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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('metagenomeSeq_1.55.0.tar.gz','quit-with-status'=TRUE)"
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── Installing metagenomeSeq ────────────────────────────────────────────────────
✔ Package installed successfully
── metagenomeSeq session metadata ──────────────────────────────────────────────
→ sourceDir: /tmp/RtmpI752gu/file2ccb9c5c600403/metagenomeSeq
→ BiocVersion: 3.24
→ Package: metagenomeSeq
→ PackageVersion: 1.55.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/metagenomeSeq.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpI752gu/file2ccb9c5c600403/metagenomeSeq
→ installDir: /tmp/RtmpI752gu/file2ccb9c76f827b3
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on metagenomeSeq ──────────────────────────────────────────
* 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 3.0 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/RtmpI752gu/file2ccb9c5c600403/metagenomeSeq/man/lungData.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpI752gu/file2ccb9c5c600403/metagenomeSeq/man/mouseData.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Transcription,
Microarray, Metabolomics, Proteomics, Epigenetics, Cheminformatics,
Transcriptomics, Preprocessing, Bayesian, Regression, ExonArray,
GeneExpression, RNASeq, OneChannel, TwoChannel, MicroRNAArray, mRNAMicroarray,
ProprietaryPlatforms, CellBiology, BiomedicalInformatics, FunctionalGenomics,
SystemsBiology, AlternativeSplicing, DifferentialSplicing, GeneSetEnrichment,
BatchEffect, 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (19%).
* 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:
    • fitTimeSeries.Rnw
    • metagenomeSeq.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • fitTimeSeries.Rnw
    • metagenomeSeq.Rnw
* Checking package installation calls in R code...
* Checking for library/require of metagenomeSeq...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/biom2MRexperiment.R (line 20, column 27)
    • ...
    • R/plotOTU.R (line 40, column 24)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • aggregateByTaxonomy.R (line 68, column 81)
    • ...
    • plotOTU.R (line 61, column 23)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/fitZig.R (line 171, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/aggregateBySample.R (line 26, column 21)
    • ...
    • R/plotRare.R (line 40, column 19)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/cumNormStat.R (line 24, column 35)
    • R/cumNormStatFast.R (line 25, column 42)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • T in R/fitZeroLogNormal.R (line 261, column 41)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • aggregateBySample.R (line 25, column 22)
    • ...
    • plotRare.R (line 25, column 26)
! WARNING: .Deprecated / .Defunct usage (found 5 times)
  • .Deprecated() in R/deprecated_metagenomeSeq_function.R (line 19, column 26)
  • ...
  • .Deprecated() in R/deprecated_metagenomeSeq_function.R (line 23, column 29)
* 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 12
functions greater than 50 lines.
  The longest 5 functions are:
    • .do_fitZig() (R/fitZig.R): 169 lines
    • ...
    • MRcoefs() (R/MRcoefs.R): 78 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/calcPosComponent.Rd
    • ...
    • man/MRihw.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • calculateEffectiveSamples.Rd
  • ...
  • ssPermAnalysis.Rd
* 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; 481 lines (9%) are > 80 characters long.
  First few lines:
    • R/aggregateBySample.R#L3 #' Using the phenoData information in th ...
    • ...
    • vignettes/metagenomeSeq.Rnw#L728 More information will be included later.
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 621 lines (12%) contain tabs.
  First few lines:
    • R/aggregateBySample.R#L25 if(class(obj)=="MRexperiment"){ ...
    • ...
    • vignettes/fitTimeSeries.Rnw#L254 \item ... - Options for ssanova ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 446 lines (8%) are
not.
  First few lines:
    • R/aggregateByTaxonomy.R#L31 if(class(obj)=="MRexperiment"){ ...
    • ...
    • vignettes/metagenomeSeq.Rnw#L638 }) ...
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 | ⚠ 5 WARNINGS | ℹ 15 NOTES
ℹ See the metagenomeSeq.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.