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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('aroma.light_3.42.0.tar.gz','quit-with-status'=TRUE)"
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── Installing aroma.light ──────────────────────────────────────────────────────
✔ Package installed successfully
── aroma.light session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpnAsKY0/file729be58ce50c2/aroma.light
→ BiocVersion: 3.23
→ Package: aroma.light
→ PackageVersion: 3.42.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/aroma.light.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpnAsKY0/file729be58ce50c2/aroma.light
→ installDir: /tmp/RtmpnAsKY0/file729be6fa9ed6d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on aroma.light ────────────────────────────────────────────
* 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 2.15.2 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...
No vignettes found.
Warning in strsplit(q[[1]], "[[:punct:]]", perl = TRUE) :
  input string 38 is invalid UTF-8
Warning in strsplit(q[[1]], "[[:punct:]]", perl = TRUE) :
  input string 77 is invalid UTF-8
Warning in strsplit(q[[1]], "[[:punct:]]", perl = TRUE) :
  input string 172 is invalid UTF-8
ℹ NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, Normalization
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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ NOTE: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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...
✖ ERROR: No 'vignettes' directory.
* Checking package installation calls in R code...
* Checking for library/require of aroma.light...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/callNaiveGenotypes.R (line 109, column 10)
    • R/normalizeDifferencesToAverage.R (line 52, column 10)
    • R/plotDensity.R (line 54, column 11)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • averageQuantile.R (line 73, column 14)
    • ...
    • wpca.R (line 172, column 18)
Warning in grepl(pattern, txt) :
  unable to translate '#   \enc{H<f6>ssjer}{Hossjer} (2006).' to a wide string
Warning in grepl(pattern, txt) : input string 28 is invalid
Warning in grepl(pattern, txt) :
  unable to translate '#   In Bengtsson & \enc{H<f6>ssjer}{Hossjer} (2006), we carry out a detailed' to a wide string
Warning in grepl(pattern, txt) : input string 67 is invalid
Warning in grepl(pattern, txt) :
  unable to translate '#   See Bengtsson & \enc{H<f6>ssjer}{Hossjer} (2006) for details.' to a wide string
Warning in grepl(pattern, txt) : input string 162 is invalid
Warning in grepl(pattern, txt) :
  unable to translate '#   [1] M. \enc{<c5>strand}{Astrand},' to a wide string
Warning in grepl(pattern, txt) : input string 122 is invalid
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/callNaiveGenotypes.R (line 116, column 18)
    • ...
    • cat() in R/print.SmoothSplineLikelihood.R (line 46, column 3)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/backtransformAffine.R (line 92, column 10)
    • ...
    • R/rowAverages.matrix.R (line 19, column 12)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 3 times:
    • F in R/distanceBetweenLines.R (line 96, column 5)
    • F in R/distanceBetweenLines.R (line 100, column 28)
    • F in R/distanceBetweenLines.R (line 100, column 41)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 7 times)
  • suppressWarnings() in R/normalizeFragmentLength.R (line 224, column 5)
  • ...
  • suppressWarnings() in R/plotXYCurve.R (line 81, column 3)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 29
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.87() (R/normalizeFragmentLength.R): 269 lines
    • ...
    • _anonymous_.98() (R/wpca.R): 168 lines
* Checking man page documentation...
Warning in grepl("^%%\\s+~", lines) :
  unable to translate '  \enc{H<f6>ssjer}{Hossjer} (2006).' to a wide string
Warning in grepl("^%%\\s+~", lines) : input string 38 is invalid
Warning in grepl("^%%\\s+~", lines) :
  unable to translate '  In Bengtsson & \enc{H<f6>ssjer}{Hossjer} (2006), we carry out a detailed' to a wide string
Warning in grepl("^%%\\s+~", lines) : input string 77 is invalid
Warning in grepl("^%%\\s+~", lines) :
  unable to translate '  See Bengtsson & \enc{H<f6>ssjer}{Hossjer} (2006) for details.' to a wide string
Warning in grepl("^%%\\s+~", lines) : input string 172 is invalid
Warning in grepl("^%%\\s+~", lines) :
  unable to translate '[4] H. Bengtsson, J. Vallon-Christersson and G. \enc{J<f6>nsson}{Jonsson}, \emph{Calibration and assessment of channel-specific biases in microarray data with extended dynamical range}, BMC Bioinformatics, 5:177, 2004.' to a wide string
Warning in grepl("^%%\\s+~", lines) : input string 110 is invalid
Warning in grepl("^%%\\s+~", lines) :
  unable to translate '[5] Henrik Bengtsson and Ola \enc{H<f6>ssjer}{Hossjer}, \emph{Methodological Study of Affine Transformations of Gene Expression Data}, Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dime...' to a wide string
Warning in grepl("^%%\\s+~", lines) : input string 113 is invalid
Warning in grepl("^%%\\s+~", lines) :
  unable to translate '  [1] H. Bengtsson, J. Vallon-Christersson and G. \enc{J<f6>nsson}{Jonsson}, \emph{Calibration and assessment of channel-specific biases in microarray data with extended dynamical range}, BMC Bioinformatics, 5:177, 2004.' to a wide string
Warning in grepl("^%%\\s+~", lines) : input string 135 is invalid
Warning in grepl("^%%\\s+~", lines) :
  unable to translate '  [1] Henrik Bengtsson and Ola \enc{H<f6>ssjer}{Hossjer}, \emph{Methodological Study of Affine Transformations of Gene Expression Data}, Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-di...' to a wide string
Warning in grepl("^%%\\s+~", lines) : input string 138 is invalid
Warning in grepl("^%%\\s+~", lines) :
  unable to translate '  [1] M. \enc{<c5>strand}{Astrand},' to a wide string
Warning in grepl("^%%\\s+~", lines) : input string 133 is invalid
Warning in grepl("^%%\\s+~", lines) :
  unable to translate '  [2] Henrik Bengtsson and Ola \enc{H<f6>ssjer}{Hossjer}, \emph{Methodological Study of Affine Transformations of Gene Expression Data}, Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-di...' to a wide string
Warning in grepl("^%%\\s+~", lines) : input string 136 is invalid
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/1._Calibration_and_Normalization.Rd
    • man/plotDensity.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • aroma.light-package.Rd
    • ...
    • print.SmoothSplineLikelihood.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 3% of man
pages use at least one of these tags.
  Found in files:
    • calibrateMultiscan.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • calibrateMultiscan.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...
Warning in grepl("\t", lines) :
  unable to translate '#   \enc{H<f6>ssjer}{Hossjer} (2006).' to a wide string
Warning in grepl("\t", lines) : input string 28 is invalid
Warning in grepl("\t", lines) :
  unable to translate '#   In Bengtsson & \enc{H<f6>ssjer}{Hossjer} (2006), we carry out a detailed' to a wide string
Warning in grepl("\t", lines) : input string 67 is invalid
Warning in grepl("\t", lines) :
  unable to translate '#   See Bengtsson & \enc{H<f6>ssjer}{Hossjer} (2006) for details.' to a wide string
Warning in grepl("\t", lines) : input string 162 is invalid
Warning in regexpr("^([ ]+)", lines) :
  unable to translate '#   \enc{H<f6>ssjer}{Hossjer} (2006).' to a wide string
Warning in regexpr("^([ ]+)", lines) : input string 28 is invalid
Warning in regexpr("^([ ]+)", lines) :
  unable to translate '#   In Bengtsson & \enc{H<f6>ssjer}{Hossjer} (2006), we carry out a detailed' to a wide string
Warning in regexpr("^([ ]+)", lines) : input string 67 is invalid
Warning in regexpr("^([ ]+)", lines) :
  unable to translate '#   See Bengtsson & \enc{H<f6>ssjer}{Hossjer} (2006) for details.' to a wide string
Warning in regexpr("^([ ]+)", lines) : input string 162 is invalid
Warning in grepl("\t", lines) :
  unable to translate '#   [1] M. \enc{<c5>strand}{Astrand},' to a wide string
Warning in grepl("\t", lines) : input string 122 is invalid
Warning in regexpr("^([ ]+)", lines) :
  unable to translate '#   [1] M. \enc{<c5>strand}{Astrand},' to a wide string
Warning in regexpr("^([ ]+)", lines) : input string 122 is invalid
Warning in grepl("\t", lines) :
  unable to translate '  \enc{H<f6>ssjer}{Hossjer} (2006).' to a wide string
Warning in grepl("\t", lines) : input string 38 is invalid
Warning in grepl("\t", lines) :
  unable to translate '  In Bengtsson & \enc{H<f6>ssjer}{Hossjer} (2006), we carry out a detailed' to a wide string
Warning in grepl("\t", lines) : input string 77 is invalid
Warning in grepl("\t", lines) :
  unable to translate '  See Bengtsson & \enc{H<f6>ssjer}{Hossjer} (2006) for details.' to a wide string
Warning in grepl("\t", lines) : input string 172 is invalid
Warning in regexpr("^([ ]+)", lines) :
  unable to translate '  \enc{H<f6>ssjer}{Hossjer} (2006).' to a wide string
Warning in regexpr("^([ ]+)", lines) : input string 38 is invalid
Warning in regexpr("^([ ]+)", lines) :
  unable to translate '  In Bengtsson & \enc{H<f6>ssjer}{Hossjer} (2006), we carry out a detailed' to a wide string
Warning in regexpr("^([ ]+)", lines) : input string 77 is invalid
Warning in regexpr("^([ ]+)", lines) :
  unable to translate '  See Bengtsson & \enc{H<f6>ssjer}{Hossjer} (2006) for details.' to a wide string
Warning in regexpr("^([ ]+)", lines) : input string 172 is invalid
Warning in grepl("\t", lines) :
  unable to translate '[4] H. Bengtsson, J. Vallon-Christersson and G. \enc{J<f6>nsson}{Jonsson}, \emph{Calibration and assessment of channel-specific biases in microarray data with extended dynamical range}, BMC Bioinformatics, 5:177, 2004.' to a wide string
Warning in grepl("\t", lines) : input string 110 is invalid
Warning in grepl("\t", lines) :
  unable to translate '[5] Henrik Bengtsson and Ola \enc{H<f6>ssjer}{Hossjer}, \emph{Methodological Study of Affine Transformations of Gene Expression Data}, Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dime...' to a wide string
Warning in grepl("\t", lines) : input string 113 is invalid
Warning in regexpr("^([ ]+)", lines) :
  unable to translate '[4] H. Bengtsson, J. Vallon-Christersson and G. \enc{J<f6>nsson}{Jonsson}, \emph{Calibration and assessment of channel-specific biases in microarray data with extended dynamical range}, BMC Bioinformatics, 5:177, 2004.' to a wide string
Warning in regexpr("^([ ]+)", lines) : input string 110 is invalid
Warning in regexpr("^([ ]+)", lines) :
  unable to translate '[5] Henrik Bengtsson and Ola \enc{H<f6>ssjer}{Hossjer}, \emph{Methodological Study of Affine Transformations of Gene Expression Data}, Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dime...' to a wide string
Warning in regexpr("^([ ]+)", lines) : input string 113 is invalid
Warning in grepl("\t", lines) :
  unable to translate '  [1] H. Bengtsson, J. Vallon-Christersson and G. \enc{J<f6>nsson}{Jonsson}, \emph{Calibration and assessment of channel-specific biases in microarray data with extended dynamical range}, BMC Bioinformatics, 5:177, 2004.' to a wide string
Warning in grepl("\t", lines) : input string 135 is invalid
Warning in regexpr("^([ ]+)", lines) :
  unable to translate '  [1] H. Bengtsson, J. Vallon-Christersson and G. \enc{J<f6>nsson}{Jonsson}, \emph{Calibration and assessment of channel-specific biases in microarray data with extended dynamical range}, BMC Bioinformatics, 5:177, 2004.' to a wide string
Warning in regexpr("^([ ]+)", lines) : input string 135 is invalid
Warning in grepl("\t", lines) :
  unable to translate '  [1] Henrik Bengtsson and Ola \enc{H<f6>ssjer}{Hossjer}, \emph{Methodological Study of Affine Transformations of Gene Expression Data}, Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-di...' to a wide string
Warning in grepl("\t", lines) : input string 138 is invalid
Warning in regexpr("^([ ]+)", lines) :
  unable to translate '  [1] Henrik Bengtsson and Ola \enc{H<f6>ssjer}{Hossjer}, \emph{Methodological Study of Affine Transformations of Gene Expression Data}, Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-di...' to a wide string
Warning in regexpr("^([ ]+)", lines) : input string 138 is invalid
Warning in grepl("\t", lines) :
  unable to translate '  [1] M. \enc{<c5>strand}{Astrand},' to a wide string
Warning in grepl("\t", lines) : input string 133 is invalid
Warning in grepl("\t", lines) :
  unable to translate '  [2] Henrik Bengtsson and Ola \enc{H<f6>ssjer}{Hossjer}, \emph{Methodological Study of Affine Transformations of Gene Expression Data}, Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-di...' to a wide string
Warning in grepl("\t", lines) : input string 136 is invalid
Warning in regexpr("^([ ]+)", lines) :
  unable to translate '  [1] M. \enc{<c5>strand}{Astrand},' to a wide string
Warning in regexpr("^([ ]+)", lines) : input string 133 is invalid
Warning in regexpr("^([ ]+)", lines) :
  unable to translate '  [2] Henrik Bengtsson and Ola \enc{H<f6>ssjer}{Hossjer}, \emph{Methodological Study of Affine Transformations of Gene Expression Data}, Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-di...' to a wide string
Warning in regexpr("^([ ]+)", lines) : input string 136 is invalid
ℹ NOTE: Consider shorter lines; 375 lines (3%) are > 80 characters long.
  First few lines:
    • R/999.package.R#L18 # \item see @see "calibrateMultiscan ...
    • ...
    • man/wpca.Rd#L62 \item{vt}{An KxK \code{\link[base]{mat ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • aroma.light/NAMESPACE#L38 "predict", "sd", "smooth.spline", "w ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3399 lines (29%) are
not.
  First few lines:
    • R/averageQuantile.R#L49 # - - - - - - - - - - - - - - - - - - ...
    • ...
    • man/wpca.Rd#L230 \pkg{pcurve}. ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 2 WARNINGS | ℹ 17 NOTES
ℹ See the aroma.light.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.