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Tasklist

FS#74609 - [r] R with LTO breaks some R library packages

Attached to Project: Community Packages
Opened by Christoph Fink (peippo) - Sunday, 01 May 2022, 14:21 GMT
Last edited by Antonio Rojas (arojas) - Monday, 02 May 2022, 17:25 GMT
Task Type Bug Report
Category Packages
Status Closed
Assigned To Antonio Rojas (arojas)
Architecture All
Severity Low
Priority Normal
Reported Version
Due in Version Undecided
Due Date Undecided
Percent Complete 100%
Votes 1
Private No

Details

Description:

`r-rsamtools` statically links `r-rhtslib` and fails to build properly if either of those two packages or R is built with `option(lto)` (i.e., all three need to be built with `!lto`).


Additional info:

r 4.2.0-1
r-rhtslib 1.28.0-1 (AUR)
r-rsamtools 2.12.0-1 (AUR)

Upstream bug report against r-rsamtools: https://github.com/Bioconductor/Rsamtools/issues/36


Steps to reproduce:

A. fails:
1. install `r` from community repository
2. build and install `r-rhtslib` from AUR
3. build `r-rsamtools` from AUR

Last step fails with:

```
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘Rsamtools’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/christoph/Dokumente/Tools/aur/r-rsamtools/src/00LOCK-Rsamtools/00new/Rsamtools/libs/Rsamtools.so':
/home/christoph/Dokumente/Tools/aur/r-rsamtools/src/00LOCK-Rsamtools/00new/Rsamtools/libs/Rsamtools.so: undefined symbol: hts_open_format
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/christoph/Dokumente/Tools/aur/r-rsamtools/src/Rsamtools’
* restoring previous ‘/home/christoph/Dokumente/Tools/aur/r-rsamtools/src/Rsamtools’
```

B. works:
1. Build `r` locally with `options=(!lto)`
2. build and install `r-rhtslib` from AUR
3. build and install `r-rsamtools` from AUR
This task depends upon

Closed by  Antonio Rojas (arojas)
Monday, 02 May 2022, 17:25 GMT
Reason for closing:  Fixed
Additional comments about closing:  r 4.2.0-2
Comment by Christoph Fink (peippo) - Sunday, 01 May 2022, 14:29 GMT
This affects other packages from BioConductor as well, it seems: https://github.com/BioArchLinux/Packages/issues/40

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