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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('HTqPCR_1.67.0.tar.gz','quit-with-status'=TRUE)"
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── Installing HTqPCR ───────────────────────────────────────────────────────────
✔ Package installed successfully
── HTqPCR session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpa1wFRi/fileb1bce4af5a95c/HTqPCR
→ BiocVersion: 3.24
→ Package: HTqPCR
→ PackageVersion: 1.67.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/HTqPCR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpa1wFRi/fileb1bce4af5a95c/HTqPCR
→ installDir: /tmp/Rtmpa1wFRi/fileb1bce3c9e775b
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on HTqPCR ─────────────────────────────────────────────────
* 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...
* 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: Transcription,
Sequencing, Microarray, Metabolomics, Proteomics, Epigenetics, Cheminformatics,
Transcriptomics, Normalization, Bayesian, Clustering, Regression, ExonArray,
RNASeq, OneChannel, TwoChannel, MicroRNAArray, mRNAMicroarray,
ProprietaryPlatforms, CellBiology, BiomedicalInformatics, FunctionalGenomics,
SystemsBiology, ImmunoOncology, AlternativeSplicing, DifferentialSplicing,
GeneSetEnrichment, BatchEffect, TimeCourse
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 (36%).
* 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:
    • HTqPCR.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • HTqPCR.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • HTqPCR.Rnw
* Checking package installation calls in R code...
* Checking for library/require of HTqPCR...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/cbind.qPCRset.R (line 44, column 21)
    • ...
    • R/ttestCtData.R (line 65, column 30)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • cbind.qPCRset.R (line 11, column 48)
    • ...
    • ttestCtData.R (line 60, column 103)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/filterCtData.R (line 21, column 25)
    • ...
    • print() in R/setCategory.R (line 113, column 25)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/plotCtVariation.R (line 27, column 41)
    • ...
    • R/plotCtVariation.R (line 30, column 56)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/cbind.qPCRset.R (line 20, column 33)
    • ...
    • R/readCtData.R (line 163, column 25)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • clusterCt.R (line 13, column 21)
    • ...
    • plotCtVariation.R (line 20, column 28)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/plotCtPairs.R (line 33, column 9)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 19
functions greater than 50 lines.
  The longest 5 functions are:
    • readCtData() (R/readCtData.R): 154 lines
    • ...
    • plotCtSignificance() (R/plotCtSignificance.R): 121 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/filterCategory.Rd
  • man/plotCtArray.Rd
  • man/setCategory.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • heatmapSig.Rd
  • ...
  • ttestCtData.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; 760 lines (13%) are > 80 characters long.
  First few lines:
    • R/cbind.qPCRset.R#L20 warning(paste(qset.names[i], "has a d ...
    • ...
    • vignettes/HTqPCR.Rnw#L1145 % Use the function \Rfunction{news} to s ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2117 lines (38%) contain tabs.
  First few lines:
    • R/cbind.qPCRset.R#L3 dotsenv <- parent.frame() ...
    • ...
    • vignettes/HTqPCR.Rnw#L178 \includegraphics{objects.png} ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 563 lines (10%) are
not.
  First few lines:
    • R/heatmapSig.R#L14 data <- sapply(qDE, function(x) x$ddCt ...
    • ...
    • vignettes/HTqPCR.Rnw#L974 \item[\Rfunction{rbind}] combines data ...
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 ───────────────────────────────────────────────────
✖ 4 ERRORS | ⚠ 2 WARNINGS | ℹ 18 NOTES
ℹ See the HTqPCR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.