[ Started: 2022-04-25 13:49:35 ] Loading required package: BiocCheck ─ BiocCheckVersion: 1.31.37 ─ BiocVersion: 3.15 ─ Package: liana ─ PackageVersion: 0.1.0 ─ sourceDir: /tmp/RtmpvRzvfZ/file386d8a123f9692/liana ─ installDir: /tmp/RtmpvRzvfZ/file386d8a319ee6e1 ─ BiocCheckDir: /home/omnipath/testing/liana/bioc-3.15/2022-04-25_1340/liana/liana.BiocCheck ─ platform: unix ─ isTarBall: TRUE * Installing package... * Checking package dependencies... [2022-04-25 13:50:27] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2022-04-25 13:50:27] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2022-04-25 13:50:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2022-04-25 13:50:27] [INFO] [OmnipathR] Welcome to OmnipathR! [2022-04-25 13:50:27] [TRACE] [OmnipathR] Cache locked: FALSE * Checking if other packages can import this one... * ERROR: Packages providing 18 object(s) used in this package should be imported in the NAMESPACE file, otherwise packages importing this package may fail. * Checking to see if we understand object initialization... * NOTE: Consider clarifying how 281 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... * ERROR: Package dependencies must be on CRAN or Bioconductor. Remove 'Remotes:' from DESCRIPTION * Checking for 'LazyData: true' usage... * Checking version number... * Checking for version number mismatch... * Checking version number validity... Package version 0.1.0; pre-release * Checking R version dependency... * NOTE: Update R version dependency from 4.0 to 4.2.0. * Checking package size... * ERROR: Package tarball exceeds the Bioconductor size requirement. * Checking individual file sizes... * Checking biocViews... * Checking that biocViews are present... * ERROR: No biocViews terms found. 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... * WARNING: Description field in the DESCRIPTION file is too concise * 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... * WARNING: Import utils in NAMESPACE as well as DESCRIPTION. * WARNING: Import OmnipathR in DESCRIPTION as well as NAMESPACE. * Checking .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... * ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as 'VignetteEngine' in any vignettes: * WARNING: Vignette(s) missing Vignette metadata. See http://r-pkgs.had.co.nz/vignettes.html * ERROR: No 'VignetteEngine' specified in vignette or DESCRIPTION. * WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette Title}'. Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' * NOTE: 'sessionInfo' not found in vignette(s) * Checking package installation calls in R code... * Checking for library/require of liana... * Checking coding practice... * NOTE: Avoid sapply(); use vapply() * NOTE: Avoid 1:...; use seq_len() or seq_along() * 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 * ERROR: Avoid references to external hosting platforms * WARNING: Remove set.seed usage (found 3 times) * Checking parsed R code in R directory, examples, vignettes... Found @ in vignettes/liana_nichenet.Rmd Found @ in vignettes/liana_ortho.Rmd * NOTE: Use accessors; don't access S4 class slots via '@' in examples/vignettes. * NOTE: Avoid '<<-' if possible (found 2 times) * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times) * Checking function lengths... * NOTE: Recommended function length <= 50 lines.There are 20 functions > 50 lines. * Checking man page documentation... Warning in nzchar(fpath) && !is.na(fpath) : 'length(x) = 37 > 1' in coercion to 'logical(1)' Warning in nzchar(fpath) && !is.na(fpath) : 'length(x) = 37 > 1' in coercion to 'logical(1)' * WARNING: Add non-empty \value sections to the following man pages: man/account_missing.Rd, man/assign_ligrecs.Rd, man/cellchat_formatDB.Rd, man/check_if_dissociated.Rd, man/conn_formatDB.Rd, man/cytotalk_score.Rd, man/dot-aggregate_rank.Rd, man/dot-antilog1m.Rd, man/dot-filt_liana_pipe.Rd, man/dot-format_idents.Rd, man/dot-generate_complex_dict.Rd, man/dot-get_invcounts.Rd, man/dot-score_housekeep.Rd, man/dot-select_cap.Rd, man/fast_mean.Rd, man/FormatConnectome.Rd, man/FormatiTALK.Rd, man/FormatSCA.Rd, man/generate_orthologs.Rd, man/genesymbol_to_uniprot.Rd, man/get_cellchat_missing.Rd, man/get_partners.Rd, man/get_up_dict.Rd, man/intercell_connections.Rd, man/italk_formatDB.Rd, man/liana_message.Rd, man/liana_prep.Rd, man/logg.Rd, man/map_custom.Rd, man/minmax.Rd, man/omni_to_NATMI.Rd, man/omnipath_partners.Rd, man/recode.character2.Rd, man/sca_formatDB.Rd, man/select_resource.Rd, man/show_methods.Rd, man/show_resources.Rd * ERROR: At least 80% of man pages documenting exported objects must have runnable examples. The following pages do not: call_cellchat.Rd, call_connectome.Rd, call_italk.Rd, call_natmi.Rd, call_sca.Rd, call_squidpy.Rd, cellchat_formatDB.Rd, compile_ligrec.Rd, conn_formatDB.Rd, decomplexify.Rd, FormatConnectome.Rd, FormatiTALK.Rd, FormatSCA.Rd, generate_omni.Rd, generate_orthologs.Rd, get_connectome.Rd, get_curated_omni.Rd, get_logfc.Rd, get_lr_resources.Rd, get_natmi.Rd, get_sca.Rd, get_scconnect.Rd, italk_formatDB.Rd, liana_call.Rd, liana_dotplot.Rd, liana_pipe.Rd, liana_prep.Rd, mean0.Rd, recomplexify.Rd, sca_formatDB.Rd, select_resource.Rd, show_methods.Rd, show_resources.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; 461 lines (5%) are > 80 characters long. * NOTE: Consider multiples of 4 spaces for line indents; 1294 lines (15%) 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. * ERROR: Maintainer must add package name to Watched Tags on the support site; Edit your Support Site User Profile to add Watched Tags. ─ BiocCheck results ── 9 ERRORS | 8 WARNINGS | 14 NOTES See the liana.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details. [ Finished: 2022-04-25 13:50:45 ]