[ Started: 2024-11-02 13:46:42 CET ]
[ mistyR v1.10.0 for BioC-3.20 from https://github.com/saezlab/mistyR@master (8bb8ba9 2024-03-25 14:10:38) ]

Loading required package: BiocCheck
── Installing mistyR ───────────────────────────────────────────────────────────
✔ Package installed successfully
── mistyR session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpS4IlgV/filea9ea842c21582/mistyR
→ BiocVersion: 3.20
→ Package: mistyR
→ PackageVersion: 1.10.0
→ BiocCheckDir: /mnt/disk0/build/bioc-check/mistyr/bioc-3.20/2024-11-02_1344/mistyR/mistyR.BiocCheck
→ BiocCheckVersion: 1.42.0
→ sourceDir: /tmp/RtmpS4IlgV/filea9ea842c21582/mistyR
→ installDir: /tmp/RtmpS4IlgV/filea9ea84a9e7fa9
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on mistyR ─────────────────────────────────────────────────
* 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...
ℹ NOTE: Update R version dependency from 4.0 to 4.4.0.
* 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 proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
! WARNING: 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.
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking package installation calls in R code...
* Checking for library/require of mistyR...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• model-functions.R (line 196, column 27)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/plots.R (line 73, column 3)
• ...
• print() in R/plots.R (line 619, column 5)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 16
functions greater than 50 lines.
The longest 5 functions are:
• run_misty() (R/misty.R): 239 lines
• ...
• collect_results() (R/utils.R): 110 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/reexports.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...
ℹ NOTE: Consider shorter lines; 146 lines (4%) are > 80 characters long.
First few lines:
• R/data.R#L2 # Copyleft (ɔ) 2020 Jovan Tanevski, Atti ...
• ...
• vignettes/mistyR.Rmd#L277 Here is the output of `sessionInfo()` at ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 845 lines (25%) are
not.
First few lines:
• R/misty.R#L7 packageStartupMessage("mistyR is able ...
• ...
• vignettes/mistyR.Rmd#L207 arrange(mean.p) ...
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.
* Checking if package already exists in CRAN...
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
* Checking for bioc-devel mailing list subscription...
ℹ 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...
ℹ Maintainer is registered at support site.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.42.0 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 2 WARNINGS | • 7 NOTES
ℹ See the mistyR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.
[ Finished: 2024-11-02 13:46:55 CET ]