##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('pathwayPCA_1.29.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing pathwayPCA ───────────────────────────────────────────────────────
✔ Package installed successfully
── pathwayPCA session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpqUU7Gx/filefd69f3e01e26a/pathwayPCA
→ BiocVersion: 3.24
→ Package: pathwayPCA
→ PackageVersion: 1.29.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/pathwayPCA.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpqUU7Gx/filefd69f3e01e26a/pathwayPCA
→ installDir: /tmp/RtmpqUU7Gx/filefd69f79149a72
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on pathwayPCA ─────────────────────────────────────────────
* 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 3.1 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...
ℹ NOTE: Consider adding these automatically suggested biocViews:
ExperimentalDesign
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...
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • Supplement1-Quickstart_Guide.Rmd
    • ...
    • Supplement5-Analyse_Results.Rmd
* Checking package installation calls in R code...
* Checking for library/require of pathwayPCA...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/aesPC_extract_OmicsPath_PCs.R (line 124, column 50)
    • ...
    • library() in R/superPC_wrapper.R (line 214, column 50)
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/createOmics_CheckAssay.R (line 99, column 7)
    • ...
    • print() in R/utils_load_test_data_onto_PCs.R (line 88, column 5)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/createOmics_Wrapper.R (line 140, column 10)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/aesPC_calculate_AESPCA.R (line 157, column 15)
    • R/superPC_model_train.R (line 89, column 10)
    • R/superPC_model_train.R (line 93, column 10)
* 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 26
functions greater than 50 lines.
  The longest 5 functions are:
    • definition() (R/superPC_wrapper.R): 246 lines
    • ...
    • superpc.st() (R/superPC_model_tStats.R): 147 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • aespca.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:
    • aespca.Rd
    • CreateOmicsPathway.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • aespca.Rd
    • CreateOmicsPathway.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; 380 lines (4%) are > 80 characters long.
  First few lines:
    • R/accessClass_pathwayCollection.R#L24 #' object, then create a new one
    with ...
    • ...
    • vignettes/Supplement5-Analyse_Results.Rmd#L494 We are exploring options
    to connect this ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2307 lines (22%) are
not.
  First few lines:
    • R/accessClass_OmicsPath.R#L84 function(object, ...){ ...
    • ...
    • vignettes/Supplement5-Analyse_Results.Rmd#L478 ) ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | ℹ 15 NOTES
ℹ See the pathwayPCA.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.