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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('MEIGOR_1.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing MEIGOR ───────────────────────────────────────────────────────────
✔ Package installed successfully
── MEIGOR session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR
→ BiocVersion: 3.24
→ Package: MEIGOR
→ PackageVersion: 1.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/MEIGOR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR
→ installDir: /tmp/RtmpLUsy0R/filed29596514ebb8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MEIGOR ─────────────────────────────────────────────────
* 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 4.6.0
* 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...
! WARNING: Invalid BiocViews term(s):
  • 'Optimization'
* Checking for recommended biocViews...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR/man/cnolist_cellnopt.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR/man/cnolist.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR/man/eucl_dist.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR/man/ith_essR.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR/man/ith_VNSR.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR/man/model_cellnopt.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR/man/model.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR/man/optim_fobj.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR/man/paramsOpt.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR/man/rvnds_local.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR/man/solnp_fobj.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR/man/ssm_beyond.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR/man/ssm_defaults.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR/man/ssm_isdif2.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR/man/ssm_localsolver.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR/man/ssm_optset.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR/man/ssm_penalty_function.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR/man/ssm_round_int.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR/man/vns_defaults.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLUsy0R/filed295922da2be8/MEIGOR/man/vns_optset.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Proteomics,
CellBasedAssays, CellBiology, ImmunoOncology, TimeCourse
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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (25%).
* 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: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/MEIGOR-vignette.Rmd (chunk no. 10, line 359, column 1)
    • ...
    • vignettes/MEIGOR-vignette.Rmd (chunk no. 14, line 479, column 31)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/MEIGOR-vignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of MEIGOR...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/CeSSR.R (line 54, column 35)
    • library() in R/CeVNSR.R (line 74, column 31)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • calculate_hessian.R (line 162, column 12)
    • ...
    • vns_optset.R (line 11, column 27)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/CeSSR.R (line 48, column 17)
    • ...
    • cat() in R/vns_optset.R (line 14, column 33)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/accept_move.R (line 83, column 13)
    • ...
    • R/vns_optset.R (line 21, column 13)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/initialize.R (line 193, column 7)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 10 times)
  • <<- in R/nls_fobj.R (line 7, column 20)
  • ...
  • <<- in R/ssm_localsolver.R (line 9, column 15)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 12
functions greater than 50 lines.
  The longest 5 functions are:
    • essR() (R/essR.R): 1190 lines
    • ...
    • rvnds_hamming() (R/rvnds_hamming.R): 201 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/CeVNSR.Rd
  • man/vns_defaults.Rd
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/cnolist_cellnopt.Rd
    • ...
    • man/paramsOpt.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/dhc.Rd
    • ...
    • man/vns_optset.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • CeVNSR.Rd
    • essR_multistart.Rd
* 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; 640 lines (7%) are > 80 characters long.
  First few lines:
    • R/accept_move.R#L2 #' @description "accept_move" updates th ...
    • ...
    • vignettes/MEIGOR-vignette.Rmd#L1075 ```{r
    CellNOptRExamplePlotOptModel,inclu ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1362 lines (16%) contain tabs.
  First few lines:
    • R/CeSSR.R#L2 ...
    • ...
    • vignettes/MEIGOR-vignette.Rmd#L1064 aggr=0, local_search_type=1,
    decomp=1, ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1488 lines (17%) are
not.
  First few lines:
    • R/accept_move.R#L84 output$accept_prior = output$test_prio ...
    • ...
    • vignettes/MEIGOR-vignette.Rmd#L1035 ...
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 | ⚠ 6 WARNINGS | ℹ 17 NOTES
ℹ See the MEIGOR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.