Build/check report for BioC 3.24 - BIOCCHECK results for SMITE on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4890
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

BIOCCHECK results for SMITE on nebbiolo2

To the developers/maintainers of the SMITE package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SMITE.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: SMITE

Version: 1.41.0

Command: /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('SMITE_1.41.0.tar.gz','quit-with-status'=TRUE)"

StartedAt: 2026-05-09 07:44:39 -0400 (Sat, 09 May 2026)

EndedAt: 2026-05-09 07:45:56 -0400 (Sat, 09 May 2026)

EllapsedTime: 77.1 seconds

RetCode: 1

Status: ERRORS

CheckDir: None

Warnings: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('SMITE_1.41.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing SMITE ────────────────────────────────────────────────────────────
✔ Package installed successfully
── SMITE session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE
→ BiocVersion: 3.24
→ Package: SMITE
→ PackageVersion: 1.41.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/SMITE.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE
→ installDir: /tmp/RtmpZVlv7s/file133e9c1dceba8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SMITE ──────────────────────────────────────────────────
* 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 3.5 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE/man/addShadowText.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE/man/annotateExpression.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE/man/annotateModification.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE/man/convertGeneIds.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE/man/curated_expression.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE/man/extractExpression.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE/man/extractModules.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE/man/genes_for_conversiontest.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE/man/histone_h3k4me1.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE/man/makePvalueAnnotation.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE/man/makePvalueObject.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE/man/methylationdata.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE/man/normalizePval.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE/man/plotCompareScores.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE/man/plotDensityPval.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE/man/removeModification.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE/man/runBioNet.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE/man/runGOseq.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE/man/scorePval.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZVlv7s/file133e9c31f2b1e5/SMITE/man/test_annotation_score_data.Rd'
* 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (36%).
* 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:
    • SMITE.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/SMITE.Rmd
* Checking package installation calls in R code...
* Checking for library/require of SMITE...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/SMITE-plot.R (line 381, column 26)
    • ...
    • R/SMITE.R (line 1442, column 21)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • SMITE-plot.R (line 146, column 27)
    • ...
    • SMITE.R (line 1439, column 38)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/SMITE-plot.R (line 147, column 66)
    • ...
    • R/SMITE.R (line 1055, column 44)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/SMITE-plot.R (line 25, column 18)
    • ...
    • R/SMITE.R (line 1052, column 25)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/SMITE.R (line 261, column 21)
    • ...
    • R/SMITE.R (line 1125, column 18)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 2 times:
    • T in R/SMITE-plot.R (line 365, column 34)
    • F in R/SMITE-plot.R (line 371, column 34)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • SMITE-plot.R (line 127, column 31)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 7 times)
  • suppressWarnings() in R/SMITE.R (line 99, column 17)
  • ...
  • suppressWarnings() in R/SMITE.R (line 1140, column 21)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 3
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.401() (R/SMITE.R): 109 lines
    • _anonymous_.416() (R/SMITE.R): 91 lines
    • definition() (R/SMITE-plot.R): 61 lines
* Checking man page documentation...


* Checking package NEWS...
* 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; 256 lines (5%) are > 80 characters long.
  First few lines:
    • R/SMITE-generics.R#L28 promoter_upstream_dista ...
    • ...
    • vignettes/SMITE.Rmd#L206 plotModule(test_annotation, which_networ ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 389 lines (8%) are
not.
  First few lines:
    • R/SMITE-generics.R#L28 promoter_upstream_dista ...
    • ...
    • vignettes/SMITE.Rmd#L181 load(system.file("data","Reactome.Symbo ...
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.
ℹ Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | ℹ 15 NOTES
ℹ See the SMITE.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.