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satijalab / azimuth

A Shiny web app for mapping datasets using Seurat v4
https://satijalab.org/azimuth
GNU General Public License v3.0
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Error in installing package #191

Open czfoo opened 11 months ago

czfoo commented 11 months ago

Hi,

I get the error below when trying to install Azimuth:

ERROR: dependencies ‘hdf5r’, ‘SeuratDisk’ are not available for package ‘Azimuth’

Do you by any chance know what's going on?

Thank you.

Niubile001 commented 11 months ago

Hi,

I get the error below when trying to install Azimuth:

ERROR: dependencies ‘hdf5r’, ‘SeuratDisk’ are not available for package ‘Azimuth’

  • removing ‘/home/czf316/R/x86_64-pc-linux-gnu-library/4.2/Azimuth’ Warning messages: 1: In i.p(...) : installation of package ‘hdf5r’ had non-zero exit status 2: In i.p(...) : installation of package ‘/tmp/RtmpSEHAHd/filefb6440ce03aa/SeuratDisk_0.0.0.9021.tar.gz’ had non-zero exit status 3: In i.p(...) : installation of package ‘hdf5r’ had non-zero exit status 4: In i.p(...) : installation of package ‘/tmp/RtmpSEHAHd/filefb64510e02cd/Azimuth_0.5.0.tar.gz’ had non-zero exit status

Do you by any chance know what's going on?

Thank you.

Try following scripts in Ubuntu terminal: apt-get install libhdf5-dev conda install -c conda-forge r-hdf5r

MWRR commented 10 months ago

Hi,

I get the error below when trying to install Azimuth:

ERROR: dependencies ‘hdf5r’, ‘SeuratDisk’ are not available for package ‘Azimuth’

  • removing ‘/home/czf316/R/x86_64-pc-linux-gnu-library/4.2/Azimuth’ Warning messages: 1: In i.p(...) : installation of package ‘hdf5r’ had non-zero exit status 2: In i.p(...) : installation of package ‘/tmp/RtmpSEHAHd/filefb6440ce03aa/SeuratDisk_0.0.0.9021.tar.gz’ had non-zero exit status 3: In i.p(...) : installation of package ‘hdf5r’ had non-zero exit status 4: In i.p(...) : installation of package ‘/tmp/RtmpSEHAHd/filefb64510e02cd/Azimuth_0.5.0.tar.gz’ had non-zero exit status

Do you by any chance know what's going on?

Thank you.

@czfoo I am facing a similar issue. Did you find a solution? remotes::install_github('satijalab/azimuth', ref = 'master') and the error was

── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────✔  checking for file ‘/tmp/Rtmp3mA7hZ/remotes153175d0dc545/satijalab-azimuth-f3c7904/DESCRIPTION’ ...
─  preparing ‘Azimuth’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
   Omitted ‘LazyData’ from DESCRIPTION
─  building ‘Azimuth_0.4.6.tar.gz’
   Warning: invalid uid value replaced by that for user 'nobody'
   Warning: invalid gid value replaced by that for user 'nobody'

Installing package into ‘/home/user/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
ERROR: dependencies ‘hdf5r’, ‘SeuratDisk’ are not available for package ‘Azimuth’
* removing ‘/home/user/R/x86_64-pc-linux-gnu-library/4.2/Azimuth’
Warning messages:
1: In i.p(...) : installation of package ‘hdf5r’ had non-zero exit status
2: In i.p(...) :
  installation of package ‘/tmp/Rtmp3mA7hZ/file1531758beb003/SeuratDisk_0.0.0.9021.tar.gz’ had non-zero exit status
3: In i.p(...) : installation of package ‘hdf5r’ had non-zero exit status
4: In i.p(...) :
  installation of package ‘/tmp/Rtmp3mA7hZ/file1531745915c1c/Azimuth_0.4.6.tar.gz’ had non-zero exit status
NicoHadas commented 8 months ago

I am facing a similar issue as well

aseemmehta commented 5 months ago

I was having the same issue, after installing https://cran.r-project.org/bin/windows/Rtools/rtools44/rtools.html and restarting rStudio, installation was successful