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remotes::install_github("satijalab/seurat-data", quiet = TRUE) does not work #8933

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asmlgkj opened this issue May 25, 2024 · 3 comments
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@asmlgkj
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asmlgkj commented May 25, 2024

remotes::install_github("satijalab/seurat-data", quiet = TRUE)

Warning message:
In i.p(...) :
The exit status was not 0 when installing package 'SeuratData_0.2.2.9001.tar.gz'

in centos8 or win11, the same error.
Thanks a lot

@asmlgkj asmlgkj added the bug Something isn't working label May 25, 2024
@Y-CBob
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Y-CBob commented May 26, 2024

same here. Warning message is : "
Installing 2 packages: uwot, SeuratObject
Warning: dependency ‘Matrix’ is not available
Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘uwot’ ‘SeuratObject’
installing the source packages ‘uwot’, ‘SeuratObject’

Error: Failed to install 'Seurat' from GitHub:
! System command 'Rcmd.exe' failed
In addition: Warning messages:
1: In untar2(tarfile, files, list, exdir, restore_times) :
skipping pax global extended headers
2: In untar2(tarfile, files, list, exdir, restore_times) :
skipping pax global extended headers
3: In i.p(...) : installation of package ‘uwot’ had non-zero exit status
4: In i.p(...) :
installation of package ‘SeuratObject’ had non-zero exit status
"

@asmlgkj
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asmlgkj commented May 28, 2024

error: Failed to install 'Seurat' from GitHub:
! System command 'R' failed
on today

@longmanz
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Hi,
Please install Seurat and SeuratObject directly from CRAN using install.packages() function and then try to install the SeuratData again. Please feel free to re-open it if the issue persists.

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