[ Started: 2022-04-26 15:55:32 ] Loading required package: BiocCheck ─ BiocCheckVersion: 1.31.37 ─ BiocVersion: 3.15 ─ Package: CARNIVAL ─ PackageVersion: 2.5.1 ─ sourceDir: /tmp/RtmpooyE7f/file3d1be6567dc7e3/CARNIVAL ─ installDir: /tmp/RtmpooyE7f/file3d1be637c2f8e5 ─ BiocCheckDir: /home/omnipath/testing/carnival/bioc-3.15/2022-04-26_1553/CARNIVAL/CARNIVAL.BiocCheck ─ platform: unix ─ isTarBall: TRUE * Installing package... * Checking package dependencies... * Checking if other packages can import this one... * Checking to see if we understand object initialization... * NOTE: Consider clarifying how 35 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... * Checking build system compatibility... * Checking for blank lines in DESCRIPTION... * Checking if DESCRIPTION is well formatted... * Checking for proper Description: field... * NOTE: The Description field in the DESCRIPTION is made up by less than 3 sentences. Please consider expanding this field, and structure it as a full paragraph * 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 CARNIVAL... * 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 * NOTE: Avoid the use of 'paste' in condition signals * Checking parsed R code in R directory, examples, vignettes... * NOTE: Avoid '<<-' if possible (found 2 times) * Checking function lengths... * NOTE: Recommended function length <= 50 lines.There are 5 functions > 50 lines. * Checking man page documentation... * NOTE: Consider adding runnable examples to the following man pages which document exported objects: defaultCbcSolveCarnivalOptions.Rd, getOptionsList.Rd, getSupportedSolvers.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; 286 lines (6%) are > 80 characters long. * NOTE: Consider multiples of 4 spaces for line indents; 1572 lines (31%) 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 | 0 WARNINGS | 14 NOTES See the CARNIVAL.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details. [ Finished: 2022-04-26 15:56:05 ]