##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('genArise_1.89.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing genArise ─────────────────────────────────────────────────────────
✔ Package installed successfully
── genArise session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpUJhuBt/filea2c916b55ea6b/genArise
→ BiocVersion: 3.24
→ Package: genArise
→ PackageVersion: 1.89.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/genArise.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpUJhuBt/filea2c916b55ea6b/genArise
→ installDir: /tmp/RtmpUJhuBt/filea2c911daf664f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on genArise ───────────────────────────────────────────────
* 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 1.7.1 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/RtmpUJhuBt/filea2c916b55ea6b/genArise/man/analysis.window.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUJhuBt/filea2c916b55ea6b/genArise/man/genArise.init.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUJhuBt/filea2c916b55ea6b/genArise/man/graphic.choose.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUJhuBt/filea2c916b55ea6b/genArise/man/help.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUJhuBt/filea2c916b55ea6b/genArise/man/note.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUJhuBt/filea2c916b55ea6b/genArise/man/old.project.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUJhuBt/filea2c916b55ea6b/genArise/man/principal.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUJhuBt/filea2c916b55ea6b/genArise/man/projects.select.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUJhuBt/filea2c916b55ea6b/genArise/man/set.grid.properties.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUJhuBt/filea2c916b55ea6b/genArise/man/set.path.project.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUJhuBt/filea2c916b55ea6b/genArise/man/set.project.properties.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUJhuBt/filea2c916b55ea6b/genArise/man/swap.select.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUJhuBt/filea2c916b55ea6b/genArise/man/trim.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: GUI
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...
ℹ NOTE: License 'file LICENSE' unknown; refer to
$R_HOME/share/licenses/license.db
ℹ and https://choosealicense.com/appendix/ for more info.
* 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:
    • genArise.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • genArise.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/genArise.Rnw
* Checking package installation calls in R code...
* Checking for library/require of genArise...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/applications.R (line 2, column 1)
    • ...
    • require() in R/operations.R (line 1, column 1)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/input.R (line 40, column 16)
    • ...
    • R/Zscore.R (line 46, column 39)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • applications.R (line 192, column 16)
    • ...
    • Zscore.R (line 33, column 31)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/base.R (line 61, column 3)
    • ...
    • cat() in R/postAnalysis.R (line 99, column 5)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 35 times:
    • F in R/baseGUI.R (line 135, column 55)
    • ...
    • F in R/openProyect.R (line 13, column 20)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/applications.R (line 47, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 13 times)
  • <<- in R/applications.R (line 159, column 14)
  • ...
  • <<- in R/genArise.R (line 8, column 14)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 24
functions greater than 50 lines.
  The longest 5 functions are:
    • analysis.window() (R/baseGUI.R): 633 lines
    • ...
    • swap.select() (R/openswap.R): 224 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/classes.Rd
    • ...
    • man/Zscore.points.Rd
Warning in fun(libname, pkgname) : couldn't connect to display ":1.0"
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • analysis.window.Rd
    • ...
    • Zscore.points.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; 784 lines (14%) are > 80 characters long.
  First few lines:
    • R/applications.R#L5 annotations <- function(specie.data, sp ...
    • ...
    • vignettes/genArise.Rnw#L649 Clicking the \textbf{Zscore} option menu ...
ℹ NOTE: Consider 4 spaces instead of tabs; 160 lines (3%) contain tabs.
  First few lines:
    • R/classes.R#L8 representation(name ="character", spo ...
    • ...
    • vignettes/genArise.Rnw#L301 \caption{Filtered data, R vs I plot. \la ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2337 lines (41%) are
not.
  First few lines:
    • R/applications.R#L6 species <- c("Mus musculus","Saccharom ...
    • ...
    • vignettes/genArise.Rnw#L638 Two factors are computed to describe th ...
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 | ⚠ 5 WARNINGS | ℹ 19 NOTES
ℹ See the genArise.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.