Installation Fails on Debian Bullseye

[DarioS]

There is a problem with compiled code.

** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘flowWorkspace’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/dskh/nobackup/biostat/Rpackages/v4/00LOCK-flowWorkspace/00new/flowWorkspace/libs/flowWorkspace.so':
  /dskh/nobackup/biostat/Rpackages/v4/00LOCK-flowWorkspace/00new/flowWorkspace/libs/flowWorkspace.so: undefined symbol: _ZN2pb15GatingHierarchyC1EPN6google8protobuf5ArenaE
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/dskh/nobackup/biostat/Rpackages/v4/flowWorkspace’

I am installing onto a Debian 11 departmental server.

> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 11 (bullseye)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.13.so

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

[mikejiang]

Make sure RProtoBufLib and cytolib are installed properly via BiocManager::install,

[DarioS]

Thanks for the suggestion. They were previously installed and are at the latest release versions. Any other checks I should do?

> library(cytolib)
> library(RProtoBufLib)
> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 11 (bullseye)

other attached packages:
[1] RProtoBufLib_2.8.0 cytolib_2.8.0

[mikejiang]

Could you please paste or attach the entire output of biocManager::install("flowWorkspace")?

[DarioS]

I could.

> .libPaths("/tmp/testInstall") # Empty directory.
> install.packages("BiocManager") # Installs version 1.30.18 of BiocManager.
> logLines <- system2("Rscript", "-e \".libPaths('/tmp/testInstall/');BiocManager::install('flowWorkspace');\"", stdout = TRUE, stderr = TRUE)
> writeLines(logLines, "installation.txt")

The log of installation is attached.

[mikejiang]

skip .libPaths("/tmp/testInstall") , and run BiocManager::install(c('RProtoBufLib', 'cytolib', 'flowWorkspace'); then reattach the log

[DarioS]

Never mind. One of the package installations was failing because it was looking for TMPDIR that is on another server.