Installation Error

[Exceret]

Hello,

I encountered an error when trying to install scrapper:

packageVersion("assorthead")
# [1] ‘1.5.13’
pak::pkg_install("libscran/scrapper")
#                                                                            
# → Will install 1 package.
# → The package (0 B) is cached.
# + scrapper   1.5.13 [bld][cmp] (GitHub: f004c4f) + ✔ make
# ✔ All system requirements are already installed.
#   
# ℹ No downloads are needed, 1 pkg is cached
# ℹ Building scrapper 1.5.13
# ✖ Failed to build scrapper 1.5.13 (24.3s)                          
#                                                                    
# Error:
# ! ! error in pak subprocess
# Caused by error in `stop_task_build(state, worker)`:
# ! Failed to build source package scrapper.
# Full installation output:
# * installing *source* package ‘scrapper’ ...
# ** this is package ‘scrapper’ version ‘1.5.13’
# staged installation is only possible with locking
# ** using non-staged installation
# ** libs
# using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
# using C++17
# g++ -std=gnu++17 -I"/opt/R/4.5.1/lib/R/include" -DNDEBUG -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/Rigraphlib/igraph/include/igraph' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/Rcpp/include' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/assorthead/include' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/beachmat/include' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/BiocNeighbors/include' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -pedantic -fdiagnostics-color=always  -c RcppExports.cpp -o RcppExports.o
# g++ -std=gnu++17 -I"/opt/R/4.5.1/lib/R/include" -DNDEBUG -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/Rigraphlib/igraph/include/igraph' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/Rcpp/include' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/assorthead/include' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/beachmat/include' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/BiocNeighbors/include' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -pedantic -fdiagnostics-color=always  -c adt_quality_control.cpp -o adt_quality_control.o
# g++ -std=gnu++17 -I"/opt/R/4.5.1/lib/R/include" -DNDEBUG -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/Rigraphlib/igraph/include/igraph' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/Rcpp/include' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/assorthead/include' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/beachmat/include' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/BiocNeighbors/include' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -pedantic -fdiagnostics-color=always  -c aggregate_across_cells.cpp -o aggregate_across_cells.o
# g++ -std=gnu++17 -I"/opt/R/4.5.1/lib/R/include" -DNDEBUG -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/Rigraphlib/igraph/include/igraph' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/Rcpp/include' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/assorthead/include' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/beachmat/include' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/BiocNeighbors/include' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -pedantic -fdiagnostics-color=always  -c aggregate_across_genes.cpp -o aggregate_across_genes.o
# g++ -std=gnu++17 -I"/opt/R/4.5.1/lib/R/include" -DNDEBUG -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/Rigraphlib/igraph/include/igraph' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/Rcpp/include' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/assorthead/include' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/beachmat/include' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/BiocNeighbors/include' -I'/home/yyx/R/x86_64-pc-linux-gnu-library/4.5/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -pedantic -fdiagnostics-color=always  -c build_snn_graph.cpp -o build_snn_graph.o
# In file included from /home/yyx/R/x86_64-pc-linux-gnu-library/4.5/assorthead/include/raiigraph/raiigraph.hpp:4,
#                  from /home/yyx/R/x86_64-pc-linux-gnu-library/4.5/assorthead/include/scran_graph_cluster/build_snn_graph.hpp:13,
#                  from build_snn_graph.cpp:7:
# /home/yyx/R/x86_64-pc-linux-gnu-library/4.5/assorthead/include/raiigraph/RNGScope.hpp: In constructor ‘raiigraph::RNGScope::RNGScope(igraph_uint_t, const igraph_rng_type_t*)’:
# /home/yyx/R/x86_64-pc-linux-gnu-library/4.5/assorthead/include/raiigraph/RNGScope.hpp:46:42: error: void value not ignored as it ought to be
#    46 |         previous = igraph_rng_set_default(&current);
#       |                    ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
(too long, so I just pasted part of it here)

sessioninfo::session_info()
# ─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#  setting  value
#  version  R version 4.5.1 (2025-06-13)
#  os       Ubuntu 24.04.3 LTS
#  system   x86_64, linux-gnu
#  ui       Positron
#  language (EN)
#  collate  en_US.UTF-8
#  ctype    en_US.UTF-8
#  tz       Asia/Shanghai
#  date     2026-03-05
#  pandoc   3.2 @ /usr/local/bin/pandoc
#  quarto   1.5.57 @ /usr/local/bin/quarto
# 
# ─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#  ! package     * version date (UTC) lib source
#    askpass       1.2.1   2024-10-04 [1] RSPM (R 4.5.0)
#    BiocManager   1.30.27 2025-11-14 [1] RSPM (R 4.5.0)
#    cachem        1.1.0   2024-05-16 [1] RSPM (R 4.5.0)
#  P callr         3.7.6   2024-03-25 [2] RSPM (R 4.5.0)
#    cheapr      * 1.5.0   2026-01-08 [1] Github (NicChr/cheapr@bfb6653)
#    cli           3.6.5   2025-04-23 [1] RSPM (R 4.5.0)
#    credentials   2.0.3   2025-09-12 [1] RSPM (R 4.5.0)
#    desc          1.4.3   2023-12-10 [1] RSPM (R 4.5.0)
#    devtools      2.4.6   2025-10-03 [1] RSPM (R 4.5.0)
#    dplyr       * 1.2.0   2026-02-03 [1] CRAN (R 4.5.1)
#    ellipsis      0.3.2   2021-04-29 [1] RSPM (R 4.5.0)
#    fastmap       1.2.0   2024-05-15 [1] RSPM (R 4.5.0)
#    fs            1.6.6   2025-04-12 [1] RSPM (R 4.5.0)
#    generics      0.1.4   2025-05-09 [1] RSPM (R 4.5.0)
#    gert          2.3.1   2026-01-11 [1] RSPM (R 4.5.0)
#    glue          1.8.0   2024-09-30 [1] RSPM (R 4.5.0)
#    jsonlite      2.0.0   2025-03-27 [1] RSPM (R 4.5.0)
#    lifecycle     1.0.5   2026-01-08 [1] RSPM (R 4.5.0)
#    magrittr      2.0.4   2025-09-12 [1] RSPM (R 4.5.0)
#    memoise       2.0.1   2021-11-26 [1] RSPM (R 4.5.0)
#  V openssl       2.3.4   2026-02-26 [1] RSPM (R 4.5.0) (on disk 2.3.5)
#    pak           0.9.0   2025-05-27 [2] RSPM (R 4.5.0)
#    pillar        1.11.1  2025-09-17 [1] RSPM (R 4.5.0)
#    pkgbuild      1.4.8   2025-05-26 [1] RSPM (R 4.5.0)
#    pkgconfig     2.0.3   2019-09-22 [1] RSPM (R 4.5.0)
#    pkgload       1.5.0   2026-02-03 [1] RSPM (R 4.5.0)
#  P processx      3.8.6   2025-02-21 [2] RSPM (R 4.5.0)
#  P ps            1.9.1   2025-04-12 [2] RSPM (R 4.5.0)
#    purrr         1.2.1   2026-01-09 [1] RSPM (R 4.5.0)
#    R6            2.6.1   2025-02-15 [1] RSPM (R 4.5.0)
#    rappdirs      0.3.4   2026-01-17 [1] RSPM (R 4.5.0)
#    remotes       2.5.0   2024-03-17 [1] RSPM (R 4.5.0)
#    rlang         1.1.7   2026-01-09 [1] RSPM (R 4.5.0)
#    rprojroot     2.1.1   2025-08-26 [1] RSPM (R 4.5.0)
#    rstudioapi    0.18.0  2026-01-16 [1] RSPM (R 4.5.0)
#    sessioninfo   1.2.3   2025-02-05 [1] RSPM (R 4.5.0)
#    sys           3.4.3   2024-10-04 [1] RSPM (R 4.5.0)
#    tibble        3.3.1   2026-01-11 [1] RSPM (R 4.5.0)
#    tidyselect    1.2.1   2024-03-11 [1] RSPM (R 4.5.0)
#    usethis       3.2.1   2025-09-06 [1] RSPM (R 4.5.0)
#    vctrs         0.7.1   2026-01-23 [1] RSPM (R 4.5.0)
#    whisker       0.4.1   2022-12-05 [1] RSPM (R 4.5.0)
#    withr         3.0.2   2024-10-28 [1] RSPM (R 4.5.0)
# 
#  [1] /home/yyx/R/x86_64-pc-linux-gnu-library/4.5
#  [2] /opt/R/4.5.1/lib/R/library
# 
#  * ── Packages attached to the search path.
#  V ── Loaded and on-disk version mismatch.
#  P ── Loaded and on-disk path mismatch.
# 
# ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
packageVersion("igraph")
# [1] ‘2.2.2’

These errors seem to come from the C++ part and appear to be related to igraph? My igraph version is 2.2.2.

Thank you for your help!

[LTLA]

scrapper actually depends on Rigraphlib, rather than the official igraph R package, for various reasons that I won't go into here. If you install the development version of Rigraphlib, that particular compilation error should be resolved...

However! The GitHub versions of scrapper, Rigraphlib, etc. represent development versions of those packages, i.e., from the "BioC-devel" stream. Strictly speaking, the development versions of these packages are only compatible with development versions of their dependencies. So if you install scrapper from GitHub and install the other dependencies from BiocManager::install() (which pulls from the "BioC-release" stream by default), you'd be mixing versions from the release and devel streams, which is probably going to cause problems. For example, the development version of scrapper might rely on the latest development versions of BiocNeighbors and beachmat, both of which changed quite a bit from the release versions. So, you'd have to install the latest versions of those dependencies as well.

If you don't actually need the latest versions of all packages, I'd recommend using the standard installation method for Bioconductor packages, as this ensures that all packages are installed from the same stream (BioC-release):

BiocManager::install("scrapper")

If you want the latest development versions of everything, the "official" way to do so is to switch to the BioC-devel stream. This does require you to install R-devel, though, which is a little annoying.