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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('psichomics_1.39.0.tar.gz','quit-with-status'=TRUE)"
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── Installing psichomics ───────────────────────────────────────────────────────
✔ Package installed successfully
── psichomics session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp0xYtds/file1040676e582c0c/psichomics
→ BiocVersion: 3.24
→ Package: psichomics
→ PackageVersion: 1.39.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/psichomics.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp0xYtds/file1040676e582c0c/psichomics
→ installDir: /tmp/Rtmp0xYtds/file1040673418a98
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on psichomics ─────────────────────────────────────────────
* 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 4.0 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...
* 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (17%).
* 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:
    • AS_events_preparation.Rmd
    • custom_data.Rmd
    • GUI_tutorial.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/AS_events_preparation.Rmd
    • ...
    • vignettes/GUI_tutorial.Rmd
* Checking package installation calls in R code...
* Checking for library/require of psichomics...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/analysis_correlation.R (line 153, column 30)
    • ...
    • R/utils.R (line 503, column 38)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/analysis_survival.R (line 662, column 13)
    • ...
    • cat() in R/utils_interface.R (line 543, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/app.R (line 8, column 4)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/events.R (line 790, column 9)
    • ...
    • R/formats_vasttoolsInclusionLevels.R (line 120, column 13)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/data_inclusionLevelsFilter.R (line 67, column 21)
    • R/data_local.R (line 355, column 29)
    • R/formats.R (line 271, column 14)
* Checking parsed R code in R directory, examples, vignettes...
! WARNING: Remove browser() statements (found 1 times)
  • browser() in R/analysis.R (line 2946, column 9)
ℹ NOTE: Avoid '<<-' if possible (found 3 times)
  • <<- in R/analysis.R (line 2491, column 15)
  • <<- in R/data_local.R (line 194, column 15)
  • <<- in R/data_local.R (line 267, column 15)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 37 times)
  • suppressWarnings() in R/analysis_correlation.R (line 459, column 31)
  • ...
  • suppressWarnings() in R/utils.R (line 291, column 16)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 115
functions greater than 50 lines.
  The longest 5 functions are:
    • groupManipulation() (R/groups.R): 579 lines
    • ...
    • pcaServer() (R/analysis_dimReduction_pca.R): 302 lines
* Checking man page documentation...
Registered S3 method overwritten by 'quantmod':
  method            from
  as.zoo.data.frame zoo 
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • discardLowCoveragePSIvalues.Rd
  • ...
  • psichomics.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 4% of man
pages use at least one of these tags.
  Found in files:
    • getGtexTissues.Rd
    • ...
    • psichomics.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • getGtexTissues.Rd
    • ...
    • psichomics.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
ℹ NOTE: skip_on_bioc() found in testthat files: testDiscardLowCoveragePSIs.R
testGeneInfo.R testSRAloading.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 82 lines (0%) are > 80 characters long.
  First few lines:
    • R/analysis_dimReduction_pca.R#L238 #'
    \url{http://www.sthda.com/english/art ...
    • ...
    • vignettes/GUI_tutorial.Rmd#L642 [tutorial-custom-data]: https://nuno-ago
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs.
  First few lines:
    • R/data_inclusionLevels.R#L96 return(NULL) ...
    • R/data_inclusionLevels.R#L97 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1713 lines (6%) are
not.
  First few lines:
    • R/analysis_correlation.R#L13 "splicing quantif ...
    • ...
    • vignettes/custom_data.Rmd#L179 "SRR6368616SJ.out.t ...
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 | ⚠ 1 WARNINGS | ℹ 20 NOTES
ℹ See the psichomics.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.