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having difficult in installing Seurat #2339

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Shawn10312 opened this issue Nov 19, 2019 · 2 comments
Closed

having difficult in installing Seurat #2339

Shawn10312 opened this issue Nov 19, 2019 · 2 comments

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@Shawn10312
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It is really strange, because in the before, I can install seurat easily in R3.5.

But after update the R to 3.6.1, I confront the problem in installing seurat in Centos as following:

install.packages('Seurat')
Installing package into ‘/gpfs/ycga/home/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/Seurat_3.1.1.tar.gz'
Content type 'application/x-gzip' length 790426 bytes (771 KB)
==================================================
downloaded 771 KB

ERROR: failed to lock directory ‘/gpfs/ycga/home/R/x86_64-pc-linux-gnu-library/3.6’ for modifying
Try removing ‘/gpfs/ycga/home/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-Seurat’
Warning in install.packages :
installation of package ‘Seurat’ had non-zero exit status

The downloaded source packages are in
‘/tmp/RtmpFC9sMA/downloaded_packages’

Sys.info()
sysname release
"Linux" "3.10.0-957.38.1.el7.x86_64"
version nodename
"#1 SMP Thu Sep 26 12:15:44 EDT 2019" "c15n01.ruddle.hpc.yale.internal"
machine login
"x86_64" "unknown"
user effective_user
"y" "y"

So how can I handle this problem?

@timoast
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timoast commented Nov 19, 2019

Try removing ‘/gpfs/ycga/home/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-Seurat’

@Shawn10312
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cool, that works!
Thanks.

@timoast timoast closed this as completed Nov 19, 2019
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