octad.db

[Lionir]

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[Lionir]

Hi again,

I currently have 2 issues during the package building:

1. With merida1 sever, it can't load EH7279 from ExperimetHub for some reason (Checked on other mac machines, everything is fine): sRGES=ExperimentHub()[["EH7279"]]
2. Win server can't allocate large vector enough during the computation of one of the functions runsRGES(). This function loads ~500mb matrix into memory along with several other datasets required for computations and I assume that's the problem.

Any thoughts on how to address these issues? Thank you in advance.

[lshep]

The mac error is on our end most likely. The builder switched versions of Bioconductor and is no longer appropriate to run right now. Can you ask about the memory issue on the bioc-devel@bioconductor.org mailing list

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[lshep]

octad.db

Description

• [ ] Update to at least R 4.1

NAMESPACE

• [ ] Remove empty namespace

README

• [ ] Inlucde Bioconductor instructions

inst

• [ ] You have a citation reference in the README but no CITATION file in inst

scripts

• [ ] make-data should describe how the files on AWS were generated and include relevant source information.

man

• [ ] Have minimally a package man page.

R

• [ ] You have data references with sRGES_example and res_example but no data included in the package. The man pages were also not generated by roxygen. Please remember to do devtools::document() to auto generate man pages.

• [ ] Remove zzz.R if not utilized

vignette

• [ ] Please use a link to a Bioconductor landing page for octad rather than linking to the github

• [ ] Show example loading of data or what data is provided by the package.

general

• [ ] There needs to be better documentation on what data is provided through the package and should minimally contain source information and any relevant pre-processing performed.

---

octad

NEWS

• [ ] malformed NEWS file. Please see http://contributions.bioconductor.org/news.html . NEWS files cannot be free formed text; please use a list indicator.

README

• [ ] Remove reference to biocLite.

• [ ] Include Bioconductor installation instructions instead or in addition to github.

man

• [ ] Include a package level man page

vignette

• [ ] You might want to suppressMessgaes when doing library(octad) so the vignette is cleaner.

• [ ] Don't write to a users home directory in vignette and examples. Use a tempdir() For all code in the vignette that you are flagging output=TRUE.

• [ ] I get an ERROR when running the compute drug enrichment

> octadDrugEnrichment(sRGES = sRGES, target_type = c('chembl_targets','mesh','ChemCluster'))
snapshotDate(): 2021-11-24
Running enrichment for chembl_targets 
see ?octad.db and browseVignettes('octad.db') for documentation
loading from cache
see ?octad.db and browseVignettes('octad.db') for documentation
loading from cache
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."

[1] "Normalizing..."
Error in `rownames<-`(`*tmp*`, value = names(geneSets)) : 
  attempt to set 'rownames' on an object with no dimensions

R code

• [ ] remove unused, commented out code

• [ ] Formatting and indentation is not consistent which makes it very hard to try and read the code

• [ ] remove commented out, unused arguments from function calls

• [ ] Use message instead of print when output is user console. You won't need paste inside message calls either.

• [ ] Function arguments should have some validation and checking for correct user input.

• [ ] Data accessed from the web should be cached. We recommned BiocFileCache. You should also implement some graceful tryCatch for if the web resources is unavailable.

• [ ] I mentioned this in the email thread as well. Avoid repeated calls to the experimenthub construcutr ExperimentHub() and instead set as an environment variable upon loading package. I sent the links to the bioc-devel mailing list conversation twice.

Please address the above issues and concerns. When ready please comment back here requesting a re-review and commenting on the above items.

Cheers,

[lshep]

may we expect any updates soon?

[Lionir]

Good day, I took a break for holidays, currently refactoring code to make it more readable, will update the thread early in Jan. Also, I wondered regarding one specific problem: files in the octad.db are synthesis of several years of work by several different scientists via different tools and I'm afraid we can't provide the script that reproduces the files. We described this process in the packaging paper: https://www.nature.com/articles/s41596-020-00430-z. What should we do in this case? Thank you in advance and Merry Christmas!

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[lshep]

Were you ready for a re-review? If so please respond to the original review and explain what has updated and changed

[Lionir]

Hi,

I am having a bit of a problem with the Win version of octad.db, will let you know when will deal with it. Thanks.

Evgenii Chekalin, PhD, Sr. Bioinformatics scientist, Illumina

On Fri, Feb 11, 2022 at 9:42 AM lshep @.***> wrote:

Were you ready for a re-review? If so please respond to the original review and explain what has updated and changed

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[lshep]

Was this ready for a re-review? If so, could you please summarize your changes

[Lionir]

Not yet, almost done, want to perform a bit more graceful file catching.

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