chilampoon
commented
4 years ago BiocCheck (Bioconductor check) passed:
BiocCheck::BiocCheck("~/pkg/ReactomeGraph4R")
#> This is BiocCheck version 1.24.0. BiocCheck is a work in progress.
#> Output and severity of issues may change. Installing package...
#> Is the url 'http://localhost:7474'? (Yes/no/cancel)
#> Does Neo4J require authentication? (yes/No/cancel)
#> * Checking Package Dependencies...
#> * Checking if other packages can import this one...
#> * Checking to see if we understand object initialization...
#> * Checking for deprecated package usage...
#> * Checking for remote package usage...
#> * Checking version number...
#> * Checking version number validity...
#> Package version 0.99.0; pre-release
#> * Checking R Version dependency...
#> * Checking package size...
#> Skipped... only checked on source tarball
#> * Checking individual file sizes...
#> * Checking biocViews...
#> * Checking that biocViews are present...
#> * Checking package type based on biocViews...
#> Software
#> * Checking for non-trivial biocViews...
#> * Checking that biocViews come from the same category...
#> * Checking biocViews validity...
#> * Checking for recommended biocViews...
#> * Checking build system compatibility...
#> * Checking for blank lines in DESCRIPTION...
#> * Checking if DESCRIPTION is well formatted...
#> * Checking for whitespace in DESCRIPTION field names...
#> * Checking that Package field matches directory/tarball name...
#> * Checking for Version field...
#> * Checking for valid maintainer...
#> * Checking DESCRIPTION/NAMESPACE consistency...
#> * Checking vignette directory...
#> This is a software package
#> * Checking library calls...
#> * Checking for library/require of ReactomeGraph4R...
#> * Checking coding practice...
#> * Checking parsed R code in R directory, examples, vignettes...
#> * Checking function lengths...................
#> * NOTE: Recommended function length <= 50 lines.
#> There are 4 functions > 50 lines.
#> The longest 5 functions are:
#> matchObject() (R/queries.R, line 62): 79 lines
#> .basicErrMsgs() (R/errors.R, line 2): 61 lines
#> matchReferrals() (R/queries.R, line 445): 54 lines
#> .parse_row() (R/data.parsing.R, line 53): 52 lines
#> .WHERE() (R/cyphers.R, line 19): 46 lines
#> * Checking man page documentation...
#> * NOTE: Consider adding runnable examples to the following man
#> pages which document exported objects:
#> unnestListCol.Rd
#> * NOTE: Usage of dontrun{} / donttest{} found in man page examples.
#> 17% of man pages use one of these cases.
#> Found in the following files:
#> matchReferrals.Rd
#> unnestListCol.Rd
#> * Checking package NEWS...
#> * Checking unit tests...
#> * Checking skip_on_bioc() in tests...
#> * Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
#> and vignette source...
#> * NOTE: Consider shorter lines; 103 lines (4%) are > 80 characters
#> long.
#> First 6 lines:
#> R/cyphers.R:11 clause <- paste0("MATCH p", list.idx, " = ", clause)...
#> R/cyphers.R:31 # can't fetch data if adding Reactome/PubMed as data...
#> R/cyphers.R:40 # complete WHERE clause by adding filter arguments (eg...
#> R/cyphers.R:50 add <- paste0(node, '.speciesName = "', .matchSpec...
#> R/cyphers.R:56 tmp <- ifelse(grepl("^[0-9]+$", filters[[filter]])...
#> R/cyphers.R:61 clause <- ifelse(!grepl(node, clause), paste0(clause...
#> * NOTE: Consider multiples of 4 spaces for line indents, 655
#> lines(28%) are not.
#> First 6 lines:
#> R/cyphers.R:6 final.clause <- ""
#> R/cyphers.R:7
#> R/cyphers.R:8 # glue clauses in the list
#> R/cyphers.R:9 for (list.idx in seq(1, length(clause.list))) {
#> R/cyphers.R:13 }
#> R/cyphers.R:14 final.clause
#> See http://bioconductor.org/developers/how-to/coding-style/
#> See FormatR package:
#> https://cran.r-project.org/web/packages/formatR/index.html
#> * Checking if package already exists in CRAN...
#> * Checking for bioc-devel mailing list subscription...
#> * NOTE: 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
#> * Checking for support site registration...
#> Maintainer is registered at support site.
#>
#>
#> Summary:
#> ERROR count: 0
#> WARNING count: 0
#> NOTE count: 6
#> For detailed information about these checks, see the BiocCheck
#> vignette, available at
#> https://bioconductor.org/packages/3.11/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
#> $error
#> character(0)
#>
#> $warning
#> character(0)
#>
#> $note
#> [1] "Recommended function length <= 50 lines."
#> [2] "Consider adding runnable examples to the following man pages which document exported objects:"
#> [3] "Usage of dontrun{} / donttest{} found in man page examples."
#> [4] "Consider shorter lines; 103 lines (4%) are > 80 characters long."
#> [5] "Consider multiples of 4 spaces for line indents, 655 lines(28%) are not."
#> [6] "Cannot determine whether maintainer is subscribed to the bioc-devel\nmailing list (requires admin credentials). Subscribe here:\nhttps://stat.ethz.ch/mailman/listinfo/bioc-devel"Created on 2020-10-20 by the reprex package (v0.3.0)
multiObjects()function -- https://github.com/reactome/ReactomeGraph4R/issues/19#issue-723407109