##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('attract_1.65.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing attract ──────────────────────────────────────────────────────────
✔ Package installed successfully
── attract session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpbfwChA/file5781f3fd8f5ad/attract
→ BiocVersion: 3.24
→ Package: attract
→ PackageVersion: 1.65.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/attract.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpbfwChA/file5781f3fd8f5ad/attract
→ installDir: /tmp/RtmpbfwChA/file5781f1507ed24
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on attract ────────────────────────────────────────────────
* 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 3.4.0 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpbfwChA/file5781f3fd8f5ad/attract/man/getCustomGenes.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpbfwChA/file5781f3fd8f5ad/attract/man/getPwayGenes.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
Clustering
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 (33%).
* 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:
    • attract.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • attract.Rnw
* Checking package installation calls in R code...
* Checking for library/require of attract...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/findAttractorsStep.R (line 74, column 5)
    • ...
    • require() in R/findFuncEnrichAndCorr.R (line 31, column 13)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/findAttractorsStep.R (line 55, column 19)
    • ...
    • R/findFuncEnrichAndCorr.R (line 79, column 27)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • findAttractorsStep.R (line 96, column 82)
    • ...
    • removeFlatGenesStep.R (line 32, column 40)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/findSynexprsStep.R (line 20, column 9)
    • print() in R/findSynexprsStep.R (line 26, column 13)
    • print() in R/findSynexprsStep.R (line 35, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/findAttractorsStep.R (line 326, column 57)
    • R/findAttractorsStep.R (line 327, column 50)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/findAttractorsStep.R (line 98, column 18)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • findSynexprsStep.R (line 21, column 26)
    • findSynexprsStep.R (line 93, column 52)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/findSynexprs.Rd
ℹ Found @ in vignettes/attract.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 4
functions greater than 50 lines.
  The longest 5 functions are:
    • findAttractors() (R/findAttractorsStep.R): 286 lines
    • ...
    • calcFuncSynexprs() (R/findFuncEnrichAndCorr.R): 58 lines
* Checking man page documentation...


ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 21% of man
pages use at least one of these tags.
  Found in files:
    • attract-package.Rd
    • ...
    • calcRss.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • attract-package.Rd
    • ...
    • calcRss.Rd
* Checking package NEWS...
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 414 lines (19%) are > 80 characters long.
  First few lines:
    • R/classdef.R#L4 cellTypeTag="character", incidenceMat ...
    • ...
    • vignettes/attract.Rnw#L331 [4] Mar JC, Wells CA, Quackenbush J. 201 ...
ℹ NOTE: Consider 4 spaces instead of tabs; 358 lines (16%) contain tabs.
  First few lines:
    • R/classdef.R#L4 cellTypeTag="character", incidenceMat ...
    • ...
    • vignettes/attract.Rnw#L266 \caption{Average Expression Profiles of ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 171 lines (8%) are
not.
  First few lines:
    • R/findAttractorsStep.R#L326 names(namesInMatrix)[which(is.na(n ...
    • ...
    • vignettes/attract.Rnw#L311 ,analysis= ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 3 WARNINGS | ℹ 19 NOTES
ℹ See the attract.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.