Installation error- always end up with pak error #150
Comments
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Hi! It seems to me that omnideconv could not be installed correctly. Maybe try installing omnideconv directly and check if spacedeconv installation finishes then. |
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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)
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Maybe try installing with devtools::install_github ("omnideconv/omnideconv") to see a more detailed error description. The issue seems to be related to the omnideconv installation so maybe checkout their FAQ as well |
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Thanks a lot for your prompt reply, but we still receive this error,
→ 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
Best,
Shreshta
From: Constantin Zackl ***@***.***>
Sent: Thursday, November 28, 2024 3:22 PM
To: omnideconv/spacedeconv ***@***.***>
Cc: Vijayaraghavan, Shreshta ***@***.***>; Author ***@***.***>
Subject: Re: [omnideconv/spacedeconv] Installation error- always end up with pak error (Issue #150)
Maybe try installing with devtools::install_github ("omnideconv/omnideconv") to see a more detailed error description. The issue seems to be related to the omnideconv installation so maybe checkout their FAQ as well
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The omnidecovn team is preparing a PR that aims to solve this issue. Feel free to check out the PR: omnideconv/omnideconv#202 |
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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:
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
Type .Last.error to see the more details.
→ Will install 6 packages.
→ Will download 5 packages with unknown size.
✔ 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:
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
Type .Last.error to see the more details.
# insert reprex hereVersions
Ubuntu 22.04, R 4.2.3
[Paste the output of
sessionInfo()leaving a blank line after the details tag]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
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