pouryany / panomir Goto Github PK

Current options are ENTREZ and ENSEMBL

• error: output directory does not exist
• get Function for the clustering algorithms. Ensure a string is provided and throw a meaningful error.

WARNING from devtools::check()

Files not of a type allowed in a ‘data’ directory:
‘GeneSets’ ‘LIHC_gene.RDS’ ‘MirPathEnrichment’
‘TCGA-LIHC-DEmiRNAs.RDS’ ‘TCGA-LIHC-miRNAs_residuals.RDS’
‘preprocessed’
Please use e.g. ‘inst/extdata’ for non-R data files

Reference: https://r-pkgs.org/data.html

Variable and function name style should be snake_case.

https://github.com/pouryany/PanomiR/actions/runs/1467758678

On the other hand Bioc recommends:

Variable names
Use camelCaps: initial lowercase, then alternate case between words.
Function names
Use camelCaps: initial lower case, then alternate case between words.
https://www.bioconductor.org/developers/how-to/coding-style/

* Checking valid files...
    * ERROR: System Files found that should not be git tracked:
        PanomiR.Rproj
        .Rhistory
        .DS_Store

For detailed information about these checks, see the BiocCheck vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output

"If you are using just a few functions from another package, the recommended option is to note the package name in the Imports: field of the DESCRIPTION file and call the function(s) explicitly using ::, e.g., pkg::fun()"

https://roxygen2.r-lib.org/articles/namespace.html#imports

See also: #33

Add new methods. Including ypj

Give the ability of change colors for pathway visualization in mappingPathwaysClusters

Updating R dependency to R 4.2.0 in the DESCRIPTION file fails the release R CMD Checks. and Lint checks.

Denote the available clustering algorithms in mappingPathwaysClusters

Reported by devtools::check():

    %<>% . := E E<- ENSEMBL ES ES2 Intersect Pathway V V<- brewer.pal
    cluster_edge_betweenness coef contrasts contrasts.fit dev.off eBayes
    ends graph_from_data_frame hit hit2 induced_subgraph k
    layout.fruchterman.reingold layout_components legend lm lmFit
    makeContrasts median model.matrix p.adjust path_fdr pdf phyper pnorm
    pval qnorm relevel residuals.MArrayLM sd set_vertex_attr topTable
    write.csv x y

See also: #26

Reference:

• devtools::check giving error on dplyr column names

Errors

• "At least 80% of man pages documenting exported objects must have runnable examples. The following pages do not:"
• "Maintainer must add package name to Watched Tags on the support site; Edit your Support Site User Profile to add Watched Tags."
• "Invalid package Version, see http://www.bioconductor.org/developers/how-to/version-numbering/"
• "No biocViews terms found."
• "No 'vignettes' directory."
• "Maintainer must register at the support site; visit https://support.bioconductor.org/accounts/signup/ ."

Warnings

• "Description field in the DESCRIPTION file is too concise"
• "Evaluate more vignette chunks."
• "Remove set.seed usage (found 5 times)"
• "Avoid T/F variables; If logical, use TRUE/FALSE (found 51 times)"
• "The following files are over 5MB in size: '.git/objects/33/d794a2db6598e9fd6808ee815a21af38fb1f48 .git/objects/77/40f0f0d0abee5c3fee0c13d1eeeea044c62fa7 .git/objects/pack/pack-c37633e5c2521abc60f069884252e737552ee3dc.pack'"

Notes

• " 'sessionInfo' not found in vignette(s)"
• " Avoid the use of 'paste' in condition signals"
• "Recommended function length <= 50 lines."
• "Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements."
• "Consider shorter lines; 6 lines (0%) are > 80 characters long."
• "Consider multiples of 4 spaces for line indents, 758 lines(32%) are not."
• "Cannot determine whether maintainer is subscribed to the bioc-devel mailing list (requires admin credentials). Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel"
• " Avoid sapply(); use vapply()"
• " Avoid 1:...; use seq_len() or seq_along()"
• "'LazyData:' in the 'DESCRIPTION' should be set to false or removed" - [x] "Update R version dependency from 2.10 to 4.1.0."

R CMD check reports:

* checking installed package size ... NOTE
  installed size is 31.2Mb
  sub-directories of 1Mb or more:
    data  31.0Mb

Bioconductor says:

• The source package resulting from running R CMD build should occupy less than 5 MB on disk.
• For software packages, individual files must be <= 5MB
  https://contributions.bioconductor.org/general.html

Potential solutions:

• Remove (some of the) data files
• Move large data files into a separate package

The following build error can be avoided if we make a local version of the function bitr() from the clusterProfiler package. We can look into easier ways to address this of course.

` Error: Error: <callr_remote_error: Failed to build source package 'clusterProfiler'>
in process 9115
-->
Failed to build source package 'clusterProfiler', stdout + stderr:

OE> * installing source package ‘clusterProfiler’ ...
OE> staged installation is only possible with locking
OE> ** using non-staged installation
OE> ** R
OE> ** data
OE> ** inst
OE> ** byte-compile and prepare package for lazy loading
OE> Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
OE> object 'get_fun_from_pkg' not found
OE> Error: unable to load R code in package ‘clusterProfiler’
OE> Execution halted
OE> ERROR: lazy loading failed for package ‘clusterProfiler’
OE> * removing ‘/tmp/RtmpUL3O1s/pkg-lib239b6cc4dcf9/clusterProfiler’

Stack trace:

12. (function (...) ...
13. base:::withCallingHandlers(cli_message = function(msg) { ...
14. get("pkg_install_do_plan", asNamespace("pak"))(...)
15. pkgdepends::install_package_plan(plan = plan, lib = lib, num_workers = num_ ...
16. base:::withCallingHandlers({ ...
17. pkgdepends:::handle_events(state, events)
18. pkgdepends:::handle_event(state, i)
19. pkgdepends:::stop_task(state, worker)
20. pkgdepends:::stop_task_build(state, worker)
21. base:::throw(new_pkg_build_error("Failed to build source package {pkg}", ...
22. base:::signalCondition(cond)
23. (function (e) ...
24. base:::stop(e)
25. (function (e) ...

x Failed to build source package 'clusterProfiler'

Execution halted
Error: Process completed with exit code 1.`

WARNING from devtools::check()

Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R.

File(s) containing such objects:
‘PanomiR/Data/GeneSets/MSigDB.RDS’
‘PanomiR/data/GeneSets/improved_PCxN_MSigDB.RDS’
‘PanomiR/data/LIHC_gene.RDS’
‘PanomiR/data/MirPathEnrichment/AllGenes_AllMirs_ENRICHMENT.RDS’
‘PanomiR/data/MirPathEnrichment/AllGenes_BrainMirs_ENRICHMENT.RDS’
‘PanomiR/data/MirPathEnrichment/BrainGenes_AllMirs_ENRICHMENT.RDS’
‘PanomiR/data/MirPathEnrichment/BrainGenes_BrainMirs_ENRICHMENT.RDS’
‘PanomiR/data/TCGA-LIHC-DEmiRNAs.RDS’
‘PanomiR/data/TCGA-LIHC-miRNAs_residuals.RDS’
‘PanomiR/data/preprocessed/MSigDBPathGeneTab.RDS’
‘PanomiR/data/preprocessed/NORMALIZED_MIRSETS_TargetScan00.rds’
‘PanomiR/data/preprocessed/NORMALIZED_MIRSETS_TargetScan01.rds’
‘PanomiR/data/preprocessed/NORMALIZED_MIRSETS_TargetScan02.rds’
‘PanomiR/data/preprocessed/NORMALIZED_MIRSETS_TargetScan03.rds’
‘PanomiR/data/preprocessed/brainGenes.RDS’
‘PanomiR/data/preprocessed/brainmiRNA.RDS’

Add dependency on R >= 3.5.0?
r-lib/usethis#631

May be resolved when #24 is fixed

The vignette includes

PanomiR can be accessed via Bioconductor. To install, start R (version > "4.1) and run the following code.

Note the > and the version number are inappropriate, along with the unmatched quotation mark. You should have >= 4.1.

At the end of the vignette, head(tempEnrich) had no output.

Please attend to these before review begins. Bump the version of your github repo. @lshep

WARNING by devtools:check():

  Undocumented code objects:
    ‘COV_TCGA_LIHC’ ‘TCGA_LIHC’ ‘brainGenes’ ‘brainMicroRNAs’ ‘msigdb_c2’
    ‘path_gene_table’ ‘pcxn’ ‘targetScan_00’ ‘targetScan_01’
    ‘targetScan_02’ ‘targetScan_03’
  Undocumented data sets:
    ‘COV_TCGA_LIHC’ ‘TCGA_LIHC’ ‘brainGenes’ ‘brainMicroRNAs’ ‘msigdb_c2’
    ‘path_gene_table’ ‘pcxn’ ‘targetScan_00’ ‘targetScan_01’
    ‘targetScan_02’ ‘targetScan_03’
  All user-level objects in a package should have documentation entries.
  See chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.

Objects in data/ are always effectively exported. This means that they must be documented.
https://r-pkgs.org/data.html#documenting-data

WARNING from devtools::check():

Undocumented arguments in documentation object 'DifferentialPathwayAnalysis'
‘contrast.conds’

Undocumented arguments in documentation object 'MappingPathwaysClusters'
‘weighted’

Undocumented arguments in documentation object 'Pathway_Gene_Tab'
‘pathway.list’

Undocumented arguments in documentation object 'PrioritizeMicroRNA'
‘enriches0’ ‘mir.path.fdr.thresh’ ‘run.jack.knife’
Documented arguments not in \usage in documentation object 'PrioritizeMicroRNA':
‘enriches’ ‘mir.path.fdr.selection’

Documented arguments not in \usage in documentation object 'getDesignMatrix':
‘pathways’

Undocumented arguments in documentation object 'methodProbBase'
‘n_paths’

Undocumented arguments in documentation object 'miRNAPathwayEnrichment'
‘genes.selection’
Documented arguments not in \usage in documentation object 'miRNAPathwayEnrichment':
‘gene.selection’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.

Implement a function that takes an input gene list from users and calculates conditional correlation with all annotated pathways.