Set `StagedInstall: no` in `DESCRIPTION`

[waddella]

Hello there,

I am trying to install FLAMES with the environment variable BASILISK_USE_SYSTEM_DIR set to 1 so that python environments get installed/configured at R package installation time. I do the the following error message:

installing to /tmp/Rtmp0bBJ3T/file59fa6a23e8ef/00LOCK-FLAMES/00new/FLAMES/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
ERROR: absolute paths in ‘basilisk/flames_env/lib/libtcl8.6.so’ include the temporary installation directory: please report to the package maintainer and use ‘--no-staged-install’
* removing ‘/tmp/Rtmp0bBJ3T/file59fa6a23e8ef/FLAMES’

which is due to StagedInstall: no not being set , see

https://www.bioconductor.org/packages/release/bioc/vignettes/basilisk/inst/doc/motivation.html#setting-up-the-package

Can you please read the article and address the issue? Let me know if you need any help.

Best, Adrian

Session info is here:

> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

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-r0.3.20.so;  LAPACK version 3.10.0

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   

time zone: Etc/UTC
tzcode source: system (glibc)

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

loaded via a namespace (and not attached):
[1] compiler_4.3.1 tools_4.3.1    parallel_4.3.1
> 

[ChangqingW]

Hi Adrian,

Thanks for reporting this and sharing the article. Does commit dc9795f7669f5fa7580cd1b85acc72aa21753cd3 solve the issue on your system?

Cheers, Changqing

[waddella]

Hi, yes that looks good.