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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('phantasus_1.33.0.tar.gz','quit-with-status'=TRUE)"
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── Installing phantasus ────────────────────────────────────────────────────────
✔ Package installed successfully
── phantasus session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpj9MzGi/filefecd44e7e84f6/phantasus
→ BiocVersion: 3.24
→ Package: phantasus
→ PackageVersion: 1.33.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/phantasus.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpj9MzGi/filefecd44e7e84f6/phantasus
→ installDir: /tmp/Rtmpj9MzGi/filefecd4668f7e4e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on phantasus ──────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.3 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...
* 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (29%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • phantasus-tutorial.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/phantasus-tutorial.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/appConfig.R (line 46, column 13)
    • install.packages() in R/serve.R (line 54, column 17)
* Checking for library/require of phantasus...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/collapseDataset.R (line 62, column 42)
    • ...
    • R/utils.R (line 243, column 14)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • loadGEO.R (line 530, column 19)
    • loadGEO.R (line 609, column 23)
    • utils.R (line 244, column 20)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/appConfig.R (line 26, column 9)
    • cat() in R/appConfig.R (line 366, column 13)
    • cat() in R/convertByAnnotationDB.R (line 121, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/appConfig.R (line 13, column 16)
    • ...
    • R/utils.R (line 306, column 18)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/appConfig.R (line 25, column 17)
    • ...
    • R/utils.R (line 722, column 29)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/deseqAnalysis.R (line 69, column 14)
    • ...
    • R/utils.R (line 763, column 14)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 2 times:
    • T in R/reproduceInR.R (line 19, column 47)
    • F in R/reproduceInR.R (line 59, column 54)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • loadPreloaded.R (line 39, column 23)
    • loadPreloaded.R (line 42, column 30)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 2 times)
  • <<- in R/serve.R (line 87, column 22)
  • <<- in R/serve.R (line 96, column 18)
! WARNING: Avoid 'Sys.setenv' (found 2 times)
  • Sys.setenv() in R/appConfig.R (line 32, column 5)
  • Sys.setenv() in R/serve.R (line 66, column 9)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
  • suppressWarnings() in R/adjustDataset.R (line 48, column 50)
  • ...
  • suppressWarnings() in R/loadGEO.R (line 516, column 21)
* 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:
    • gseaPlot() (R/gseaPlot.R): 171 lines
    • ...
    • checkGPLsFallback() (R/loadGEO.R): 83 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/fgseaExample.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/getPhantasusConf.Rd
    • man/setupPhantasus.Rd
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading config from /home/biocbuild/bbs-3.24-bioc/R/site-library/opencpu/config/defaults.conf
Loading config from /home/biocbuild/.config/R/opencpu/user.conf
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • generatePreloadedSession.Rd
    • ...
    • write.gct.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 14% of man
pages use at least one of these tags.
  Found in files:
    • es.Rd
    • ...
    • servePhantasus.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • es.Rd
    • ...
    • servePhantasus.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...
ℹ NOTE: Consider shorter lines; 352 lines (8%) are > 80 characters long.
  First few lines:
    • R/adjustDataset.R#L23 #' @return Nothing. Adjusted dataset wil ...
    • ...
    • vignettes/phantasus-tutorial.Rmd#L501 Kleverov, M., Zenkova, D., Kamenev,
    V., ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs.
  First few lines:
    • R/utils.R#L147 DT_meta <- data.frame(matrix(ncol = ...
    • R/utils.R#L239 DT_meta <- data.frame(matrix(ncol = ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 300 lines (7%) are
not.
  First few lines:
    • R/adjustDataset.R#L35 log2 = FALSE, ...
    • ...
    • R/utils.R#L774 sprintf("window.PHANTASUS_BUILD='% ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 5 WARNINGS | ℹ 21 NOTES
ℹ See the phantasus.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.