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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('FindIT2_1.19.0.tar.gz','quit-with-status'=TRUE)"
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── Installing FindIT2 ──────────────────────────────────────────────────────────
✔ Package installed successfully
── FindIT2 session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpMpe3w2/file9a03d2bb99566/FindIT2
→ BiocVersion: 3.24
→ Package: FindIT2
→ PackageVersion: 1.19.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/FindIT2.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpMpe3w2/file9a03d2bb99566/FindIT2
→ installDir: /tmp/RtmpMpe3w2/file9a03d45653535
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on FindIT2 ────────────────────────────────────────────────
* 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 3.5.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
ChipOnChip, Coverage
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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (42%).
* 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:
    • FindIT2.Rmd
* Checking package installation calls in R code...
* Checking for library/require of FindIT2...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/integrateInfo.R (line 255, column 15)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • calcRP.R (line 170, column 37)
    • find_influential_TF.R (line 400, column 39)
    • find_influential_TF.R (line 864, column 49)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/find_influential_TF.R (line 1047, column 12)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/peakGeneCor.R (line 242, column 13)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 29 times)
  • suppressWarnings() in R/calcRP.R (line 72, column 20)
  • ...
  • suppressMessages() in R/peakGeneCor.R (line 267, column 27)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 21
functions greater than 50 lines.
  The longest 5 functions are:
    • findIT_regionRP() (R/find_influential_TF.R): 231 lines
    • ...
    • findIT_TFHit() (R/find_influential_TF.R): 173 lines
* Checking man page documentation...
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 7% of man
pages use at least one of these tags.
  Found in files:
    • test_geneSet.Rd
    • TF_target_database.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • test_geneSet.Rd
    • TF_target_database.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; 182 lines (4%) are > 80 characters long.
  First few lines:
    • R/calcRP.R#L23 #' Please note that because of rtracklay ...
    • ...
    • vignettes/FindIT2.Rmd#L1132 [InteractiveFindIT2](https://github.com/ ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 178 lines (3%) are
not.
  First few lines:
    • R/calcRP.R#L120 call. = FALSE ...
    • ...
    • vignettes/FindIT2.Rmd#L1128 mmAnno_corFil ...
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 | ⚠ 0 WARNINGS | ℹ 15 NOTES
ℹ See the FindIT2.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.