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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('massiR_1.49.0.tar.gz','quit-with-status'=TRUE)"
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── Installing massiR ───────────────────────────────────────────────────────────
✔ Package installed successfully
── massiR session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp9UprMF/filed036731257ef8/massiR
→ BiocVersion: 3.24
→ Package: massiR
→ PackageVersion: 1.49.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/massiR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp9UprMF/filed036731257ef8/massiR
→ installDir: /tmp/Rtmp9UprMF/filed036714e63891
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on massiR ─────────────────────────────────────────────────
* 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 3.0.2 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:
PrincipalComponent
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 (25%).
* 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...
✖ ERROR: 'NAMESPACE' contains exportPattern with '[[:alpha:]]'; use explicit
exports instead.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • massiR_Vignette.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • massiR_Vignette.Rnw
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/massiR_Vignette.Rnw (chunk no. 6, line 38, column 68)
    • ...
    • vignettes/massiR_Vignette.Rnw (chunk no. 14, line 109, column 42)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/massiR_Vignette.Rnw
* Checking package installation calls in R code...
* Checking for library/require of massiR...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/massi_cluster_plot.R (line 1, column 1)
    • ...
    • library() in R/massi_y.R (line 1, column 1)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/massi_cluster.R (line 36, column 27)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • massi_y_plot.R (line 14, column 22)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 4 times:
    • T in R/massi_cluster_plot.R (line 9, column 59)
    • ...
    • T in R/massi_y_plot.R (line 7, column 68)
* 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 3
functions greater than 50 lines.
  The longest 5 functions are:
    • massi_select() (R/massi_select.R): 72 lines
    • massi_cluster() (R/massi_cluster.R): 58 lines
    • massi_y() (R/massi_y.R): 53 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; 147 lines (12%) are > 80 characters long.
  First few lines:
    • R/massi_cluster_plot.R#L11 key=T, trace="none", dendrog ...
    • ...
    • vignettes/massiR_Vignette.Rnw#L370 This is a straightforwd way of
    obtaining ...
ℹ NOTE: Consider 4 spaces instead of tabs; 12 lines (1%) contain tabs.
  First few lines:
    • man/massi_eset.Rd#L33 .. .. ..@ varMetadata :'data.fram ...
    • ...
    • man/y_probes.Rd#L19 $ affy_hg_u133_plus_2 :'data.frame': 9 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 405 lines (32%) are
not.
  First few lines:
    • R/massi_cluster_plot.R#L4 ...
    • ...
    • vignettes/massiR_Vignette.Rnw#L403 ...
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 Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 4 WARNINGS | ℹ 15 NOTES
ℹ See the massiR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.