/cbi/shared/software/CBI/bats-support-0.3.0/src/error.bash, line 40,
    in test file /wynton/home/cbi/hb/repositories/CBI-software/CBI/.incl/tests/001.bats, line 13)
     `[[ ${#missing[@]} == 0 ]] || fail "Detected missing library dependencies: [n=${#missing[@]}] ${missing[*]}"' failed
   Scanning 915 executable files under
   Detected missing library dependencies: [n=31] /lib64/libstdc++.so.6 [version `CXXABI_1.3.11'] /lib64/libstdc++.so.6 [version `CXXABI_1.3.13'] /lib64/libstd
c++.so.6 [version `CXXABI_1.3.8'] /lib64/libstdc++.so.6 [version `CXXABI_1.3.9'] /lib64/libstdc++.so.6 [version `GLIBCXX_3.4.20'] /lib64/libstdc++.so.6 [versi
on `GLIBCXX_3.4.21'] /lib64/libstdc++.so.6 [version `GLIBCXX_3.4.22'] /lib64/libstdc++.so.6 [version `GLIBCXX_3.4.26'] /lib64/libstdc++.so.6 [version `GLIBCXX
_3.4.29'] libarchive.so.19 libbz2.so.1.0 libcrypto.so.3 libev.so.4 libffi.so.8 libfmt.so.9 libicuuc.so.58 libmamba.so.2 libncursesw.so.6 libnghttp2.so.14 libp
anelw.so.6 libpcre2-posix.so.3 libreadline.so.8 libreproc.so.14 libreproc++.so.14 libsolvext.so.1 libsolv.so.1 libssl.so.3 libtcl8.6.so libtinfow.so.6 libtk8.
6.so libyaml-cpp.so.0.7

Oh, wait. This is from dev3, so should be all good. Ah, this is because Conda will update LD_LIBRARY_PATH when the environment is activated (which loading the module doesn't do). Need to revisit idea, or find a way ...

HenrikBengtsson commented 1 year ago

Rocky 8

[devr8]$ make check-libs/ALL

22/99: cellranger
 ✗ No missing library dependencies
   Scanning 210 executable files under
   Detected missing library dependencies: [n=1] libreadline.so.8

30/99: emacs
 ✗ No missing library dependencies
   Scanning 8 executable files under
   Detected missing library dependencies: [n=2] libpng15.so.15 libtinfo.so.5

31/99: expect
 ✗ No missing library dependencies
   Scanning 44 executable files under
   Detected missing library dependencies: [n=1] libtcl8.5.so

38/99: gistic2
 ✗ No missing library dependencies
   Detected missing library dependencies: [n=188] libaudiodevice.so libavcodec.so.52 libavcodec.so.53 libavformat.so.52 libavformat.so.53 libboost_chrono.so.1.49.0 libboost_date_time.so.1.49.0 libboost_filesystem.so.1.49.0 libboost_log.so.1.49.0 libboost_regex.so.1.49.0 libboost_serialization.so.1.49.0 libboost_system.so.1.49.0 libboost_thread.so.1.49.0 libcdf.so.3 libcfitsio.so libcrypto.so.1.0.0 libcublas.so.5.5 libcudart.so.5.5 libgcrypt.so.11 libGctp.so.0 libgfortran.so.3 libgmp.so.3 libgstapp-0.10.so.0 libgstbase-0.10.so.0 libgstinterfaces-0.10.so.0 libgstreamer-0.10.so.0 libgstreamer-lite.so libgstvideo-0.10.so.0 libhdf5_hl.so.6 libhdf5.so.6 libhdfeos.so.0 libicudata.so.49 libicui18n.so.49 libicuuc.so.49 libimf.so libintlc.so.5 libITKBiasCorrection-4.2.so.1 libITKBioCell-4.2.so.1 libITKCommon-4.2.so.1 libITKDICOMParser-4.2.so.1 libITKEXPAT-4.2.so.1 libITKFEM-4.2.so.1 libitkgdcmCommon-4.2.so.1 libitkgdcmDICT-4.2.so.1 libitkgdcmDSED-4.2.so.1 libitkgdcmIOD-4.2.so.1 libitkgdcmjpeg12-4.2.so.1 libitkgdcmjpeg16-4.2.so.1 libitkgdcmjpeg8-4.2.so.1 libitkgdcmMSFF-4.2.so.1 libitkgdcmuuid-4.2.so.1 libITKgiftiio-4.2.so.1 libitkhdf5-4.2.so.1 libitkhdf5_cpp-4.2.so.1 libITKIOBioRad-4.2.so.1 libITKIOBMP-4.2.so.1 libITKIOGDCM-4.2.so.1 libITKIOGE-4.2.so.1 libITKIOGIPL-4.2.so.1 libITKIOImageBase-4.2.so.1 libITKIOIPL-4.2.so.1 libITKIOJPEG-4.2.so.1 libITKIOLSM-4.2.so.1 libITKIOMeta-4.2.so.1 libITKIONIFTI-4.2.so.1 libITKIONRRD-4.2.so.1 libITKIOPNG-4.2.so.1 libITKIOSiemens-4.2.so.1 libITKIOSpatialObjects-4.2.so.1 libITKIOStimulate-4.2.so.1 libITKIOTIFF-4.2.so.1 libITKIOTransformBase-4.2.so.1 libITKIOTransformHDF5-4.2.so.1 libITKIOTransformInsightLegacy-4.2.so.1 libITKIOTransformMatlab-4.2.so.1 libITKIOVTK-4.2.so.1 libITKIOXML-4.2.so.1 libitkjpeg-4.2.so.1 libITKKLMRegionGrowing-4.2.so.1 libITKLabelMap-4.2.so.1 libITKMesh-4.2.so.1 libITKMetaIO-4.2.so.1 libitkNetlibSlatec-4.2.so.1 libITKniftiio-4.2.so.1 libITKNrrdIO-4.2.so.1 libitkopenjpeg-4.2.so.1 libITKOptimizers-4.2.so.1 libITKPath-4.2.so.1 libitkpng-4.2.so.1 libITKPolynomials-4.2.so.1 libITKQuadEdgeMesh-4.2.so.1 libITKSpatialObjects-4.2.so.1 libITKStatistics-4.2.so.1 libitksys-4.2.so.1 libitktiff-4.2.so.1 libitkv3p_lsqr-4.2.so.1 libitkv3p_netlib-4.2.so.1 libitkvcl-4.2.so.1 libITKVideoCore-4.2.so.1 libitkvnl-4.2.so.1 libitkvnl_algo-4.2.so.1 libITKVNLInstantiation-4.2.so.1 libITKVTK-4.2.so.1 libITKWatersheds-4.2.so.1 libitkzlib-4.2.so.1 libITKznz-4.2.so.1 libjava.so libjvm.so libkdu_a63R.so libkdu_v63R.so liblept.so.2 libmat.so libmawt.so libmex.so libmwamd.so libmwarpack.so libmwaudiofilepluginmanager.so libmwaudiofileplugin.so libmwblacs.so libmwblas.so libmwcholmod.so libmwcolamd.so libmwcpp11compat.so libmwfftw3f.so.3 libmwfftw3.so.3 libmwfl.so libmwhdf5dataset.so libmwhg.so libmwi18n.so libmwJp2Adapter.so libmwlapack.so libmwlaunchermain.so libmwmathcore.so libmwmathrng.so libmwMATLAB_imagesci_res.so libmwMATLAB_res.so libmwmclmcrrt.so.8.3 libmwm_dispatcher.so libmwmfl_fft.so libmwm_interpreter.so libmwmlutil.so libmwmpath.so libmwmpicompat.so libmwmpi.so libmwms.so libmwqhull.so libmwservices.so libmwsl_solver.so libmwtamutil.so libmwtiffmexutils.so libmwudd.so libmx.so libncurses.so.5 libnetcdf.so.7 libnppc.so.5.5 libnsl.so.1 libopencv_calib3d.so.2.4 libopencv_core.so.2.4 libopencv_features2d.so.2.4 libopencv_flann.so.2.4 libopencv_gpu.so.2.4 libopencv_highgui.so.2.4 libopencv_imgproc.so.2.4 libopencv_legacy.so.2.4 libopencv_ml.so.2.4 libopencv_nonfree.so.2.4 libopencv_objdetect.so.2.4 libopencv_photo.so.2.4 libopencv_video.so.2.4 libOpenThreads.so.12 libosgDB.so.80 libosg.so.80 libosgUtil.so.80 libproj.so.0 libQtCore.so.4 libQtGui.so.4 libQtNetwork.so.4 libQtOpenGL.so.4 libQtSql.so.4 libQtSvg.so.4 libQtWebKit.so.4 libQtXmlPatterns.so.4 libQtXml.so.4 libudev.so.0 libut.so libxerces-c.so.27 /wynton/home/cbi/shared/software/CBI/gistic2-2.0.23/MATLAB_Compiler_Runtime/v83/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6 [version `CXXABI_1.3.8'] /wynton/home/cbi/shared/software/CBI/gistic2-2.0.23/MATLAB_Compiler_Runtime/v83/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6 [version `CXXABI_1.3.9']

45/99: htop
 ✗ No missing library dependencies
   Scanning 1 executable files under
   Detected missing library dependencies: [n=2] libncursesw.so.5 libtinfo.so.5

55/99: mc
 ✗ No missing library dependencies
   Scanning 52 executable files under
   Detected missing library dependencies: [n=2] libncursesw.so.5 libtinfo.so.5

56/99: miniconda3
 ✗ No missing library dependencies
   Scanning 915 executable files under
   Detected missing library dependencies: [n=18] /lib64/libstdc++.so.6 [version `CXXABI_1.3.13'] /lib64/libstdc++.so.6 [version `GLIBCXX_3.4.26'] /lib64/libstdc++.so.6 [version `GLIBCXX_3.4.29'] libarchive.so.19 libbz2.so.1.0 libcrypto.so.3 libffi.so.8 libfmt.so.9 libicuuc.so.58 libmamba.so.2 libnsl.so.1 libpcre2-posix.so.3 libreadline.so.8 libreproc++.so.14 libreproc.so.14 libssl.so.3 libtinfow.so.6 libyaml-cpp.so.0.7

70/99: r
040.libs.bats
 ✗ No missing library dependencies
   Scanning 44 executable files under
   Detected missing library dependencies: [n=6] libicui18n.so.50 libicuuc.so.50 libpng15.so.15 libreadline.so.6 libtcl8.5.so libtk8.5.so

76/99: rstudio
 ✗ No missing library dependencies
   Scanning 50 executable files under
   Detected missing library dependencies: [n=3] libicui18n.so.50 libicuuc.so.50 libreadline.so.6

77/99: rstudio-server
 ✗ No missing library dependencies
   Scanning 46 executable files under
   Detected missing library dependencies: [n=3] libicui18n.so.50 libicuuc.so.50 libreadline.so.6

80/99: samtools
 ✗ No missing library dependencies
   Scanning 22 executable files under
   Detected missing library dependencies: [n=2] libncursesw.so.5 libtinfo.so.5

86/99: sqlite
 ✗ No missing library dependencies
   Scanning 3 executable files under
   Detected missing library dependencies: [n=2] libreadline.so.6 libtinfo.so.5

88/99: star
 ✗ No missing library dependencies
   Scanning 76 executable files under
   Detected missing library dependencies: [n=2] /lib64/libm.so.6 [version `GLIBC_2.29'] /lib64/libstdc++.so.6 [version `GLIBCXX_3.4.26']

89/99: tmux
 ✗ No missing library dependencies
   Scanning 1 executable files under
   Detected missing library dependencies: [n=1] libtinfo.so.5

CentOS 7

[dev3]$ make check-libs/ALL

22/99: cellranger
 ✗ No missing library dependencies
   Scanning 210 executable files under
   Detected missing library dependencies: [n=1] libreadline.so.8

38/99: gistic2
 ✗ No missing library dependencies
   Scanning 2209 executable files under
   Detected missing library dependencies: [n=177] libaudiodevice.so libavcodec.so.52 libavcodec.so.53 libavformat.so.52 libavformat.so.53 libboost_chrono.so.1.49.0 libboost_date_time.so.1.49.0 libboost_filesystem.so.1.49.0 libboost_log.so.1.49.0 libboost_regex.so.1.49.0 libboost_serialization.so.1.49.0 libboost_system.so.1.49.0 libboost_thread.so.1.49.0 libcdf.so.3 libcfitsio.so libcrypto.so.1.0.0 libcublas.so.5.5 libcudart.so.5.5 libdf.so.0 libGctp.so.0 libgmp.so.3 libgstapp-0.10.so.0 libgstbase-0.10.so.0 libgstinterfaces-0.10.so.0 libgstreamer-0.10.so.0 libgstreamer-lite.so libgstvideo-0.10.so.0 libhdf5_hl.so.6 libhdf5.so.6 libhdfeos.so.0 libicudata.so.49 libicui18n.so.49 libicuuc.so.49 libimf.so libintlc.so.5 libITKBiasCorrection-4.2.so.1 libITKBioCell-4.2.so.1 libITKCommon-4.2.so.1 libITKDICOMParser-4.2.so.1 libITKEXPAT-4.2.so.1 libITKFEM-4.2.so.1 libitkgdcmCommon-4.2.so.1 libitkgdcmDICT-4.2.so.1 libitkgdcmDSED-4.2.so.1 libitkgdcmIOD-4.2.so.1 libitkgdcmjpeg12-4.2.so.1 libitkgdcmjpeg16-4.2.so.1 libitkgdcmjpeg8-4.2.so.1 libitkgdcmMSFF-4.2.so.1 libitkgdcmuuid-4.2.so.1 libITKgiftiio-4.2.so.1 libitkhdf5-4.2.so.1 libitkhdf5_cpp-4.2.so.1 libITKIOBioRad-4.2.so.1 libITKIOBMP-4.2.so.1 libITKIOGDCM-4.2.so.1 libITKIOGE-4.2.so.1 libITKIOGIPL-4.2.so.1 libITKIOImageBase-4.2.so.1 libITKIOIPL-4.2.so.1 libITKIOJPEG-4.2.so.1 libITKIOLSM-4.2.so.1 libITKIOMeta-4.2.so.1 libITKIONIFTI-4.2.so.1 libITKIONRRD-4.2.so.1 libITKIOPNG-4.2.so.1 libITKIOSiemens-4.2.so.1 libITKIOSpatialObjects-4.2.so.1 libITKIOStimulate-4.2.so.1 libITKIOTIFF-4.2.so.1 libITKIOTransformBase-4.2.so.1 libITKIOTransformHDF5-4.2.so.1 libITKIOTransformInsightLegacy-4.2.so.1 libITKIOTransformMatlab-4.2.so.1 libITKIOVTK-4.2.so.1 libITKIOXML-4.2.so.1 libitkjpeg-4.2.so.1 libITKKLMRegionGrowing-4.2.so.1 libITKLabelMap-4.2.so.1 libITKMesh-4.2.so.1 libITKMetaIO-4.2.so.1 libitkNetlibSlatec-4.2.so.1 libITKniftiio-4.2.so.1 libITKNrrdIO-4.2.so.1 libitkopenjpeg-4.2.so.1 libITKOptimizers-4.2.so.1 libITKPath-4.2.so.1 libitkpng-4.2.so.1 libITKPolynomials-4.2.so.1 libITKQuadEdgeMesh-4.2.so.1 libITKSpatialObjects-4.2.so.1 libITKStatistics-4.2.so.1 libitksys-4.2.so.1 libitktiff-4.2.so.1 libitkv3p_lsqr-4.2.so.1 libitkv3p_netlib-4.2.so.1 libitkvcl-4.2.so.1 libITKVideoCore-4.2.so.1 libitkvnl-4.2.so.1 libitkvnl_algo-4.2.so.1 libITKVNLInstantiation-4.2.so.1 libITKVTK-4.2.so.1 libITKWatersheds-4.2.so.1 libitkzlib-4.2.so.1 libITKznz-4.2.so.1 libjava.so libjvm.so libkdu_a63R.so libkdu_v63R.so liblept.so.2 libmat.so libmawt.so libmex.so libmfhdf.so.0 libmwamd.so libmwarpack.so libmwaudiofilepluginmanager.so libmwaudiofileplugin.so libmwblacs.so libmwblas.so libmwcholmod.so libmwcolamd.so libmwcpp11compat.so libmwfftw3f.so.3 libmwfftw3.so.3 libmwfl.so libmwhdf5dataset.so libmwhg.so libmwi18n.so libmwJp2Adapter.so libmwlapack.so libmwlaunchermain.so libmwmathcore.so libmwmathrng.so libmwMATLAB_imagesci_res.so libmwMATLAB_res.so libmwmclmcrrt.so.8.3 libmwm_dispatcher.so libmwmfl_fft.so libmwm_interpreter.so libmwmlutil.so libmwmpath.so libmwmpicompat.so libmwmpi.so libmwms.so libmwqhull.so libmwservices.so libmwsl_solver.so libmwtamutil.so libmwtiffmexutils.so libmwudd.so libmx.so libnppc.so.5.5 libopencv_calib3d.so.2.4 libopencv_core.so.2.4 libopencv_features2d.so.2.4 libopencv_flann.so.2.4 libopencv_gpu.so.2.4 libopencv_highgui.so.2.4 libopencv_imgproc.so.2.4 libopencv_legacy.so.2.4 libopencv_ml.so.2.4 libopencv_nonfree.so.2.4 libopencv_objdetect.so.2.4 libopencv_photo.so.2.4 libopencv_video.so.2.4 libOpenThreads.so.12 libosgDB.so.80 libosg.so.80 libosgUtil.so.80 libQtGui.so.4 libQtOpenGL.so.4 libQtSvg.so.4 libQtWebKit.so.4 libudev.so.0 libut.so libxerces-c.so.27

56/99: miniconda3
 ✗ No missing library dependencies
   Scanning 915 executable files under
   Detected missing library dependencies: [n=31] /lib64/libstdc++.so.6 [version `CXXABI_1.3.11'] /lib64/libstdc++.so.6 [version `CXXABI_1.3.13'] /lib64/libstdc++.so.6 [version `CXXABI_1.3.8'] /lib64/libstdc++.so.6 [version `CXXABI_1.3.9'] /lib64/libstdc++.so.6 [version `GLIBCXX_3.4.20'] /lib64/libstdc++.so.6 [version `GLIBCXX_3.4.21'] /lib64/libstdc++.so.6 [version `GLIBCXX_3.4.22'] /lib64/libstdc++.so.6 [version `GLIBCXX_3.4.26'] /lib64/libstdc++.so.6 [version `GLIBCXX_3.4.29'] libarchive.so.19 libbz2.so.1.0 libcrypto.so.3 libev.so.4 libffi.so.8 libfmt.so.9 libicuuc.so.58 libmamba.so.2 libncursesw.so.6 libnghttp2.so.14 libpanelw.so.6 libpcre2-posix.so.3 libreadline.so.8 libreproc.so.14 libreproc++.so.14 libsolvext.so.1 libsolv.so.1 libssl.so.3 libtcl8.6.so libtinfow.so.6 libtk8.6.so libyaml-cpp.so.0.7

77/99: rstudio-server
 ✗ No missing library dependencies
   Scanning 46 executable files under
   Detected missing library dependencies: [n=1] /lib64/libc.so.6 [version `GLIBC_2.18']

87/99: sratoolkit
 ✗ No missing library dependencies
   Scanning 46 executable files under
   Detected missing library dependencies: [n=2] /lib64/libstdc++.so.6 [version `GLIBCXX_3.4.20'] /lib64/libstdc++.so.6 [version `GLIBCXX_3.4.21']

88/99: star
 ✗ No missing library dependencies
   Scanning 76 executable files under
   Detected missing library dependencies: [n=5] /lib64/libm.so.6 [version `GLIBC_2.29'] /lib64/libstdc++.so.6 [version `CXXABI_1.3.8'] /lib64/libstdc++.so.6 [version `GLIBCXX_3.4.20'] /lib64/libstdc++.so.6 [version `GLIBCXX_3.4.21'] /lib6
4/libstdc++.so.6 [version `GLIBCXX_3.4.26']
HenrikBengtsson commented 1 year ago

Previously broken modules now fixed