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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('survcomp_1.63.0.tar.gz','quit-with-status'=TRUE)"
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── Installing survcomp ─────────────────────────────────────────────────────────
✔ Package installed successfully
── survcomp session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpX45NJ3/file148dac7e590d31/survcomp
→ BiocVersion: 3.24
→ Package: survcomp
→ PackageVersion: 1.63.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/survcomp.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpX45NJ3/file148dac7e590d31/survcomp
→ installDir: /tmp/RtmpX45NJ3/file148dac63cd3d87
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on survcomp ───────────────────────────────────────────────
* 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 3.4 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/RtmpX45NJ3/file148dac7e590d31/survcomp/man/breastCancerData.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX45NJ3/file148dac7e590d31/survcomp/man/mainz7g.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX45NJ3/file148dac7e590d31/survcomp/man/nki7g.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX45NJ3/file148dac7e590d31/survcomp/man/transbig7g.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX45NJ3/file148dac7e590d31/survcomp/man/unt7g.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX45NJ3/file148dac7e590d31/survcomp/man/upp7g.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX45NJ3/file148dac7e590d31/survcomp/man/vdx7g.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Regression,
Survival
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...
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...
ℹ NOTE: Provide '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...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • survcomp.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • survcomp.Rnw
* Checking package installation calls in R code...
* Checking for library/require of survcomp...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/fisherz.R (line 18, column 35)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • balanced.hazard.ratio.R (line 47, column 14)
    • ...
    • td.sens.spec.R (line 59, column 51)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/km.coxph.plot.R (line 36, column 27)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/balanced.hazard.ratio.R (line 8, column 21)
    • ...
    • R/no.at.risk.R (line 7, column 11)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/mrmr.cindex.R (line 48, column 33)
    • R/mrmr.cindex.R (line 53, column 33)
    • R/mrmr.cindex.R (line 63, column 33)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • cvpl.R (line 40, column 30)
    • D.index.R (line 47, column 22)
    • hazard.ratio.R (line 33, column 22)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/cvpl.R (line 25, column 17)
* 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 12
functions greater than 50 lines.
  The longest 5 functions are:
    • `forestplot.surv`() (R/forestplot.surv.R): 143 lines
    • ...
    • `balanced.hazard.ratio`() (R/balanced.hazard.ratio.R): 73 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/concordanceIndexC.Rd
    • ...
    • man/mrmr_cIndex.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • concordanceIndexC.Rd
  • ...
  • mrmr.cindex.ensemble.Rd
* 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; 600 lines (13%) are > 80 characters long.
  First few lines:
    • R/balanced.hazard.ratio.R#L2 function(x, surv.time, surv.event, alpha ...
    • ...
    • vignettes/survcomp.Rnw#L940 \newblock Frequency distribution of the ...
ℹ NOTE: Consider 4 spaces instead of tabs; 857 lines (18%) contain tabs.
  First few lines:
    • R/bhr.comp.R#L3 if(bhr1$n != bhr2$n) { stop("the balanc ...
    • ...
    • man/sbrier.score2proba.Rd#L29 Andersen, P. K. and Borgan, O. and Gill ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 694 lines (15%) are
not.
  First few lines:
    • R/censor.time.R#L4 sec <- surv.event ...
    • ...
    • vignettes/survcomp.Rnw#L767 ccmData <- rbind(ccmData, tt) ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 5 WARNINGS | ℹ 19 NOTES
ℹ See the survcomp.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.