Installation Error

[cmfield]

Describe the bug When the lazy loading stage is reached it crashes:

sh: line 1: 76963 Illegal instruction     (core dumped) R_TESTS= '/nfs/nas22/fs2201/biol_micro_unix_modules/modules/software/R/4.2.0-foss-2020b/lib64/R/bin/R' --no-save --no-restore --no-echo 2>&1 < '/tmp/RtmphinURs/file12a391a5471f1'

 *** caught illegal operation ***
address 0x7f4211cafcd0, cause 'illegal operand'

To Reproduce BiocManager::install("Rsamtools")

sessionInfo

Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

Matrix products: default
BLAS/LAPACK: /nfs/nas22/fs2201/biol_micro_unix_modules/modules/software/OpenBLAS/0.3.12-GCC-10.2.0/lib/libopenblas_haswellp-r0.3.12.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] BiocManager_1.30.19 compiler_4.2.0      tools_4.2.0

[mtmorgan]

You can 'see' that Rsamtools installs on the Bioconductor linux builder (under the current Bioc release using R-4.2 & Bioc devel using R-devel.

[cmfield]

Yes, and I actually managed to install it on another machine. Is it possible that an older chipset (~5yrs) could have a problem?

[mtmorgan]

My guess would be the /nfs mount. You say 'lazy load'; can you elaborate? Is it at this stage here...

* installing *source* package ‘Rsamtools’ ...
** using staged installation
** libs
...
** R
** inst
** byte-compile and prepare package for lazy loading
<illegal instruction here ???>
...

[cmfield]

My guess would be the /nfs mount. You say 'lazy load'; can you elaborate? Is it at this stage here...

* installing *source* package ‘Rsamtools’ ...
** using staged installation
** libs
...
** R
** inst
** byte-compile and prepare package for lazy loading
<illegal instruction here ???>
...

Yes, exactly at that point.

[mtmorgan]

I see this very similar report but for a different package suggesting perhaps that the cpu node being used for the installation doesn't have a full installation of Rsamtools dependencies? Maybe the immediate dependencies are satisfied, but underlying dependencies are not... You could try to install all dependencies explicitly

> db = available.packages(repos = BiocManager::repositories())
> pkgs = tools::package_dependencies("Rsamtools", db, recursive=TRUE)[[1]]
> BiocManager::install(c("Rsamtools", pkgs))

or do a sanity check

setdiff(pkgs, rownames(installed.packages())) ## should be the empty set

[cmfield]

Thanks, I'll give it a go.

[mtmorgan]

Is this issue still active?

[cmfield]

Well, I still could not get to install on the first machine and I suspect it's the chipset not supporting a recent core library because it's otherwise identical to the newer machine on which it did install - nothing I can put my finger on, but maybe a cautionary tale for others. Feel free to close the issue.