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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('STRINGdb_2.25.0.tar.gz','quit-with-status'=TRUE)"
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── Installing STRINGdb ─────────────────────────────────────────────────────────
✔ Package installed successfully
── STRINGdb session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp9aJcM4/file147f301e48ac67/STRINGdb
→ BiocVersion: 3.24
→ Package: STRINGdb
→ PackageVersion: 2.25.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/STRINGdb.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp9aJcM4/file147f301e48ac67/STRINGdb
→ installDir: /tmp/Rtmp9aJcM4/file147f30609496a6
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on STRINGdb ───────────────────────────────────────────────
* 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 2.14.0 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp9aJcM4/file147f301e48ac67/STRINGdb/man/coeffOfvar.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp9aJcM4/file147f301e48ac67/STRINGdb/man/delColDf.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp9aJcM4/file147f301e48ac67/STRINGdb/man/diff_exp_example1.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp9aJcM4/file147f301e48ac67/STRINGdb/man/interactions.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Microarray,
RNASeq
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...
! 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:
    • STRINGdb.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • STRINGdb.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/STRINGdb.Rnw
* Checking package installation calls in R code...
* Checking for library/require of STRINGdb...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/rstring.R (line 322, column 9)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • r_utils.R (line 213, column 13)
    • ...
    • rstring.R (line 1412, column 94)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/r_utils.R (line 159, column 5)
    • ...
    • print() in R/rstring.R (line 1707, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/r_utils.R (line 135, column 8)
    • R/rstring.R (line 1114, column 16)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/r_utils.R (line 135, column 14)
    • ...
    • R/rstring.R (line 1114, column 22)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 2 times:
    • T in R/r_utils.R (line 187, column 48)
    • F in R/r_utils.R (line 202, column 15)
! WARNING: .Deprecated / .Defunct usage (found 10 times)
  • .Deprecated() in R/rstring.R (line 1469, column 7)
  • ...
  • .Deprecated() in R/rstring.R (line 1908, column 7)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 28 times)
  • <<- in R/rstring.R (line 95, column 17)
  • ...
  • <<- in R/rstring.R (line 1449, column 19)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 10
functions greater than 50 lines.
  The longest 5 functions are:
    • get_enrichment_figure() (R/rstring.R): 121 lines
    • ...
    • benchmark_ppi() (R/rstring.R): 93 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/downloadAbsentFile.Rd
    • ...
    • man/set_background.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • delColDf.Rd
    • ...
    • renameColDf.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...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 573 lines (15%) are > 80 characters long.
  First few lines:
    • R/r_utils.R#L8 postFormSmart <- function(uri, .params = ...
    • ...
    • vignettes/STRINGdb.Rnw#L407 Szklarczyk D, Kirsch R, Koutrouli M, Nas ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1315 lines (35%) are
not.
  First few lines:
    • R/r_utils.R#L9 res <- POST(url = uri, body = .params, ...
    • ...
    • vignettes/STRINGdb.Rnw#L406 ...
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 | ⚠ 6 WARNINGS | ℹ 16 NOTES
ℹ See the STRINGdb.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.