[ Started: 2024-08-15 23:58:58 CEST ] [ CARNIVAL v2.7.2 for BioC-3.20 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ] Loading required package: BiocCheck ── Installing CARNIVAL ───────────────────────────────────────────────────────── ✔ Package installed successfully ── CARNIVAL session metadata ─────────────────────────────────────────────────── → sourceDir: /tmp/RtmpbWtXke/file166ca42047d08/CARNIVAL → BiocVersion: 3.20 → Package: CARNIVAL → PackageVersion: 2.7.2 → BiocCheckDir: /mnt/disk0/build/bioc-check/carnival/bioc-3.20/2024-08-15_2338/CARNIVAL/CARNIVAL.BiocCheck → BiocCheckVersion: 1.41.12 → sourceDir: /tmp/RtmpbWtXke/file166ca42047d08/CARNIVAL → installDir: /tmp/RtmpbWtXke/file166ca2ad96dea → isTarBall: TRUE → platform: unix ── Running BiocCheck on CARNIVAL ─────────────────────────────────────────────── ℹ Checking for deprecated package usage... ✔ Checking for deprecated package usage... [11ms] ℹ Checking for remote package usage... ✔ Checking for remote package usage... [12ms] ℹ Checking for 'LazyData: true' usage... ✔ Checking for 'LazyData: true' usage... [6ms] ℹ Checking version number... ✔ Checking version number... [6ms] ℹ Checking for version number mismatch... ✔ Checking for version number mismatch... [6ms] ℹ Checking version number validity... ✔ Checking version number validity... [6ms] ℹ Checking R version dependency... ✔ Checking R version dependency... [6ms] ℹ N: Update R version dependency from 4.0 to 4.4.0. ℹ Checking package size... ✔ Checking package size... [10ms] ℹ Checking individual file sizes... ✔ Checking individual file sizes... [6ms] ℹ Checking biocViews... ✔ Checking biocViews... [6ms] ℹ Checking that biocViews are present... ✔ Checking that biocViews are present... [6ms] ℹ Checking package type based on biocViews... ✔ Checking package type based on biocViews... [6ms] → Software ℹ Checking for non-trivial biocViews... ✔ Checking for non-trivial biocViews... [10ms] ℹ Checking that biocViews come from the same category... ✔ Checking that biocViews come from the same category... [6ms] ℹ Checking biocViews validity... ✔ Checking biocViews validity... [10ms] ℹ Checking for recommended biocViews... ✔ Checking for recommended biocViews... [6ms] ℹ Checking build system compatibility... ✔ Checking build system compatibility... [7ms] ℹ Checking for proper Description: field... ✔ Checking for proper Description: field... [10ms] ℹ Checking if DESCRIPTION is well formatted... ✔ Checking if DESCRIPTION is well formatted... [6ms] ℹ Checking for whitespace in DESCRIPTION field names... ✔ Checking for whitespace in DESCRIPTION field names... [6ms] ℹ Checking that Package field matches directory/tarball name... ✔ Checking that Package field matches directory/tarball name... [6ms] ℹ Checking for Version: field... ✔ Checking for Version: field... [6ms] ℹ N: Consider adding the maintainer's ORCID iD in 'Authors@R' with 'comment=c(ORCID="...")' ℹ Checking License: for restrictive use... ✔ Checking License: for restrictive use... [6ms] ℹ Checking for recommended DESCRIPTION fields... ✔ Checking for recommended DESCRIPTION fields... [6ms] ℹ Checking for Bioconductor software dependencies... ✔ Checking for Bioconductor software dependencies... [6ms] ! W: No Bioconductor dependencies detected. Note that some infrastructure packages may not have Bioconductor dependencies. For more information, reach out to the Bioconductor community and/or consider a CRAN submission. ℹ Checking for pinned package versions in DESCRIPTION... ✔ Checking for pinned package versions in DESCRIPTION... [6ms] ℹ Checking .Rbuildignore... ✔ Checking .Rbuildignore... [6ms] ℹ Checking for stray BiocCheck output folders... ✔ Checking for stray BiocCheck output folders... [6ms] ℹ Checking vignette directory... ✔ Checking vignette directory... [6ms] ℹ Checking package installation calls in R code... ✔ Checking package installation calls in R code... [9ms] ℹ Checking for library/require of CARNIVAL... ✔ Checking for library/require of CARNIVAL... [10ms] ℹ Checking coding practice... ✔ Checking coding practice... [7ms] ℹ N: Avoid sapply(); use vapply() ℹ N: Avoid 1:...; use seq_len() or seq_along() 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org ℹ N: Avoid 'cat' and 'print' outside of 'show' methods ℹ N: Avoid using '=' for assignment and use '<-' instead ℹ N: Avoid the use of 'paste' in condition signals ℹ N: Avoid system() ; use system2() ℹ Checking parsed R code in R directory, examples, vignettes... ✔ Checking parsed R code in R directory, examples, vignettes... [6ms] ℹ N: Avoid '<<-' if possible (found 2 times) ℹ Checking function lengths... ✔ Checking function lengths... [6ms] ℹ N: The recommended function length is 50 lines or less. There are 6 functions greater than 50 lines. ℹ Checking man page documentation... ✔ Checking man page documentation... [6ms] ℹ N: Consider adding runnable examples to man pages that document exported objects. ℹ Checking package NEWS... ✔ Checking package NEWS... [6ms] ! W: Fix formatting of NEWS.md. Malformed package NEWS will not be included in Bioconductor release announcements. ℹ Checking unit tests... ✔ Checking unit tests... [6ms] ℹ Checking skip_on_bioc() in tests... ✔ Checking skip_on_bioc() in tests... [6ms] ℹ Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vigne… ✔ Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vigne… ℹ N: Consider shorter lines; 275 lines (7%) are > 80 characters long. ℹ N: Consider multiples of 4 spaces for line indents; 1522 lines (39%) are not. ℹ See https://contributions.bioconductor.org/r-code.html ℹ See styler package: https://cran.r-project.org/package=styler as described in the BiocCheck vignette. ℹ Checking if package already exists in CRAN... ✔ Checking if package already exists in CRAN... [6ms] 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org ℹ Checking for bioc-devel mailing list subscription... ✔ Checking for bioc-devel mailing list subscription... [6ms] ℹ N: 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 ℹ Checking for support site registration... ✔ Checking for support site registration... [6ms] ℹ Maintainer is registered at support site. ℹ Package is in the Support Site Watched Tags. ── BiocCheck v1.41.12 results ────────────────────────────────────────────────── ✖ 0 ERRORS | ⚠ 2 WARNINGS | • 14 NOTES ℹ See the CARNIVAL.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details. [ Finished: 2024-08-15 23:59:18 CEST ]