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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('CFAssay_1.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing CFAssay ──────────────────────────────────────────────────────────
✔ Package installed successfully
── CFAssay session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp9A1yZh/file642d25fdccd4c/CFAssay
→ BiocVersion: 3.24
→ Package: CFAssay
→ PackageVersion: 1.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/CFAssay.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp9A1yZh/file642d25fdccd4c/CFAssay
→ installDir: /tmp/Rtmp9A1yZh/file642d26d0f1522
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CFAssay ────────────────────────────────────────────────
* 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 2.10.0 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp9A1yZh/file642d25fdccd4c/CFAssay/man/pes.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp9A1yZh/file642d25fdccd4c/CFAssay/man/plotExp.default.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp9A1yZh/file642d25fdccd4c/CFAssay/man/plotExp.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp9A1yZh/file642d25fdccd4c/CFAssay/man/print.cellsurvLQdiff.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp9A1yZh/file642d25fdccd4c/CFAssay/man/sfpmean.Rd'
* 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...
! WARNING: 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...
✖ 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:
    • cfassay.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • cfassay.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/cfassay.Rnw
* Checking package installation calls in R code...
* Checking for library/require of CFAssay...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/cellsurvLQdiff.R (line 46, column 8)
    • ...
    • R/sfpmean.R (line 37, column 12)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • cellsurvLQdiff.R (line 46, column 15)
    • ...
    • sfpmean.R (line 42, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/cellsurvLQdiff.R (line 3, column 33)
    • ...
    • print() in R/cfa2way.R (line 35, column 11)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • plot.cellsurvLQfit.R (line 4, column 23)
    • ...
    • print.cfa2way.R (line 27, column 27)
* 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 7
functions greater than 50 lines.
  The longest 5 functions are:
    • cellsurvLQdiff() (R/cellsurvLQdiff.R): 142 lines
    • ...
    • print.cellsurvLQfit() (R/print.cellsurvLQfit.R): 81 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/plot.cellsurvLQfit.Rd
    • ...
    • man/print.cfa2way.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 23% of man
pages use at least one of these tags.
  Found in files:
    • plotExp.default.Rd
    • plotExp.Rd
    • sfpmean.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • plotExp.default.Rd
    • plotExp.Rd
    • sfpmean.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; 213 lines (13%) are > 80 characters long.
  First few lines:
    • R/cellsurvLQdiff.R#L10 lcells <- NULL # to suppress R CMD ch ...
    • ...
    • vignettes/cfassay.Rnw#L170 Detailed results are shown with function ...
ℹ NOTE: Consider 4 spaces instead of tabs; 633 lines (39%) contain tabs.
  First few lines:
    • R/cellsurvLQdiff.R#L3 catln <- function(...) {cat(...,"\n")} ...
    • ...
    • vignettes/cfassay.Rnw#L108 plotExp(fit) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 89 lines (5%) are not.
  First few lines:
    • R/cfa2way.R#L22 X$lnS <- log(X$ncolonies/X$ncells) ...
    • ...
    • vignettes/cfassay.Rnw#L179 dev.off() ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 4 WARNINGS | ℹ 16 NOTES
ℹ See the CFAssay.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.