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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ExiMiR_2.55.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ExiMiR ───────────────────────────────────────────────────────────
✔ Package installed successfully
── ExiMiR session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpKwNKsV/file97dd04fed329e/ExiMiR
→ BiocVersion: 3.24
→ Package: ExiMiR
→ PackageVersion: 2.55.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ExiMiR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpKwNKsV/file97dd04fed329e/ExiMiR
→ installDir: /tmp/RtmpKwNKsV/file97dd0114c2439
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ExiMiR ─────────────────────────────────────────────────
* 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 2.10 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/RtmpKwNKsV/file97dd04fed329e/ExiMiR/man/bg.correct.miR.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpKwNKsV/file97dd04fed329e/ExiMiR/man/GSE19183.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpKwNKsV/file97dd04fed329e/ExiMiR/man/GSE20122.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
Metabolomics, Proteomics, Epigenetics, Cheminformatics, Transcriptomics,
Normalization, Bayesian, Clustering, Regression, ExonArray, RNASeq,
MicroRNAArray, mRNAMicroarray, ProprietaryPlatforms, CellBiology,
BiomedicalInformatics, FunctionalGenomics, SystemsBiology, ImmunoOncology,
AlternativeSplicing, DifferentialExpression, DifferentialSplicing,
GeneSetEnrichment, BatchEffect, MultipleComparison, QualityControl, TimeCourse,
DataImport
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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* 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 (50%).
* 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:
    • ExiMiR-vignette.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/ExiMiR-vignette.Rnw
* Checking package installation calls in R code...
* Checking for library/require of ExiMiR...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • createAB.R (line 162, column 49)
    • ...
    • NormiR.R (line 811, column 18)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/createAB.R (line 54, column 41)
    • ...
    • cat() in R/read.exi.R (line 107, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/createAB.R (line 65, column 25)
    • ...
    • R/read.exi.R (line 39, column 33)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/createAB.R (line 25, column 22)
    • ...
    • R/NormiR.methods.R (line 36, column 22)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/read.exi.R (line 41, column 30)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • createAB.R (line 24, column 26)
    • ...
    • NormiR.methods.R (line 35, column 26)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 8
functions greater than 50 lines.
  The longest 5 functions are:
    • createAB() (R/createAB.R): 444 lines
    • ...
    • NormiR() (R/NormiR.R): 69 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/galenv.Rd
    • man/GSE19183.Rd
    • man/GSE20122.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • createAB.Rd
    • ...
    • ReadExi.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 17% of man
pages use at least one of these tags.
  Found in files:
    • make.gal.env.Rd
    • ReadExi.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • make.gal.env.Rd
    • ReadExi.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; 455 lines (14%) are > 80 characters long.
  First few lines:
    • R/createAB.R#L11 ######################################## ...
    • ...
    • vignettes/ExiMiR-vignette.Rnw#L784 12
    GSM503413_Hy3_Exiqon_14114413_S01_Cro ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1828 lines (54%) contain tabs.
  First few lines:
    • R/createAB.R#L14 verbose=TRUE, ...
    • ...
    • vignettes/ExiMiR-vignette.Rnw#L784 12
    GSM503413_Hy3_Exiqon_14114413_S01_Cro ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 70 lines (2%) are not.
  First few lines:
    • R/createAB.R#L15 ref.channel = "R", ...
    • ...
    • vignettes/ExiMiR-vignette.Rnw#L379 ...) ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 3 WARNINGS | ℹ 18 NOTES
ℹ See the ExiMiR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.