New R issue ('ape' package fail) - With solution

[biobrad]

I have encountered a new issue when running tormes-setup with the installation of 'ape'

** R
Error in parse(outFile) :
  /tmp/RtmpICny7q/R.INSTALLe8ec84fdd251b/ape/R/rtt.R:37:27: unexpected '>'
36:             X[,2] <- x
37:             lm.fit(X, y) |>
                              ^
ERROR: unable to collate and parse R files for package 'ape'
* removing '/home/harbj019/mambaforge/envs/tormes/lib/R/library/ape'
* installing *source* package 'rvcheck' ...
** package 'rvcheck' successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rvcheck)
ERROR: dependency 'ape' is not available for package 'tidytree'
* removing '/home/harbj019/mambaforge/envs/tormes/lib/R/library/tidytree'
ERROR: dependencies 'ape', 'tidytree' are not available for package 'treeio'
* removing '/home/harbj019/mambaforge/envs/tormes/lib/R/library/treeio'
ERROR: dependencies 'ape', 'tidytree', 'treeio' are not available for package 'ggtree'
* removing '/home/harbj019/mambaforge/envs/tormes/lib/R/library/ggtree'

After a lot of trial and error, i was able to get the tormes report to generate after adding the following packages to my tormes environment

EDIT: Doesn't need 'r-ape' installed to avoid the error in tormes-setup ***Second Edit: adding channel in the mamba install command

mamba install -c bioconda bioconductor-ggtree=2.0.0

This is the amended .yml file if you want to start from a fresh install.

https://github.com/biobrad/Tormes-Meta-Create/blob/main/tormes-1.3.0.yml

I have tested from a fresh install with this .yml and it stops the errors from occuring with ggtree during the tormes-setup process.

[nmquijada]

Hi Brad,

This is great! Thanks a lot for all your trials. I hope we stop hearing from ggtree issues in a while... I will leave this issue open so other users can see, but I will move this solution (and https://github.com/nmquijada/tormes/issues/60) to the installation instructions in the main repo.

Thanks a lot! Narciso

[Khabibullin543]

I have the same issue. I tried to install ggtree, as you wrote, but encountered the following error:

(tormes-1.3.0) khabibullinnr@microbgenome:~$ mamba install bioconductor-ggtree=2.0.0

              __    __    __    __
             /  \  /  \  /  \  /  \
            /    \/    \/    \/    \

███████████████/ /██/ /██/ /██/ /████████████████████████ / / \ / \ / \ / \ _ / / _/ _/ _/ \ o _, / _/ ___/ ` |/ ███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗ ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗ ██╔████╔██║███████║██╔████╔██║██████╔╝███████║ ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║ ██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║ ╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝

    mamba (1.3.1) supported by @QuantStack

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

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

Looking for: ['bioconductor-ggtree=2.0.0']

pkgs/main/linux-64 No change pkgs/r/linux-64 No change pkgs/r/noarch No change pkgs/main/noarch No change

Pinned packages:

• python 3.6.*

Could not solve for environment specs Encountered problems while solving:

• nothing provides requested bioconductor-ggtree 2.0.0**

The environment can't be solved, aborting the operation

[biobrad]

Try:

Mamba install -c bioconda bioconductor-ggtree=2.0.0

On Wed, 1 Mar 2023, 11:00 pm Khabibullin543, @.***> wrote:

I have the same issue. I tried to install ggtree, as you wrote, but encountered the following error:

(tormes-1.3.0) @.***:~$ mamba install bioconductor-ggtree=2.0.0

          __    __    __    __
         /  \  /  \  /  \  /  \
        /    \/    \/    \/    \

███████████████/ /██/ /██/ /██/ /████████████████████████ / / \ / \ / \ / \ _ / / / / / \ o *, / / */ ` |/ ███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗ ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗ ██╔████╔██║███████║██╔████╔██║██████╔╝███████║ ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║ ██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║ ╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝

mamba (1.3.1) supported by @QuantStack

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

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

Looking for: ['bioconductor-ggtree=2.0.0']

pkgs/main/linux-64 No change pkgs/r/linux-64 No change pkgs/r/noarch No change pkgs/main/noarch No change

Pinned packages:

• python 3.6.*

Could not solve for environment specs Encountered problems while solving:

• nothing provides requested bioconductor-ggtree 2.0.0**

The environment can't be solved, aborting the operation

— Reply to this email directly, view it on GitHub https://github.com/nmquijada/tormes/issues/62#issuecomment-1450071929, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANITBGTOO4SGLJZJI2ZSN4LWZ46N3ANCNFSM6AAAAAAVIJTZGQ . You are receiving this because you authored the thread.Message ID: @.***>

[nmquijada]

Solution added to the Installation section.

Thanks a lot! N