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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('AMARETTO_1.29.0.tar.gz','quit-with-status'=TRUE)"
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── Installing AMARETTO ─────────────────────────────────────────────────────────
✔ Package installed successfully
── AMARETTO session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpv9bhy4/file53d2b7c96aa4d/AMARETTO
→ BiocVersion: 3.24
→ Package: AMARETTO
→ PackageVersion: 1.29.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/AMARETTO.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpv9bhy4/file53d2b7c96aa4d/AMARETTO
→ installDir: /tmp/Rtmpv9bhy4/file53d2b3598cf2f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on AMARETTO ───────────────────────────────────────────────
* 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 3.6 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...
ℹ NOTE: Consider adding these automatically suggested biocViews:
NetworkInference, Pathways, 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...
✖ 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...
ℹ Bioconductor dependencies found in Imports & Depends (16%).
* 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:
    • amaretto.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/Rtmpv9bhy4/file53d2b7c96aa4d/AMARETTO/vignettes/amaretto.Rmd
* Checking package installation calls in R code...
* Checking for library/require of AMARETTO...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/amaretto_htmlreport.R (line 184, column 46)
    • ...
    • R/amaretto_preprocess.R (line 628, column 9)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • amaretto_download.R (line 255, column 37)
    • ...
    • amaretto_run.R (line 310, column 22)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/amaretto_download.R (line 101, column 17)
    • ...
    • print() in R/amaretto_vizualize.R (line 158, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/amaretto_download.R (line 29, column 13)
    • ...
    • R/amaretto_vizualize.R (line 134, column 14)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/amaretto_download.R (line 147, column 21)
    • R/amaretto_functions.R (line 66, column 14)
! WARNING: Remove set.seed usage (found 3 times)
  • set.seed() in R/amaretto_functions.R (line 69, column 7)
  • set.seed() in R/amaretto_run.R (line 123, column 15)
  • set.seed() in R/amaretto_run.R (line 151, column 23)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 6 times)
  • suppressMessages() in R/amaretto_download.R (line 39, column 13)
  • ...
  • suppressWarnings() in R/amaretto_vizualize.R (line 144, column 7)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 11
functions greater than 50 lines.
  The longest 5 functions are:
    • AMARETTO_HTMLreport() (R/amaretto_htmlreport.R): 195 lines
    • ...
    • AMARETTO_LearnRegulatoryProgramsLarsen() (R/amaretto_run.R): 120 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • AMARETTO_HTMLreport.Rd
  • AMARETTO_Preprocess.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 5% of man
pages use at least one of these tags.
  Found in files:
    • AMARETTO_HTMLreport.Rd
    • AMARETTO_Initialize.Rd
    • AMARETTO_Preprocess.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • AMARETTO_HTMLreport.Rd
    • AMARETTO_Initialize.Rd
    • AMARETTO_Preprocess.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; 326 lines (12%) are > 80 characters long.
  First few lines:
    • R/amaretto_download.R#L21 #' TargetDirectory <- file.path(getwd(), ...
    • ...
    • vignettes/amaretto.Rmd#L210 "arian serous cystaden ...
ℹ NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain tabs.
  First few lines:
    • vignettes/amaretto.Rmd#L195 1. Champion, M. et al. Module Analysis C ...
    • vignettes/amaretto.Rmd#L196 2. Gevaert, O., Villalobos, V., Sikic, B ...
    • vignettes/amaretto.Rmd#L197 3. Gevaert, O. MethylMix: an R package f ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 754 lines (27%) are
not.
  First few lines:
    • R/amaretto_download.R#L132 # "Max.")], dateData)] ...
    • ...
    • vignettes/amaretto.Rmd#L213 "thymoma","endometrial ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 1 WARNINGS | ℹ 20 NOTES
ℹ See the AMARETTO.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.