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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('hermes_1.17.0.tar.gz','quit-with-status'=TRUE)"
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── Installing hermes ───────────────────────────────────────────────────────────
✔ Package installed successfully
── hermes session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpuHazHH/fileafb8663a8f6a9/hermes
→ BiocVersion: 3.24
→ Package: hermes
→ PackageVersion: 1.17.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/hermes.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpuHazHH/fileafb8663a8f6a9/hermes
→ installDir: /tmp/RtmpuHazHH/fileafb86732306c1
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on hermes ─────────────────────────────────────────────────
* 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 4.1 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: Sequencing,
Coverage
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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (39%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* 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:
    • hermes.Rmd
* Checking package installation calls in R code...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHazHH/fileafb8663a8f6a9/hermes/man/h_diff_expr_deseq2.Rd:40: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHazHH/fileafb8663a8f6a9/hermes/man/h_diff_expr_voom.Rd:41: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHazHH/fileafb8663a8f6a9/hermes/man/h_diff_expr_voom.Rd:43: unknown macro '\insertRef'
* Checking for library/require of hermes...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/utils.R (line 391, column 3)
    • cat() in R/utils.R (line 392, column 3)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
  The longest 5 functions are:
    • draw_boxplot() (R/draw_boxplot.R): 51 lines
* Checking man page documentation...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHazHH/fileafb8663a8f6a9/hermes/man/h_diff_expr_deseq2.Rd:40: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHazHH/fileafb8663a8f6a9/hermes/man/h_diff_expr_voom.Rd:41: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHazHH/fileafb8663a8f6a9/hermes/man/h_diff_expr_voom.Rd:43: unknown macro '\insertRef'
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/assertion_arguments.Rd
    • man/GeneSpec.Rd
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHazHH/fileafb8663a8f6a9/hermes/man/h_diff_expr_deseq2.Rd:40: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHazHH/fileafb8663a8f6a9/hermes/man/h_diff_expr_voom.Rd:41: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHazHH/fileafb8663a8f6a9/hermes/man/h_diff_expr_voom.Rd:43: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHazHH/fileafb8663a8f6a9/hermes/man/h_diff_expr_deseq2.Rd:40: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHazHH/fileafb8663a8f6a9/hermes/man/h_diff_expr_voom.Rd:41: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpuHazHH/fileafb8663a8f6a9/hermes/man/h_diff_expr_voom.Rd:43: unknown macro '\insertRef'
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
ℹ NOTE: skip_on_bioc() found in testthat files: test-connections.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 362 lines (7%) are > 80 characters long.
  First few lines:
    • R/assertthat.R#L17 #' @param class2 (`character` or class d ...
    • ...
    • vignettes/hermes.Rmd#L497 The `hermes` R package provides classes, ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1121 lines (21%) are
not.
  First few lines:
    • R/assertthat.R#L24 is(x, class2) ...
    • ...
    • vignettes/hermes.Rmd#L449 data = as.data.frame(colData(object_no ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | ℹ 11 NOTES
ℹ See the hermes.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.