what dependencies that gapseq needs?

[B-1991-ing]

Dear gapseq developer,

Can you list the dependencies before loading gapseq module on HPC?

I am getting an error that package 'XXX' was built under R version 4.2.2, maybe similar to question - #176. So, I can't get the .xml file finally, only RDS files, which I can't successfully open yet.

Which R version should I load before "module load gapseq/1.2"?

Error file
gapseq_binny_I01R01.000048_C91_P97_Synechococcus.err.txt

Best,

Bing

[Waschina]

Dear Bing,

When you load gapseq with module load gapseq/1.2, it indicates that gapseq was installed system-wide by the administrators of your HPC facility. In that case, please contact your HPC-administrators to ask for help using the gapseq module.

Alternatively, if you have the option to create and use conda environments on the HPC, you can install gapseq yourself in an own conda environment by following those instructions: https://gapseq.readthedocs.io/en/latest/install.html#conda

Best
Silvio

[B-1991-ing]

When you load gapseq with module load gapseq/1.2, it indicates that gapseq was installed system-wide by the administrators of your HPC facility. In that case, please contact your HPC-administrators to ask for help using the gapseq module.

Thank you for your reply, Silvio. I am installing the gapseq using the miniconda3/4.14.0, and some incompatible packages there are examining.

Maybe bacause I loaded the anaconda before submitting the gapseq job, so I may want to rerun later. But, does the gapseq itself have a requirement on the R version?

Best,

Bing

[B-1991-ing]

I tried the conda installation step by step twice, but "Could not find conda environment: gapseq-dev".

Any idea on this problem?

Best,

Bing

[Waschina]

Using the conda installation instruction, a suitable R-Version is automatically chosen by conda.

From the output/error you send I cannot say what might went wrong. Did you notice any error when going through the conda installation instructions step-by-step?

Especially the output logs from conda env create -n gapseq-dev --file gapseq_env.yml would be helpful.

[B-1991-ing]

Especially the output logs from conda env create -n gapseq-dev --file gapseq_env.yml would be helpful.

module load tools #pre for miniconda3/4.14.0
module load miniconda3/4.14.0

Cloning the development version of gapseq

git clone https://github.com/jotech/gapseq
cd gapseq

Create and activate a conda environment "gapseq-dev"

conda env create -n gapseq-dev --file gapseq_env.yml
conda activate gapseq-dev

For the detailed information on the "Output in format: Requested package -> Available versions", I didn't paste, so many lines.

[Waschina]

Could you try to activate the conda base environment using

conda activate

and then

conda env create -n gapseq-dev --file gapseq_env.yml

?

Also, may I ask you to share the console output in text or text files instead of screenshots?

[B-1991-ing]

Could you tell me how to write all logs into one file?
conda env create -n gapseq-dev --file gapseq_env.yml 2>& log.txt

[Waschina]

Small modification: conda env create -n gapseq-dev --file gapseq_env.yml > log.txt should work. After the command, you can upload the file log.txt to GitHub.

Meanwhile, I tested the conda installation instruction again, which worked without issues. Since the problem happens during the installation of conda packages, it's not a gapseq-specific issue, and I would recommend contacting your HPC support to ask for help. They can likely identify the underlying issue quickly.

[B-1991-ing]

Meanwhile, I tested the conda installation instruction again, which worked without issues. Since the problem happens during the installation of conda packages, it's not a gapseq-specific issue, and I would recommend contacting your HPC support to ask for help. They can likely identify the underlying issue quickly.

Normally the HPC will say it is not their responsibility and let contact you again... I reran the gapseq script no to see any changes will happen.

Actually my question is that I only have the RDS file and tbl file, no xml file, so no figures generated.

[Waschina]

xml-files are not figures. They are text files and, in this case, in SBML format.

Perhaps I can help if you provide the full command line output of conda env create -n gapseq-dev --file gapseq_env.yml. Otherwise, I am afraid I cannot determine the cause of the issue.

Actually my question is that I only have the RDS file and tbl file, no xml file, so no figures generated.

That XML files are not generated with the HPC-installation of gapseq is likely due to a missing libsbml or sybilSBML installation. Since your HPC administrators have installed gapseq, they would need to test that and correct it if necessary.

[B-1991-ing]

Perhaps I can help if you provide the full command line output of conda env create -n gapseq-dev --file gapseq_env.yml. Otherwise, I am afraid I cannot determine the cause of the issue.

module load tools #pre for miniconda3/4.14.0
module load miniconda3/4.14.0

Cloning the development version of gapseq

git clone https://github.com/jotech/gapseq
cd gapseq

Create and activate a conda environment "gapseq-dev"

conda activate
conda env create -n gapseq-dev --file gapseq_env.yml > log.txt
conda activate gapseq-dev

log
log.txt
The log file seems like no useful information?

[B-1991-ing]

That XML files are not generated with the HPC-installation of gapseq is likely due to a missing libsbml or sybilSBML installation. Since your HPC administrators have installed gapseq, they would need to test that and correct it if necessary.

The reply from the HPC manager.
Note: BOTH packages are deprecated in CRAN for failing to correct reported issues - you should probably address this with gapsec maintainers, and generally use gapsec with extreme caution.
Package ‘sybil’ was removed from the CRAN repository. [https://cran.r-project.org/web/packages/sybil/index.html]
Package ‘sybilSBML’ was removed from the CRAN repository. [https://cran.r-project.org/web/packages/sybilSBML/index.html]

[Waschina]

Thanks for forwarding the reply.SybilSBML and sybil were indeed removed from CRAN. However, that does not explain this issue and should not interfere with the installation of gapseq.

To briefly state this:

• sybilSBML was removed due to errors in the automatic installation tests by CRAN on MacOS system: https://www.stats.ox.ac.uk/pub/bdr/M1mac/sybilSBML.log
• sybilSBML was removed because it can use a commercial LP-Solver (IBM's cplex), but it also works without it. CRAN does not allow suggests dependencies to IBM cplex.

In short, the removal from CRAN of these packages has nothing to do with security issues. It is still possible to install sybil using conda (https://anaconda.org/conda-forge/r-sybil) and sybilSBML as explained here and here.

As for the issue you have with the conda installation workflow, it is impossible to identify the underlying problem without additional information.

[Waschina]

Feel free to re-open this issue if more information on the problem can be provided.