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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('sva_3.60.0.tar.gz','quit-with-status'=TRUE)"
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── Installing sva ──────────────────────────────────────────────────────────────
✔ Package installed successfully
── sva session metadata ────────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpg37XGC/file9982046a14d91/sva
→ BiocVersion: 3.23
→ Package: sva
→ PackageVersion: 3.60.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/sva.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/Rtmpg37XGC/file9982046a14d91/sva
→ installDir: /tmp/Rtmpg37XGC/file99820b5b7561
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on sva ────────────────────────────────────────────────────
* 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 3.2 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:
GeneExpression, GenomicVariation, Regression
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 that Package field matches directory/tarball name...
* 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 (44%).
* 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:
    • sva.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • sva.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • sva.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/sva.Rnw
* Checking package installation calls in R code...
* Checking for library/require of sva...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/helper.R (line 1, column 1)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/ComBat_seq.R (line 60, column 16)
    • ...
    • R/helper_seq.R (line 28, column 11)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • ComBat_seq.R (line 50, column 17)
    • ...
    • twostepsva.build.R (line 70, column 16)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/ComBat_seq.R (line 63, column 3)
    • ...
    • cat() in R/svaseq.R (line 80, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/ComBat_seq.R (line 105, column 7)
    • ...
    • R/svaseq.R (line 64, column 10)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/num.sv.R (line 33, column 12)
    • R/sva.R (line 48, column 12)
    • R/svaseq.R (line 56, column 12)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/empirical.controls.R (line 32, column 44)
    • ...
    • R/svaseq.R (line 56, column 18)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • psva.R (line 41, column 19)
    • psva.R (line 41, column 44)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/num.sv.R (line 42, column 24)
* 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 5
functions greater than 50 lines.
  The longest 5 functions are:
    • ComBat() (R/ComBat.R): 261 lines
    • ...
    • twostepsva.build() (R/twostepsva.build.R): 54 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; 275 lines (12%) are > 80 characters long.
  First few lines:
    • R/ComBat_seq.R#L1 #' Adjust for batch effects using an emp ...
    • ...
    • vignettes/sva.Rnw#L380 \item Parker HS, Leek JT, Favorov AV, Co ...
ℹ NOTE: Consider 4 spaces instead of tabs; 56 lines (3%) contain tabs.
  First few lines:
    • R/helper_seq.R#L40 res <- list(gamma_star=pos_res[, "gamm ...
    • ...
    • R/sva_network.R#L33 return(dat.adjusted) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 452 lines (20%) are
not.
  First few lines:
    • R/ComBat_seq.R#L37 shrink=FALSE, shr ...
    • ...
    • vignettes/sva.Rnw#L213 ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 4 WARNINGS | ℹ 18 NOTES
ℹ See the sva.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.