Loading required package: BiocCheck
This is BiocCheck version 1.28.0. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
[2022-01-09 07:03:30] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2022-01-09 07:03:30] [INFO] [OmnipathR] Welcome to OmnipathR!
* 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 for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* WARNING: y of x.y.z version should be even in release
* Checking R Version dependency...
* NOTE: Update R version dependency from 4.0 to 4.1.
* Checking package size...
* 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...
* NOTE: Consider adding these automatically suggested biocViews:
GenePrediction
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking library calls...
* Checking for library/require of OmnipathR...
* Checking coding practice...
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details
replacement repositories:
CRAN: https://cloud.r-project.org
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths......................................................................................................................................................................................................................................
* NOTE: Recommended function length <= 50 lines.
There are 41 functions > 50 lines.
The longest 5 functions are:
download_base() (R/internals.R, line 129): 168 lines
filter_intercell_network() (R/intercell.R, line 853): 166 lines
import_intercell_network() (R/intercell.R, line 437): 161 lines
obo_parser() (R/obo.R, line 82): 149 lines
nichenet_optimization() (R/nichenet.R, line 311): 125 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
go_annot_slim.Rd, inbiomap_download.Rd, inbiomap_raw.Rd,
kegg_pathway_annotations.Rd, kegg_pathways_download.Rd,
nichenet_gr_network_remap.Rd, nichenet_ligand_activities.Rd,
nichenet_ligand_target_links.Rd, nichenet_ligand_target_matrix.Rd,
nichenet_main.Rd, nichenet_optimization.Rd,
nichenet_signaling_network_inbiomap.Rd, nichenet_test.Rd,
nichenet_workarounds.Rd, omnipath_cache_autoclean.Rd,
omnipath_cache_latest_version.Rd, omnipath_cache_wipe.Rd,
omnipath_load_config.Rd, omnipath_log.Rd, omnipath_reset_config.Rd,
omnipath_save_config.Rd, remap_filtered.Rd,
remap_tf_target_download.Rd, zenodo_download.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
16% of man pages use one of these cases.
Found in the following files:
go_annot_slim.Rd
inbiomap_download.Rd
inbiomap_raw.Rd
kegg_pathway_annotations.Rd
kegg_pathways_download.Rd
nichenet_build_model.Rd
nichenet_gr_network_remap.Rd
nichenet_gr_network.Rd
nichenet_ligand_activities.Rd
nichenet_ligand_target_links.Rd
nichenet_ligand_target_matrix.Rd
nichenet_main.Rd
nichenet_networks.Rd
nichenet_optimization.Rd
nichenet_signaling_network_inbiomap.Rd
nichenet_test.Rd
nichenet_workarounds.Rd
omnipath_cache_autoclean.Rd
omnipath_cache_latest_or_new.Rd
omnipath_cache_remove.Rd
omnipath_cache_wipe.Rd
omnipath_load_config.Rd
omnipath_log.Rd
omnipath_reset_config.Rd
omnipath_save_config.Rd
OmnipathR.Rd
remap_filtered.Rd
remap_tf_target_download.Rd
zenodo_download.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
go_annot_slim.Rd
inbiomap_download.Rd
inbiomap_raw.Rd
kegg_pathway_annotations.Rd
kegg_pathways_download.Rd
nichenet_build_model.Rd
nichenet_gr_network_remap.Rd
nichenet_gr_network.Rd
nichenet_ligand_activities.Rd
nichenet_ligand_target_links.Rd
nichenet_ligand_target_matrix.Rd
nichenet_main.Rd
nichenet_networks.Rd
nichenet_optimization.Rd
nichenet_signaling_network_inbiomap.Rd
nichenet_test.Rd
nichenet_workarounds.Rd
omnipath_cache_autoclean.Rd
omnipath_cache_latest_or_new.Rd
omnipath_cache_remove.Rd
omnipath_cache_wipe.Rd
omnipath_load_config.Rd
omnipath_log.Rd
omnipath_reset_config.Rd
omnipath_save_config.Rd
OmnipathR.Rd
remap_filtered.Rd
remap_tf_target_download.Rd
zenodo_download.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; 21 lines (0%) are > 80 characters
long.
First 6 lines:
R/annotations.R:37 #' \url{https://archive.omnipathdb.org/omnipath_webs...
R/remap.R:36 #' \url{https://github.com/saezlab/dorothea/blob/master/in...
man/ancestors.Rd:11 relations = c("is_a", "part_of", "occurs_in", "re...
man/descendants.Rd:11 relations = c("is_a", "part_of", "occurs_in", "...
man/go_ontology_download.Rd:11 relations = c("is_a", "part_of", "occu...
man/obo_parser.Rd:9 relations = c("is_a", "part_of", "occurs_in", "re...
* NOTE: Consider multiples of 4 spaces for line indents, 524
lines(2%) are not.
First 6 lines:
man/ancestors.Rd:8 terms,
man/ancestors.Rd:9 db_key = "go_basic",
man/ancestors.Rd:10 ids = TRUE,
man/ancestors.Rd:11 relations = c("is_a", "part_of", "occurs_in", "re...
man/curated_ligand_receptor_interactions.Rd:8 curated_resources = c("...
man/curated_ligand_receptor_interactions.Rd:10 cellphonedb = TRUE,
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details
replacement repositories:
CRAN: https://cloud.r-project.org
* 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.
Package name is in support site watched tags.
Summary:
ERROR count: 0
WARNING count: 1
NOTE count: 9
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
$error
character(0)
$warning
[1] "y of x.y.z version should be even in release"
$note
[1] "Update R version dependency from 4.0 to 4.1."
[2] "Consider adding these automatically suggested biocViews: GenePrediction"
[3] "Recommended function length <= 50 lines."
[4] "Consider adding runnable examples to the following man pages which document exported objects:"
[5] "Usage of dontrun{} / donttest{} found in man page examples."
[6] "Use donttest{} instead of dontrun{}."
[7] "Consider shorter lines; 21 lines (0%) are > 80 characters long."
[8] "Consider multiples of 4 spaces for line indents, 524 lines(2%) are not."
[9] "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"