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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('multiMiR_1.35.0.tar.gz','quit-with-status'=TRUE)"
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── Installing multiMiR ─────────────────────────────────────────────────────────
✔ Package installed successfully
── multiMiR session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpYB0OMe/filef36d12347ac3/multiMiR
→ BiocVersion: 3.24
→ Package: multiMiR
→ PackageVersion: 1.35.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/multiMiR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpYB0OMe/filef36d12347ac3/multiMiR
→ installDir: /tmp/RtmpYB0OMe/filef36d13c1e5b1
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on multiMiR ───────────────────────────────────────────────
* 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 3.4 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ ExperimentData
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* 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 (22%).
* 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:
    • multiMiR.Rmd
* Checking package installation calls in R code...
* Checking for library/require of multiMiR...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/mmquery.R (line 167, column 15)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • listdata.R (line 47, column 35)
    • mirnasummary.R (line 25, column 29)
    • mirnasummary.R (line 72, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/dbinfo.R (line 93, column 5)
    • cat() in R/getdata.R (line 293, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/externallinks.R (line 164, column 7)
    • R/mirnasummary.R (line 73, column 18)
    • R/mirnasummary.R (line 74, column 18)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/dbversion.R (line 50, column 13)
    • ...
    • R/search.R (line 93, column 14)
! WARNING: .Deprecated / .Defunct usage (found 3 times)
  • .Deprecated() in R/getdata.R (line 220, column 5)
  • .Deprecated() in R/listdata.R (line 71, column 5)
  • .Deprecated() in R/search.R (line 48, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/get_multimir.Rd
ℹ Found @ in vignettes/multiMiR.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* 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:
    • add.multimir.links() (R/externallinks.R): 155 lines
    • get_multimir() (R/getdata.R): 88 lines
    • multimir.summary() (R/mirnasummary.R): 86 lines
* Checking man page documentation...
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 33 lines (1%) are > 80 characters long.
  First few lines:
    • R/getdata.R#L198 rtnobject <- if (legacy.out) as.mmqu ...
    • ...
    • vignettes/multiMiR.Rmd#L636 [http://multimir.org/cgi-bin/multimir.pl ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 270 lines (10%) are
not.
  First few lines:
    • R/buildquery.R#L21 target = sq ...
    • ...
    • vignettes/multiMiR.Rmd#L662 i.pubmed_id ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | ℹ 15 NOTES
ℹ See the multiMiR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.