[ Started: 2022-05-04 15:23:54 ] Loading required package: BiocCheck ─ BiocCheckVersion: 1.31.37 ─ BiocVersion: 3.15 ─ Package: OmnipathR ─ PackageVersion: 3.2.9 ─ sourceDir: /tmp/RtmpZdbztK/file107be313bd40d9/OmnipathR ─ installDir: /tmp/RtmpZdbztK/file107be3341bdf2c ─ BiocCheckDir: /home/omnipath/testing/omnipathr/bioc-3.14/2022-05-04_1502/OmnipathR/OmnipathR.BiocCheck ─ platform: unix ─ isTarBall: TRUE * Installing package... * Checking package dependencies... [2022-05-04 15:24:15] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2022-05-04 15:24:16] [INFO] [OmnipathR] Welcome to OmnipathR! [2022-05-04 15:24:16] [TRACE] [OmnipathR] Cache locked: FALSE * Checking if other packages can import this one... * Checking to see if we understand object initialization... * NOTE: Consider clarifying how 2 object(s) are initialized. Maybe they are part of a data set loaded with data(), or perhaps part of an object referenced in with() or within(). * 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... * Checking R version dependency... * NOTE: Update R version dependency from 4.0 to 4.2.0. * 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 Search 'biocViews' at https://contributions.bioconductor.org * 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 for pinned package versions... * Checking DESCRIPTION/NAMESPACE consistency... * Checking .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' * Checking package installation calls in R code... * Checking for library/require of OmnipathR... * Checking coding practice... * NOTE: Avoid 'cat' and 'print' outside of 'show' methods * NOTE: Avoid using '=' for assignment and use '<-' instead * WARNING: Avoid class membership checks with class() / is() and == / !=; Use is(x, 'class') for S4 classes * Checking parsed R code in R directory, examples, vignettes... * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 6 times) * Checking function lengths... * NOTE: Recommended function length <= 50 lines.There are 32 functions > 50 lines. * Checking man page documentation... [2022-05-04 15:24:51] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2022-05-04 15:24:51] [INFO] [OmnipathR] Welcome to OmnipathR! [2022-05-04 15:24:51] [TRACE] [OmnipathR] Cache locked: FALSE * NOTE: Consider adding runnable examples to the following man pages which document exported objects: consensuspathdb_download.Rd, 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_cpdb.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.18% of man pages use one of these cases. * NOTE: Use donttest{} instead of dontrun{}. * 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. * NOTE: Consider multiples of 4 spaces for line indents; 503 lines (2%) are not. 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... * 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. ─ BiocCheck results ── 0 ERRORS | 1 WARNINGS | 13 NOTES See the OmnipathR.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details. [ Finished: 2022-05-04 15:24:56 ]