tormes html report file could not be created

[ryobon-dev]

Hi,

I installed Tormes-1.3.0 using conda and performed the program.

I encountered the error in below. It tells that there is no package called "ggtree".

Could you please let me know how to solve this issue ?

processing file: tormes_report.Rmd |. | 2% ordinary text without R code

|... | 4% label: unnamed-chunk-1 (with options) List of 3 $ echo : logi FALSE $ message: logi FALSE $ warning: logi FALSE

Quitting from lines 7-17 (tormes_report.Rmd) Error in library(ggtree) : there is no package called 'ggtree' Calls: ... withCallingHandlers -> withVisible -> eval -> eval -> library

Execution halted

[nmquijada]

Hi @ryobon-dev

I am afraid this is an issue of the R package ggtree, that for some users is failing in their installation. Some users have posted their solutions in different isues, see https://github.com/nmquijada/tormes/issues/47 and https://github.com/nmquijada/tormes/issues/50 and check if those solutions worked for you.

Please let me know if they worked or we will try to find an alternative solution instead.

Best, Narciso

[ryobon-dev]

I am still facing on the issue.

Is there any solution ?

[biobrad]

• Uninstall tormes

conda env remove -n tormes-1.3.0

• clean conda environment

conda clean --all

• download tormes .yml file:

wget https://anaconda.org/nmquijada/tormes-1.3.0/2021.06.08.113021/download/tormes-1.3.0.yml

• Run this line to update the .yml file:

sed -i 's/dependencies\:/dependencies:\n \- r\-rvcheck\=0\.1\.8/' tormes-1.3.0.yml

• Then re-install tormes:

conda env create -n tormes-1.3.0 --file tormes-1.3.0.yml

That should sort it out.

Cheers Brad

[ryobon-dev]

Sorry to bother you but I encountered the error in below after uninstalled tormes and re-installed.

Could you please help me again ?

tormes-1.3.0.yml.11 100%[=================================================>] 867 --.-KB/s in 0s

2022-09-01 18:07:12 (90.6 MB/s) - ‘tormes-1.3.0.yml.11’ saved [867/867]

(base) kansensho@DESKTOP-QBEDU0F:~$ sed -i 's/dependencies\:/dependencies:\n - r-rvcheck\=0.1.8/' tormes-1.3.0.yml (base) kansensho@DESKTOP-QBEDU0F:~$ conda env create -n tormes-1.3.0 --file tormes-1.3.0.yml

CondaValueError: invalid package specification: r-rvcheck=0.1.8 - abricate=1.0.1 - ant=1.10.0 - barrnap=0.9 - biopython=1.77 - blast=2.10.1 - cgecore=1.5.6 - fasttree=2.1.10 - git=2.28.0 - imagemagick=7.0.10_28 - kaptive=0.7.3 - kraken2=2.0.9beta - mauve=2.4.0 - mauvealigner=1.2.0 - megahit=1.2.9 - mlst=2.19.0 - parallel=20200722 - perl-data-dumper=2.173 - perl-try-tiny=0.30 - bioconda::perl-try-tiny-retry=0.004 - prinseq=0.20.4 - prokka=1.14.6 - python=3.6.11 - quast=5.0.2 - r-base=3.6.3 - r-biocmanager=1.30.10 - r-dt=0.5 - r-essentials=3.6 - r-plotly=4.9.0 - r-rmarkdown=2.1 - r-stringi=1.4.6 - rdptools=2.0.3 - roary=3.13.0 - sickle-trim=1.33 - sistr_cmd=1.1.1 - spades=3.15.2 - tabulate=0.8.7 - tormes=1.3.0 - trimmomatic=0.39

[biobrad]

Firstly, delete all tormes yml files. You have 11 of them saved.

rm -rf tormes-1.3.0.yml*

download the .yml file again and instead of using the sed command, open the file with an editor such as nano by typing nano tormes-1.3.0.yml

Then just under where it says dependencies: add in

• r-rvcheck=0.1.8

Be sure that it aligns with the others in terms of formatting.

Save the file by using holding down ctrl key and pressing X Then write yes and hit enter.

Make sure you are outside of the conda base environment before attempting install again by typing conda deactivate

(Base) at the start of your commamd line should be gone.

Then run the install command from the tormes website again.

On Thu, 1 Sept 2022, 6:53 pm ryobon-dev, @.***> wrote:

Sorry to bother you but I encountered the error in below after uninstalled tormes and re-installed.

Could you please help me again ?

tormes-1.3.0.yml.11 100%[=================================================>] 867 --.-KB/s in 0s

2022-09-01 18:07:12 (90.6 MB/s) - ‘tormes-1.3.0.yml.11’ saved [867/867]

(base) @.:$ sed -i 's/dependencies:/dependencies:\n - r-rvcheck=0.1.8/' tormes-1.3.0.yml (base) @.:$ conda env create -n tormes-1.3.0 --file tormes-1.3.0.yml

CondaValueError: invalid package specification: r-rvcheck=0.1.8 - abricate=1.0.1 - ant=1.10.0 - barrnap=0.9 - biopython=1.77 - blast=2.10.1 - cgecore=1.5.6 - fasttree=2.1.10 - git=2.28.0 - imagemagick=7.0.10_28 - kaptive=0.7.3 - kraken2=2.0.9beta - mauve=2.4.0 - mauvealigner=1.2.0 - megahit=1.2.9 - mlst=2.19.0 - parallel=20200722 - perl-data-dumper=2.173 - perl-try-tiny=0.30 - bioconda::perl-try-tiny-retry=0.004 - prinseq=0.20.4 - prokka=1.14.6 - python=3.6.11 - quast=5.0.2 - r-base=3.6.3 - r-biocmanager=1.30.10 - r-dt=0.5 - r-essentials=3.6 - r-plotly=4.9.0 - r-rmarkdown=2.1 - r-stringi=1.4.6 - rdptools=2.0.3 - roary=3.13.0 - sickle-trim=1.33 - sistr_cmd=1.1.1 - spades=3.15.2 - tabulate=0.8.7 - tormes=1.3.0 - trimmomatic=0.39

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[ryobon-dev]

Thanks, Tormes_report created. From the log file, Tormes finished without any problems.

However, the following warning messages appeared. Is this related to the current Tormes version ?

Output created: tormes_report.html Warning messages: 1: data_frame() was deprecated in tibble 1.1.0. Please use tibble() instead. This warning is displayed once every 8 hours. Call lifecycle::last_warnings() to see where this warning was generated. 2: mutate_() was deprecated in dplyr 0.7.0. Please use mutate() instead. See vignette('programming') for more help This warning is displayed once every 8 hours. Call lifecycle::last_warnings() to see where this warning was generated.

[biobrad]

Ignore all those. They are just warnings wanting you to upgrade. These will all be a thing of the past in the next release.

On Tue, 6 Sept 2022, 9:21 am ryobon-dev, @.***> wrote:

Thanks, Tormes_report created. From the log file, Tormes finished without any problems.

However, the following warning messages appeared. Is this related to the current Tormes version ?

Output created: tormes_report.html Warning messages: 1: data_frame() was deprecated in tibble 1.1.0. Please use tibble() instead. This warning is displayed once every 8 hours. Call lifecycle::lastwarnings() to see where this warning was generated. 2: mutate() was deprecated in dplyr 0.7.0. Please use mutate() instead. See vignette('programming') for more help This warning is displayed once every 8 hours. Call lifecycle::last_warnings() to see where this warning was generated.

— Reply to this email directly, view it on GitHub https://github.com/nmquijada/tormes/issues/53#issuecomment-1237531048, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANITBGSWI5UOANSQW5NTI6LV42BQJANCNFSM5X6FUMFA . You are receiving this because you commented.Message ID: @.***>

[ryobon-dev]

Thanks,