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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('hapFabia_1.55.0.tar.gz','quit-with-status'=TRUE)"
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── Installing hapFabia ─────────────────────────────────────────────────────────
✔ Package installed successfully
── hapFabia session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpmIG8us/fileaece5ac80d07/hapFabia
→ BiocVersion: 3.24
→ Package: hapFabia
→ PackageVersion: 1.55.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/hapFabia.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpmIG8us/fileaece5ac80d07/hapFabia
→ installDir: /tmp/RtmpmIG8us/fileaece5173dcc01
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on hapFabia ───────────────────────────────────────────────
* 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 3.6.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews:
CopyNumberVariation, Microarray, DifferentialExpression, MultipleComparison
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 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (29%).
* 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:
    • hapfabia.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • hapfabia.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • hapfabia.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/hapfabia.Rnw
* Checking package installation calls in R code...
* Checking for library/require of hapFabia...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/hapFabia.R (line 617, column 31)
    • ...
    • R/methods-IBDsegmentList-class.R (line 328, column 46)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • hapFabia.R (line 59, column 17)
    • ...
    • methods-IBDsegmentList-class.R (line 585, column 25)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/hapFabia.R (line 27, column 3)
    • cat() in R/hapFabia.R (line 28, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/hapFabia.R (line 353, column 13)
    • ...
    • R/zzz.R (line 20, column 21)
* 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 16
functions greater than 50 lines.
  The longest 5 functions are:
    • simulateIBDsegments() (R/hapFabia.R): 403 lines
    • ...
    • iterateIntervals() (R/hapFabia.R): 176 lines
* Checking man page documentation...
+----------------------------+                                          
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+----------------------------+                                          

Citation: S. Hochreiter et al.,
FABIA: Factor Analysis for Bicluster Acquisition,
Bioinformatics 26(12):1520-1527, 2010.
BibTex: enter 'toBibtex(citation("fabia"))'

Homepage: http://www.bioinf.jku.at/software/fabia/fabia.html

FABIA Package Version 2.59.0

+--------------------------+          #    #    ##    #####     
|#.....#...#.......#.#....#|          #    #   #  #   #    #    
|#.....#...#.......#.#....#|          ######  #    #  #    #    
|#.....#...#...............|          #    #  ######  #####     
|#.....#...#.......#.#....#|          #    #  #    #  #         
|#.....#...#...............|          #    #  #    #  #         
|#.....#...#.......#.#....#|  #######                           
|..................#.#....#|  #         ##    #####   #    ##   
|#.....#...#.......#.#....#|  #        #  #   #    #  #   #  #  
|..................#.#....#|  #####   #    #  #####   #  #    # 
|#.....#...#.......#.#....#|  #       ######  #    #  #  ###### 
|#.....#...#.......#.#....#|  #       #    #  #    #  #  #    # 
+--------------------------+  #       #    #  #####   #  #    # 

Citation: S. Hochreiter,
HapFABIA: Identification of very short segments of identity by descent characterized by rare variants in large sequencing data,
Nucleic Acids Research, 2013, doi: 10.1093/nar/gkt1013.
BibTex: enter 'toBibtex(citation("hapFabia"))'

Homepage: http://www.bioinf.jku.at/software/hapFabia/index.html

hapFabia Package Version 1.55.0

ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • simulateIBDsegments.Rd
  • split_sparse_matrix.Rd
  • vcftoFABIA.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 25% of man
pages use at least one of these tags.
  Found in files:
    • analyzeIBDsegments.Rd
    • ...
    • vcftoFABIA.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • analyzeIBDsegments.Rd
    • ...
    • vcftoFABIA.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; 442 lines (4%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L42 else if (!is.numeric(slot(object ...
    • ...
    • vignettes/hapfabia.Rnw#L1241 in the 1000 Genomes Project data. Additi ...
ℹ NOTE: Consider 4 spaces instead of tabs; 5 lines (0%) contain tabs.
  First few lines:
    • R/hapFabia.R#L217 ylab="", axes=FALSE, zlim=c(min,max)) ...
    • ...
    • man/IBDsegmentList-class.Rd#L74 an IBD segment, average number of ta ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1791 lines (18%) are
not.
  First few lines:
    • R/AllClasses.R#L7 representation = representation ...
    • ...
    • vignettes/hapfabia.Rnw#L941 \E \left( \z_j \mid \x_j \right) \ ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 1 WARNINGS | ℹ 19 NOTES
ℹ See the hapFabia.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.