##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('BioTIP_1.27.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing BioTIP ───────────────────────────────────────────────────────────
✔ Package installed successfully
── BioTIP session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpTH9dRY/file5e2592c04cfc8/BioTIP
→ BiocVersion: 3.24
→ Package: BioTIP
→ PackageVersion: 1.27.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/BioTIP.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpTH9dRY/file5e2592c04cfc8/BioTIP
→ installDir: /tmp/RtmpTH9dRY/file5e2593fe423c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on BioTIP ─────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 3.6 to 4.6.0
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews:
FunctionalGenomics, GeneTarget
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (14%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • BioTIP.Rmd
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • BioTIP.Rmd (code line 195, column 18)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/BioTIP.Rmd (chunk no. 26, line 333, column 48)
    • vignettes/BioTIP.Rmd (chunk no. 26, line 362, column 42)
* Checking package installation calls in R code...
* Checking for library/require of BioTIP...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/BioTIP_update_06232025.R (line 468, column 9)
    • ...
    • require() in R/BioTIP_update_06232025.R (line 3448, column 3)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/BioTIP_update_06232025.R (line 167, column 22)
    • ...
    • R/BioTIP_update_06232025.R (line 2235, column 15)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • BioTIP_update_06232025.R (line 339, column 26)
    • ...
    • BioTIP_update_06232025.R (line 3495, column 30)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/BioTIP_update_06232025.R (line 473, column 9)
    • ...
    • print() in R/BioTIP_update_06232025.R (line 3457, column 106)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/BioTIP_update_06232025.R (line 126, column 8)
    • ...
    • R/BioTIP_update_06232025.R (line 3539, column 47)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/BioTIP_update_06232025.R (line 1298, column 13)
    • ...
    • R/BioTIP_update_06232025.R (line 3396, column 13)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 3 times:
    • T in R/BioTIP_update_06232025.R (line 3462, column 105)
    • T in R/BioTIP_update_06232025.R (line 3463, column 111)
    • T in R/BioTIP_update_06232025.R (line 3464, column 109)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • BioTIP_update_06232025.R (line 119, column 23)
    • ...
    • BioTIP_update_06232025.R (line 3216, column 36)
* 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 14
functions greater than 50 lines.
  The longest 5 functions are:
    • BioTIP.wrap() (R/BioTIP_update_06232025.R): 473 lines
    • ...
    • cor.shrink() (R/BioTIP_update_06232025.R): 98 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • optimize.sd_selection.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 6% of man
pages use at least one of these tags.
  Found in files:
    • getBiotypes.Rd
    • getReadthrough.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • getBiotypes.Rd
    • getReadthrough.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 649 lines (14%) are > 80 characters long.
  First few lines:
    • R/BioTIP_update_06232025.R#L3 ## Email: zhezhen@uchicago.edu;andrewgol
    ...
    • ...
    • vignettes/BioTIP.Rmd#L992 * Wang, Z. Z., J. M. Cunningham and X. H ...
ℹ NOTE: Consider 4 spaces instead of tabs; 259 lines (6%) contain tabs.
  First few lines:
    • R/BioTIP_update_06232025.R#L14 ## 12/24/2024 rename the function myplot
    ...
    • ...
    • R/BioTIP_update_06232025.R#L3541 if(n>64) warning('only the first 65 cas
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1164 lines (25%) are
not.
  First few lines:
    • R/BioTIP_update_06232025.R#L118 # require(GenomicRanges) ...
    • ...
    • vignettes/BioTIP.Rmd#L996 ...
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...
* 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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 5 WARNINGS | ℹ 21 NOTES
ℹ See the BioTIP.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.