Installation error related to 'dbplyr'

[anikaliu]

Hello:)
I'm having trouble installing liana and was wondering if you'd be able to help with that?
It seems to be related to dbplyr which I have re-installed now and works fine, so I'm not sure what is going wrong...
When I try to install it, this is the error I receive:

`> devtools::install_github('saezlab/liana')
Downloading GitHub repo saezlab/liana@HEAD
✔  checking for file ‘/tmp/Rtmp2PPIY4/remotes1ac085225ff03/saezlab-liana-965def5/DESCRIPTION’
─  preparing ‘liana’:
✔  checking DESCRIPTION meta-information ... OK
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘liana_0.0.1.tar.gz’
   
Installing package into ‘/home/al862/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package ‘liana’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘purrr::list_along’ by ‘rlang::list_along’ when loading ‘liana’
Warning: replacing previous import ‘purrr::invoke’ by ‘rlang::invoke’ when loading ‘liana’
Warning: replacing previous import ‘purrr::flatten_raw’ by ‘rlang::flatten_raw’ when loading ‘liana’
Warning: replacing previous import ‘purrr::modify’ by ‘rlang::modify’ when loading ‘liana’
Warning: replacing previous import ‘purrr::as_function’ by ‘rlang::as_function’ when loading ‘liana’
Warning: replacing previous import ‘purrr::flatten_dbl’ by ‘rlang::flatten_dbl’ when loading ‘liana’
Warning: replacing previous import ‘purrr::flatten_lgl’ by ‘rlang::flatten_lgl’ when loading ‘liana’
Warning: replacing previous import ‘purrr::flatten_int’ by ‘rlang::flatten_int’ when loading ‘liana’
Warning: replacing previous import ‘purrr::%@%’ by ‘rlang::%@%’ when loading ‘liana’
Warning: replacing previous import ‘purrr::flatten_chr’ by ‘rlang::flatten_chr’ when loading ‘liana’
Warning: replacing previous import ‘purrr::splice’ by ‘rlang::splice’ when loading ‘liana’
Warning: replacing previous import ‘purrr::flatten’ by ‘rlang::flatten’ when loading ‘liana’
Warning: replacing previous import ‘purrr::prepend’ by ‘rlang::prepend’ when loading ‘liana’
Error in completeSubclasses(classDef2, class1, obj, where) : 
  trying to get slot "subclasses" from an object of a basic class ("NULL") with no slots
Error: package or namespace load failed for ‘dbplyr’:
 .onLoad failed in loadNamespace() for 'dbplyr', details:
  call: setClass(cl, contains = c(prevClass, "VIRTUAL"), where = where)
  error: error in contained classes ("character") for class “ident”; class definition removed from ‘dbplyr’
Error in .requirePackage(package) : 
  unable to find required package ‘dbplyr’
Calls: <Anonymous> ... .recacheSubclasses -> getClassDef -> .requirePackage
Execution halted
ERROR: lazy loading failed for package ‘liana’
* removing ‘/home/al862/R/x86_64-pc-linux-gnu-library/4.0/liana’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/Rtmp2PPIY4/file1ac0894fb358/liana_0.0.1.tar.gz’ had non-zero exit status`

My session info is:

> sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0

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

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

loaded via a namespace (and not attached):
 [1] rstudioapi_0.13   magrittr_2.0.1    usethis_2.0.1     devtools_2.4.2   
 [5] pkgload_1.2.1     R6_2.5.0          rlang_0.4.11      fastmap_1.1.0    
 [9] tools_4.0.5       pkgbuild_1.2.0    sessioninfo_1.1.1 cli_3.0.1        
[13] withr_2.4.2       ellipsis_0.3.2    remotes_2.4.0     rprojroot_2.0.2  
[17] lifecycle_1.0.0   crayon_1.4.1      processx_3.5.2    purrr_0.3.4      
[21] callr_3.7.0       fs_1.5.0          ps_1.6.0          testthat_3.0.4   
[25] curl_4.3.2        memoise_2.0.0     glue_1.4.2        cachem_1.0.5     
[29] compiler_4.0.5    desc_1.3.0        prettyunits_1.1.1

As side note, someone has previously had a similar error over here: tidyverse/dbplyr#619
However, I was able to install both packages where the error was observed there.

Best wishes,
Anika

[dbdimitrov]

Hi Anika,

Thanks for using liana :)

Honestly, I have not seen this error and I'm not sure if I can reproduce it and hence fix it. I was also unable to find any further information than the one that you shared about it.

Perhaps, installing it in renv (i.e. a clean environment) might resolve the issue.
If you prefer I could share a renv snapshot of my own that I know is working.

Best wishes,
Daniel

[deeenes]

Hi Anika,

Are all your installed packages up to date and built under the current R version? You can check by old.packages() and use update.packages() to update all.

[anikaliu]

Hi Denes,
good call.. I see that "Matrix" which was pointed out as troublemaker in the link I added is outdated. However, it's a system library that I don't have rights to update on our server. Will try to find a workaround and let you know:)

[deeenes]

Maybe you can install it in your home dir:

packages <- 'Matrix'
local_lib <- '~/r_packages'
.libPaths(new = local_lib)

for(pkg in packages){

    if(!require(pkg, character.only = TRUE)){

        dir.create(local_lib, showWarnings = FALSE)
        install.packages(pkg, lib = local_lib)
        library(pkg, character.only = TRUE)

    }

}

renv does this by a more systematic way (do this in your project working directory):

library(renv)
renv::install('Matrix')
renv::update('Matrix')
renv::snapshot()

[anikaliu]

Hi Denes and Daniel,
all packages were updated now by the person in control of the server and it's still not working:/ Will give renv a try (probably good to start using it anyways) and will then wait for the next update:)

Thanks for you help so far,
Anika

[deeenes]

I afraid renv won't make a miracle here, as all packages are already installed, it will simply copy them to your project directory. The issue can be related also to some outdated dependency outside R, C libraries such as BLAS, lxml, etc.

You are getting the error during installation. To see better what's going on, you could try to load the package and report a traceback:

mkdir liana_tmp
cd liana_tmp
git clone --depth 1 https://github.com/saezlab/liana .
R

And:

library(devtools)
load_all()
# error happens
traceback()