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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('fCI_1.43.0.tar.gz','quit-with-status'=TRUE)"
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── Installing fCI ──────────────────────────────────────────────────────────────
✔ Package installed successfully
── fCI session metadata ────────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpg7EsiZ/file9933e4850885a/fCI
→ BiocVersion: 3.24
→ Package: fCI
→ PackageVersion: 1.43.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/fCI.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpg7EsiZ/file9933e4850885a/fCI
→ installDir: /tmp/Rtmpg7EsiZ/file9933e142f8b1f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on fCI ────────────────────────────────────────────────────
* 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 3.1 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/Rtmpg7EsiZ/file9933e4850885a/fCI/man/compute.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpg7EsiZ/file9933e4850885a/fCI/man/fci.data.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpg7EsiZ/file9933e4850885a/fCI/man/multi.dimensional.fci.data.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpg7EsiZ/file9933e4850885a/fCI/man/report.target.summary.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpg7EsiZ/file9933e4850885a/fCI/man/setfCI.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpg7EsiZ/file9933e4850885a/fCI/man/show.targets.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, Transcriptomics, DifferentialExpression
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...
! 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...
✖ ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
  • knitr
! WARNING: Vignette(s) missing Vignette metadata. See
https://r-pkgs.org/vignettes.html
  Update the following files:
    • fCI.Rmd
✖ ERROR: 'VignetteEngine' specified but not in the DESCRIPTION.
  Add 'VignetteEngine' to DESCRIPTION from the following:
    • vignettes/fCI.Rmd
! WARNING: Package listed as VignetteEngine or VignetteBuilder but not
currently Suggested.
  Add the following to Suggests in DESCRIPTION:
    • %knitr
! WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette Title}'.
  Update the following files:
    • fCI.Rmd
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • fCI.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/fCI.Rmd
* Checking package installation calls in R code...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
  Found in files:
    • install.packages() in R/callfCI.R (line 211, column 14)
    • install.packages() in R/callfCI.R (line 214, column 11)
    • install.packages() in R/callfCI.R (line 217, column 11)
* Checking for library/require of fCI...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • buildfCI.R (line 18, column 21)
    • ...
    • utils.R (line 71, column 12)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/findDivergencefCI.R (line 119, column 9)
    • cat() in R/postProcessfCI.R (line 27, column 7)
    • cat() in R/precomputefCI.R (line 113, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/buildfCI.R (line 10, column 16)
    • ...
    • R/utils.R (line 91, column 15)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/get.npci.distance.matrix.Rd
ℹ Found @ in man/npci.index.reconsidered.Rd
ℹ Found @ in man/summarize.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
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:
    • _anonymous_.120() (R/buildfCI.R): 110 lines
    • ...
    • _anonymous_.92() (R/plotfCI.R): 58 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/call.npci-methods.Rd
    • ...
    • man/venndiagram-methods.Rd
Warning: 'rgl.init' failed, will use the null device.
See '?rgl.useNULL' for ways to avoid this warning.
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 79 lines (2%) are > 80 characters long.
  First few lines:
    • R/buildfCI.R#L36 #print("You didn't provide either th ...
    • ...
    • vignettes/fCI.Rmd#L352 When multiple biological/technical repli ...
ℹ NOTE: Consider 4 spaces instead of tabs; 220 lines (7%) contain tabs.
  First few lines:
    • R/buildfCI.R#L9 ==0){ ...
    • ...
    • R/utils.R#L73 (abs(x[i]-mean(x))/sd(x))>outline.sd.c ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 798 lines (25%) are
not.
  First few lines:
    • R/buildfCI.R#L7 ...
    • ...
    • vignettes/fCI.Rmd#L342 ...
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 ───────────────────────────────────────────────────
✖ 5 ERRORS | ⚠ 5 WARNINGS | ℹ 17 NOTES
ℹ See the fCI.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.