Got error when installing the GiottoClass on Rocky Linux

[shaojunyu]

Hi,

I encountered an error while installing the GiottoClass on Rocky Linux, but I was able to successfully install it on my Mac. Here are the details of the error:

• install command

library(devtools)
install_github('drieslab/GiottoClass')

Error:

Error: extract-methods.Rd:210: no comma in argument list following \S4method

Error log:

Downloading GitHub repo drieslab/GiottoClass@HEAD
── R CMD build ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/tmp/RtmpC8LrFR/remotes1e7e91ec18380/drieslab-GiottoClass-848d41d/DESCRIPTION’ ...
─ preparing ‘GiottoClass’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts (563ms)
─ checking for empty or unneeded directories
─ building ‘GiottoClass_0.3.2.tar.gz’

Installing package into ‘/home/user/R/x86_64-pc-linux-gnu-library/4.4’
(as ‘lib’ is unspecified)

• installing source package ‘GiottoClass’ ...
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  in method for ‘as.sp’ with signature ‘"sf"’: no definition for class “sf”

....

Error: extract-methods.Rd:210: no comma in argument list following \S4method

• removing ‘/home/user/R/x86_64-pc-linux-gnu-library/4.4/GiottoClass’
  Warning message:
  In i.p(...) :
  installation of package ‘/tmp/RtmpC8LrFR/file1e7e9586b98ff/GiottoClass_0.3.2.tar.gz’ had non-zero exit status

• sessionInfo

> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Rocky Linux 8.10 (Green Obsidian)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.15.so;  LAPACK version 3.9.0

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

time zone: UTC
tzcode source: system (glibc)

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

other attached packages:
[1] devtools_2.4.5 usethis_3.0.0

loaded via a namespace (and not attached):
 [1] miniUI_0.1.1.1    compiler_4.4.1    promises_1.3.0    Rcpp_1.0.13
 [5] stringr_1.5.1     callr_3.7.6       later_1.3.2       fastmap_1.2.0
 [9] mime_0.12         R6_2.5.1          pak_0.7.2         curl_5.2.1
[13] htmlwidgets_1.6.4 desc_1.4.3        profvis_0.3.8     shiny_1.9.0
[17] rlang_1.1.4       cachem_1.1.0      stringi_1.8.4     httpuv_1.6.15
[21] fs_1.6.4          pkgload_1.4.0     memoise_2.0.1     cli_3.6.3
[25] magrittr_2.0.3    ps_1.7.7          processx_3.8.4    digest_0.6.36
[29] xtable_1.8-4      remotes_2.5.0     lifecycle_1.0.4   vctrs_0.6.5
[33] glue_1.7.0        urlchecker_1.0.1  sessioninfo_1.2.2 pkgbuild_1.4.4
[37] purrr_1.0.2       tools_4.4.1       ellipsis_0.3.2    htmltools_0.5.8.1

Thanks for your help!

[jiajic]

Hi, thanks for reporting this!
I'm not too sure what is going wrong here. It appears that somehow building the documentation is breaking the install.
Could you try reinstalling roxygen2 on Linux and seeing if that fixes it? I am on roxygen2 7.3.2

Thanks
George

[shaojunyu]

I have tried reinstalling roxygen2 (v 7.3.2), but the issue persists. I also attempted to install the latest commit of this tool, but encountered the same error. It is puzzling because I tested the installation with R 4.4.1 on three different operating systems: Mac OS Sonoma, Debian 12.6, and Rocky 8.10. This issue only occurs for R 4.4.1 on Rocky Linux; it works fine on the other two platforms.

[jiajic]

I think this is now solved on the dev branch, which should be merged in soon.

It was an issue with one of the methods not having all the params defined by the generic.

[jiajic]

Closing as completed, please reopen is not solved