R Fails to Start and `swupd` Segmentation Fault

[hakoyamah]

I encountered two related issues on Clear Linux, starting from a recent version (observed in build 43720):

1. R fails to start due to unresolved library paths.
2. swupd crashes with a segmentation fault when trying to manage the openblas bundle.

The segmentation fault appears to be caused by a bug or corruption in swupd, and R’s failure to start is due to missing or incorrectly linked libraries (libopenblas.so.0, libR.so, libRblas.so) that previously worked without manual configuration.

Problem Description

• When attempting to run R on Clear Linux, the following error occurs, and R cannot start:

  /usr/lib64/R/bin/exec/R: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory
  

Steps Taken to Troubleshoot and Resolve

1. Check Linked Libraries:

   • I used the ldd command to check which libraries R is linked to:

     ldd /usr/lib64/R/bin/exec/R
     

   • The output showed that libR.so and libRblas.so are not linked, even though they exist on the system. The issue is that these libraries are present, but the path to these libraries is not correctly recognized by the R executable:

     linux-vdso.so.1 (0x00007f7fb9efc000)
     libR.so => not found
     libRblas.so => not found
     libgomp.so.1 => /usr/lib64/libgomp.so.1 (0x00007f7fb9e58000)
     libc.so.6 => /usr/lib64/libc.so.6 (0x00007f7fb9c00000)
     /lib64/ld-linux-x86-64.so.2 => /usr/lib64/ld-linux-x86-64.so.2 (0x00007f7fb9efe000)
     

   • The libraries (libR.so, libRblas.so) exist in the /usr/lib64/R/lib/ directory, but for some reason, R cannot resolve the path to these libraries, which is likely a configuration issue or a missing environment variable.

2. Check for Missing OpenBLAS Library (libopenblas.so.0):

   • I confirmed that libopenblas.so.0 was missing, though OpenBLAS was reported as installed.:

     sudo find /usr/lib64 -name 'libopenblas.so*'
     

3. Segmentation Fault when Removing OpenBLAS:

   • Next, I attempted to remove the OpenBLAS bundle to reinstall it and resolve the missing library issue:

     sudo swupd bundle-remove openblas
     

   • However, this resulted in a Segmentation Fault:

     Segmentation fault
     

   • This crash occurred every time I tried to remove the OpenBLAS bundle.

4. Other Troubleshooting Steps Taken:

   • Ran sudo swupd repair --picky to attempt to fix any broken packages or configurations, but no issues were detected or repaired, leaving the problem unresolved.