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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('GEM_1.39.0.tar.gz','quit-with-status'=TRUE)"
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── Installing GEM ──────────────────────────────────────────────────────────────
✔ Package installed successfully
── GEM session metadata ────────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpb4pJ5Y/filea25a67a37a0a1/GEM
→ BiocVersion: 3.24
→ Package: GEM
→ PackageVersion: 1.39.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/GEM.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpb4pJ5Y/filea25a67a37a0a1/GEM
→ installDir: /tmp/Rtmpb4pJ5Y/filea25a61c447ce2
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GEM ────────────────────────────────────────────────────
* 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 3.3 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/Rtmpb4pJ5Y/filea25a67a37a0a1/GEM/man/SlicedData-class.Rd'
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • user_guide.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/user_guide.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/Rtmpb4pJ5Y/filea25a67a37a0a1/GEM/vignettes/user_guide.Rmd
* Checking package installation calls in R code...
* Checking for library/require of GEM...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/Matrix_eQTL_engine2.R (line 1559, column 20)
    • ...
    • R/Matrix_eQTL_engine2.R (line 1562, column 20)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • GEM_model.R (line 312, column 22)
    • ...
    • Matrix_eQTL_engine2.R (line 1835, column 19)
✖ ERROR: Use double colon for qualified imports: 'pkg::foo()'
  Found in files:
    • Matrix_eQTL_engine2.R (line 425, column 58)
    • ...
    • Matrix_eQTL_engine2.R (line 868, column 75)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/GEM_model.R (line 86, column 9)
    • ...
    • print() in R/GEM_model.R (line 333, column 19)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/GEM_GUI.R (line 218, column 19)
    • ...
    • R/Matrix_eQTL_engine2.R (line 1922, column 18)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • Matrix_eQTL_engine2.R (line 45, column 58)
    • ...
    • Matrix_eQTL_engine2.R (line 1141, column 39)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 78 times)
  • <<- in R/Matrix_eQTL_engine2.R (line 32, column 44)
  • ...
  • <<- in R/Matrix_eQTL_engine2.R (line 956, column 55)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/Matrix_eQTL_engine2.R (line 83, column 48)
  • suppressWarnings() in R/Matrix_eQTL_engine2.R (line 1270, column 41)
* 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:
    • Matrix_eQTL_engine2() (R/Matrix_eQTL_engine2.R): 769 lines
    • ...
    • LoadFile() (R/Matrix_eQTL_engine2.R): 99 lines
* Checking man page documentation...
Warning in fun(libname, pkgname) : couldn't connect to display ":1.0"
* 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; 368 lines (12%) are > 80 characters long.
  First few lines:
    • R/GEM_GUI.R#L1 #' GEM: Fast association study for the i ...
    • ...
    • vignettes/user_guide.Rmd#L190 [3] Teh AL, Pan H, Chen L, Ong ML, Dogra
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 93 lines (3%) contain tabs.
  First few lines:
    • R/Matrix_eQTL_engine2.R#L49 # rns ...
    • ...
    • vignettes/user_guide.Rmd#L115 2.5 **snp.txt** - A subset of genotype d
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 700 lines (23%) are
not.
  First few lines:
    • R/GEM_GUI.R#L75 covariate ...
    • ...
    • vignettes/user_guide.Rmd#L17 ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 2 WARNINGS | ℹ 16 NOTES
ℹ See the GEM.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.