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

To the developers/maintainers of the SIMAT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SIMAT.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: SIMAT

Version: 1.45.0

Command: /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('SIMAT_1.45.0.tar.gz','quit-with-status'=TRUE)"

StartedAt: 2026-05-09 07:43:15 -0400 (Sat, 09 May 2026)

EndedAt: 2026-05-09 07:43:38 -0400 (Sat, 09 May 2026)

EllapsedTime: 23.0 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('SIMAT_1.45.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing SIMAT ────────────────────────────────────────────────────────────
✔ Package installed successfully
── SIMAT session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT
→ BiocVersion: 3.24
→ Package: SIMAT
→ PackageVersion: 1.45.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/SIMAT.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT
→ installDir: /tmp/Rtmp1y1nEW/file131f6c58e08c94
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SIMAT ──────────────────────────────────────────────────
* 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 3.5.0 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/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/getEIC.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/getPeak.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/getPeakScore.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/getRI.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/getRIStandard.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/getScore.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/getTarget.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/getTargetTable.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/Library.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/optFrag.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/plotEIC.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/plotTIC.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/putTargetTable.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/readCDF.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/readMSL.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/RItable.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/Run.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/SIMAT-package.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/target.table.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/Targets.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/writeMSL.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/man/writeResult.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1y1nEW/file131f6c7ef8164b/SIMAT/vignettes/SIMAT-vignette.Rnw'
* 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 (12%).
* 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...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • SIMAT-vignette.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/SIMAT-vignette.Rnw
* Checking package installation calls in R code...
* Checking for library/require of SIMAT...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/writeResult.R (line 55, column 22)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • getEIC.R (line 17, column 14)
    • ...
    • writeResult.R (line 62, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/getPeak.R (line 87, column 13)
    • ...
    • print() in R/plotTIC.R (line 20, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/getTargetTable.R (line 47, column 28)
    • ...
    • R/plotTIC.R (line 44, column 22)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/getTarget.R (line 28, column 18)
    • ...
    • R/optFrag.R (line 93, column 21)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/getEIC.R (line 18, column 14)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 11
functions greater than 50 lines.
  The longest 5 functions are:
    • optFrag() (R/optFrag.R): 203 lines
    • ...
    • readMSL() (R/readMSL.R): 95 lines
* Checking man page documentation...
* 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; 156 lines (6%) are > 80 characters long.
  First few lines:
    • R/getEIC.R#L135 tempScoreArea <- getScore(tr ...
    • ...
    • vignettes/SIMAT-vignette.Rnw#L223 Improved peak detection and more
    options ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 76 lines (3%) are not.
  First few lines:
    • R/getEIC.R#L4 sp0 = numeric(), rt0 ...
    • ...
    • vignettes/SIMAT-vignette.Rnw#L204 forceOpt = TRUE) ...
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 Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | ℹ 14 NOTES
ℹ See the SIMAT.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.