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Can't install package using mamba #37

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mblue9 opened this issue Nov 19, 2021 · 5 comments
Open

Can't install package using mamba #37

mblue9 opened this issue Nov 19, 2021 · 5 comments

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@mblue9
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mblue9 commented Nov 19, 2021

Hello,

Was trying out installing an R package in Galaxy EU RStudio terminal, following the instructions in the RStudio console mamba install package, but it didn't work with mamba (conda seems to work, or at least get further). Should I be able to install using mamba?

(base) rstudio@5ae69c5d7494:~$ mamba install bioconductor-mageckflute

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (0.15.2) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████


Looking for: ['bioconductor-mageckflute']

conda-forge/linux-64     [<=>                 ] (00m:00s) 15  B / ?? (42.00  B/s)
conda-forge/noarch       [<=>                 ] (00m:00s) 15  B / ?? (42.00  B/s)
bioconda/linux-64        [<=>                 ] (00m:00s) 15  B / ?? (42.00  B/s)
bioconda/noarch          [<=>                 ] (00m:00s) 15  B / ?? (42.00  B/s)
ERROR   Could not open file for download /data/dnb03/galaxy_db/job_working_directory/034/556/34556106/tmp/mambafpMraRzhVSy: Permission denied

(base) rstudio@5ae69c5d7494:~$ conda install bioconductor-mageckflute
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /opt/miniconda

  added / updated specs:
    - bioconductor-mageckflute


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    bioconductor-clusterprofiler-4.0.0|    r41hdfd78af_0         693 KB  bioconda
    bioconductor-do.db-2.9     |   r41hdfd78af_11           8 KB  bioconda
    bioconductor-dose-3.18.0   |    r41hdfd78af_0         6.4 MB  bioconda
    bioconductor-enrichplot-1.12.0|    r41hdfd78af_0         277 KB  bioconda
    bioconductor-fgsea-1.18.0  |    r41h399db7b_0         1.4 MB  bioconda
    bioconductor-ggtree-3.0.1  |    r41hdfd78af_0         825 KB  bioconda
    bioconductor-go.db-3.13.0  |    r41hdfd78af_0           8 KB  bioconda
    bioconductor-gosemsim-2.18.0|    r41h399db7b_0         904 KB  bioconda
    bioconductor-mageckflute-1.12.0|    r41hdfd78af_0        13.3 MB  bioconda
    bioconductor-qvalue-2.24.0 |    r41hdfd78af_0         2.7 MB  bioconda
    bioconductor-treeio-1.16.1 |    r41hdfd78af_0         802 KB  bioconda
    ca-certificates-2021.10.8  |       ha878542_0         139 KB  conda-forge
    certifi-2021.10.8          |   py39hf3d152e_1         145 KB  conda-forge
    conda-4.10.3               |   py39hf3d152e_3         3.1 MB  conda-forge
    r-ape-5.5                  |    r41h306847c_0         3.1 MB  conda-forge
    r-aplot-0.1.1              |    r41hc72bb7e_0          61 KB  conda-forge
    r-downloader-0.4           | r41hc72bb7e_1003          34 KB  conda-forge
    r-fastmatch-1.1_3          |    r41hcfec24a_0          47 KB  conda-forge
    r-ggforce-0.3.3            |    r41h03ef668_0         1.9 MB  conda-forge
    r-ggfun-0.0.4              |    r41hc72bb7e_0         137 KB  conda-forge
    r-ggplotify-0.1.0          |    r41hc72bb7e_0         153 KB  conda-forge
    r-ggraph-2.0.5             |    r41h03ef668_0         3.9 MB  conda-forge
    r-graphlayouts-0.7.1       |    r41h03ef668_0         2.4 MB  conda-forge
    r-gridgraphics-0.5_1       |    r41hc72bb7e_0         262 KB  conda-forge
    r-rvcheck-0.2.1            |    r41hc72bb7e_0          41 KB  conda-forge
    r-scatterpie-0.1.6         |    r41hc72bb7e_0         359 KB  conda-forge
    r-shadowtext-0.0.9         |    r41hc72bb7e_0         246 KB  conda-forge
    r-tidygraph-1.2.0          |    r41h03ef668_0         526 KB  conda-forge
    r-tidytree-0.3.6           |    r41hc72bb7e_0         273 KB  conda-forge
    r-tweenr-1.0.2             |    r41h03ef668_0         344 KB  conda-forge
    r-yulab.utils-0.0.4        |    r41hc72bb7e_0          35 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        44.3 MB

The following NEW packages will be INSTALLED:

  bioconductor-clus~ bioconda/noarch::bioconductor-clusterprofiler-4.0.0-r41hdfd78af_0
  bioconductor-do.db bioconda/noarch::bioconductor-do.db-2.9-r41hdfd78af_11
  bioconductor-dose  bioconda/noarch::bioconductor-dose-3.18.0-r41hdfd78af_0
  bioconductor-enri~ bioconda/noarch::bioconductor-enrichplot-1.12.0-r41hdfd78af_0
  bioconductor-fgsea bioconda/linux-64::bioconductor-fgsea-1.18.0-r41h399db7b_0
  bioconductor-ggtr~ bioconda/noarch::bioconductor-ggtree-3.0.1-r41hdfd78af_0
  bioconductor-go.db bioconda/noarch::bioconductor-go.db-3.13.0-r41hdfd78af_0
  bioconductor-gose~ bioconda/linux-64::bioconductor-gosemsim-2.18.0-r41h399db7b_0
  bioconductor-mage~ bioconda/noarch::bioconductor-mageckflute-1.12.0-r41hdfd78af_0
  bioconductor-qval~ bioconda/noarch::bioconductor-qvalue-2.24.0-r41hdfd78af_0
  bioconductor-tree~ bioconda/noarch::bioconductor-treeio-1.16.1-r41hdfd78af_0
  r-ape              conda-forge/linux-64::r-ape-5.5-r41h306847c_0
  r-aplot            conda-forge/noarch::r-aplot-0.1.1-r41hc72bb7e_0
  r-downloader       conda-forge/noarch::r-downloader-0.4-r41hc72bb7e_1003
  r-fastmatch        conda-forge/linux-64::r-fastmatch-1.1_3-r41hcfec24a_0
  r-ggforce          conda-forge/linux-64::r-ggforce-0.3.3-r41h03ef668_0
  r-ggfun            conda-forge/noarch::r-ggfun-0.0.4-r41hc72bb7e_0
  r-ggplotify        conda-forge/noarch::r-ggplotify-0.1.0-r41hc72bb7e_0
  r-ggraph           conda-forge/linux-64::r-ggraph-2.0.5-r41h03ef668_0
  r-graphlayouts     conda-forge/linux-64::r-graphlayouts-0.7.1-r41h03ef668_0
  r-gridgraphics     conda-forge/noarch::r-gridgraphics-0.5_1-r41hc72bb7e_0
  r-rvcheck          conda-forge/noarch::r-rvcheck-0.2.1-r41hc72bb7e_0
  r-scatterpie       conda-forge/noarch::r-scatterpie-0.1.6-r41hc72bb7e_0
  r-shadowtext       conda-forge/noarch::r-shadowtext-0.0.9-r41hc72bb7e_0
  r-tidygraph        conda-forge/linux-64::r-tidygraph-1.2.0-r41h03ef668_0
  r-tidytree         conda-forge/noarch::r-tidytree-0.3.6-r41hc72bb7e_0
  r-tweenr           conda-forge/linux-64::r-tweenr-1.0.2-r41h03ef668_0
  r-yulab.utils      conda-forge/noarch::r-yulab.utils-0.0.4-r41hc72bb7e_0

The following packages will be UPDATED:

  ca-certificates                      2021.5.30-ha878542_0 --> 2021.10.8-ha878542_0
  certifi                          2021.5.30-py39hf3d152e_0 --> 2021.10.8-py39hf3d152e_1
  conda                               4.10.3-py39hf3d152e_0 --> 4.10.3-py39hf3d152e_3


Proceed ([y]/n)? y


Downloading and Extracting Packages
bioconductor-do.db-2 | 8 KB      | ##################################################### | 100% 
bioconductor-treeio- | 802 KB    | ##################################################### | 100% 
ca-certificates-2021 | 139 KB    | ##################################################### | 100% 
r-tweenr-1.0.2       | 344 KB    | ##################################################### | 100% 
r-ggfun-0.0.4        | 137 KB    | ##################################################### | 100% 
bioconductor-cluster | 693 KB    | ##################################################### | 100% 
r-fastmatch-1.1_3    | 47 KB     | ##################################################### | 100% 
r-ggraph-2.0.5       | 3.9 MB    | ##################################################### | 100% 
bioconductor-go.db-3 | 8 KB      | ##################################################### | 100% 
bioconductor-mageckf | 13.3 MB   | ##################################################### | 100% 
bioconductor-fgsea-1 | 1.4 MB    | ##################################################### | 100% 
r-ggplotify-0.1.0    | 153 KB    | ##################################################### | 100% 
bioconductor-dose-3. | 6.4 MB    | ##################################################### | 100% 
r-ape-5.5            | 3.1 MB    | ##################################################### | 100% 
r-aplot-0.1.1        | 61 KB     | ##################################################### | 100% 
conda-4.10.3         | 3.1 MB    | ##################################################### | 100% 
r-rvcheck-0.2.1      | 41 KB     | ##################################################### | 100% 
r-tidytree-0.3.6     | 273 KB    | ##################################################### | 100% 
r-shadowtext-0.0.9   | 246 KB    | ##################################################### | 100% 
r-scatterpie-0.1.6   | 359 KB    | ##################################################### | 100% 
r-downloader-0.4     | 34 KB     | ##################################################### | 100% 
bioconductor-ggtree- | 825 KB    | ##################################################### | 100% 
bioconductor-enrichp | 277 KB    | ##################################################### | 100% 
certifi-2021.10.8    | 145 KB    | ##################################################### | 100% 
r-ggforce-0.3.3      | 1.9 MB    | ##################################################### | 100% 
r-tidygraph-1.2.0    | 526 KB    | ##################################################### | 100% 
r-gridgraphics-0.5_1 | 262 KB    | ##################################################### | 100% 
r-graphlayouts-0.7.1 | 2.4 MB    | ##################################################### | 100% 
bioconductor-qvalue- | 2.7 MB    | ##################################################### | 100% 
bioconductor-gosemsi | 904 KB    | ##################################################### | 100% 
r-yulab.utils-0.0.4  | 35 KB     | ##################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
@hexylena
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Looks like the tmpdir is set to a read only filesystem, I'm not sure why that's happened.

@hexylena
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This is an issue with the UseGalaxy.eu deployment it seems. @bgruening @gmauro can help further I imagine. The temp directories are set to the job_working_directory's working dir which makes some sense

$ env | grep job_working | sort
CWD=/data/dnb03/galaxy_db/job_working_directory/034/747/34747228/working/rstudio
_GALAXY_JOB_HOME_DIR=/data/dnb03/galaxy_db/job_working_directory/034/747/34747228/home
_GALAXY_JOB_TMP_DIR=/data/dnb03/galaxy_db/job_working_directory/034/747/34747228/tmp
GALAXY_WORKING_DIR=/data/dnb03/galaxy_db/job_working_directory/034/747/34747228/working
PWD=/data/dnb03/galaxy_db/job_working_directory/034/747/34747228/tmp
TEMP=/data/dnb03/galaxy_db/job_working_directory/034/747/34747228/tmp
TMP=/data/dnb03/galaxy_db/job_working_directory/034/747/34747228/tmp
TMPDIR=/data/dnb03/galaxy_db/job_working_directory/034/747/34747228/tmp

But I'm not quite sure why that's read only. Additionally I'm not sure it makes sense to put tmp on a networked filesystem, rather than /tmp/ within the container? But maybe they can provide additional context here.

Or maybe just a mixup because the server runs as the user within the container (rstudio) and the directories have been set to rstudio-servers's permissions

(base) rstudio@ce164b22683a:/data/dnb03/galaxy_db/job_working_directory/034/747/34747228$ whoami
rstudio
(base) rstudio@ce164b22683a:/data/dnb03/galaxy_db/job_working_directory/034/747/34747228$ ls -al working _working home
home:
total 45
drwxr-xr-x.  2 rstudio-server rstudio-server   0 Nov 22 11:17 .
drwxr-xr-x. 11 rstudio-server rstudio-server 922 Nov 22 11:17 ..

_working:
total 45
drwxr-xr-x.  2 rstudio-server rstudio-server   0 Nov 22 11:17 .
drwxr-xr-x. 11 rstudio-server rstudio-server 922 Nov 22 11:17 ..

working:
total 48
drwxr-xr-x.  3 rstudio-server rstudio-server  25 Nov 22 11:17 .
drwxr-xr-x. 11 rstudio-server rstudio-server 922 Nov 22 11:17 ..
drwxr-xr-x.  4 root           root            47 Nov 22 11:17 rstudio

@mblue9
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mblue9 commented Nov 22, 2021

Ok, thanks for investigating and the info @hexylena !

@hexylena
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hexylena commented Nov 22, 2021 via email

@hexylena
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hexylena commented Jul 5, 2022

still seems to be an issue @bgruening, is there a way EU can change the permissions of the JWD tmp dir such that RStudio can write to it?

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@hexylena @mblue9