Installation error- always end up with pak error

[shrvi]

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Brief description of the problem

✔ Cached copy of spacedeconv 0.1.1 (source) is the latest build ✔ No downloads needed, all packages are cached ℹ Building spacedeconv 0.1.1 ✖ Failed to build spacedeconv 0.1.1 (41.8s) Error: ! error in pak subprocess Caused by error in stop_task_build(state, worker): ! Failed to build source package spacedeconv. Full installation output:

• installing source package ‘spacedeconv’ ... staged installation is only possible with locking using non-staged installation R data inst byte-compile and prepare package for lazy loading Note: possible error in 'layout(title = "SpatialExperiment Overview", ': unused arguments (title = "SpatialExperiment Overview", xaxis = list(title = "pxl_col_in_fullres"), yaxis = list(title = "pxl_row_in_fullres", autorange = "reversed", scaleanchor = "x", scaleratio = 1)) help installing help indices copying figures building package indices installing vignettes ** testing if installed package can be loaded → checking spacedeconv environment and dependencies Error: package or namespace load failed for ‘spacedeconv’: .onLoad failed in loadNamespace() for 'spacedeconv', details: call: Sys.setenv(PATH = paste(path.bin, Sys.getenv()["PATH"], sep = ";")) error: wrong length for argument Error: loading failed Execution halted ERROR: loading failed
• removing ‘/tmp/Rtmp257p2j/pkg-lib600d4b814e5d/spacedeconv’ Type .Last.error to see the more details.

  pak::pkg_install("omnideconv/spacedeconv", dependencies=TRUE)

→ Will install 6 packages. → Will download 5 packages with unknown size.

• CARD 1.1 [bld][cmp][dl] (GitHub: 2d64b91)
• MCMCpack 1.7-1 [bld][cmp]
• MuSiC 0.3.0 [bld][cmp][dl] (GitHub: 7b18b03)
• omnideconv 0.1.0 [bld][cmp][dl] (GitHub: 659a72f)
• Orthology.eg.db 3.16.0 [bld][dl]
• spacedeconv 0.1.1 [bld][cmp][dl] (GitHub: dc392c2) ✔ All system requirements are already installed.

ℹ Getting 5 pkgs with unknown sizes, 1 (734.83 kB) cached ✔ Cached copy of spacedeconv 0.1.1 (source) is the latest build ✔ Cached copy of omnideconv 0.1.0 (source) is the latest build ✔ Cached copy of CARD 1.1 (source) is the latest build ✔ Cached copy of MuSiC 0.3.0 (source) is the latest build ✔ Cached copy of Orthology.eg.db 3.16.0 (source) is the latest build ✔ Got MCMCpack 1.7-1 (source) (734.83 kB) ✔ Downloaded 1 package (734.83 kB) in 1.9s ℹ Building spacedeconv 0.1.1 ℹ Building Orthology.eg.db 3.16.0 ℹ Building omnideconv 0.1.0 ℹ Building MCMCpack 1.7-1 ✖ Failed to build omnideconv 0.1.0 (40s) Error: ! error in pak subprocess Caused by error in stop_task_build(state, worker): ! Failed to build source package omnideconv. Full installation output:

• installing source package ‘omnideconv’ ... staged installation is only possible with locking using non-staged installation R data moving datasets to lazyload DB inst byte-compile and prepare package for lazy loading help installing help indices * copying figures building package indices installing vignettes testing if installed package can be loaded → checking omnideconv environment and dependencies Error: package or namespace load failed for ‘omnideconv’: .onLoad failed in loadNamespace() for 'omnideconv', details: call: Sys.setenv(PATH = paste(path.bin, Sys.getenv()["PATH"], sep = ";")) error: wrong length for argument Error: loading failed Execution halted ERROR: loading failed
• removing ‘/tmp/Rtmp257p2j/pkg-lib600d38a9e00f/omnideconv’ Type .Last.error to see the more details.

# insert reprex here

Versions

Ubuntu 22.04, R 4.2.3

[Paste the output of `sessionInfo()` leaving a blank line after the details tag] > sessionInfo() R version 4.2.3 (2023-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.5 LTS Matrix products: default BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so 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 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] processx_3.8.4 compiler_4.2.3 R6_2.5.1 cli_3.6.2 tools_4.2.3 [6] callr_3.7.6 ps_1.7.6 pak_0.8.0 tcltk_4.2.3 >

[czackl]

Hi! It seems to me that omnideconv could not be installed correctly. Maybe try installing omnideconv directly and check if spacedeconv installation finishes then.

[shrvi]

i get almost the same error there - is this built for ubuntu 22? The ; error seems to be built for windows.

✖ Failed to build omnideconv 0.1.0 (30.4s) Error: ! error in pak subprocess Caused by error in stop_task_build(state, worker): ! Failed to build source package omnideconv. Full installation output:

• installing source package ‘omnideconv’ ... staged installation is only possible with locking using non-staged installation R data moving datasets to lazyload DB inst byte-compile and prepare package for lazy loading help installing help indices * copying figures building package indices installing vignettes testing if installed package can be loaded → checking omnideconv environment and dependencies Error: package or namespace load failed for ‘omnideconv’: .onLoad failed in loadNamespace() for 'omnideconv', details: call: Sys.setenv(PATH = paste(path.bin, Sys.getenv()["PATH"], sep = ";")) error: wrong length for argument Error: loading failed Execution halted ERROR: loading failed
• removing ‘/tmp/RtmpKoDaA5/pkg-lib3e9026618fb71b/omnideconv’ Type .Last.error to see the more details.