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Bioconductor / BiocCheck

http://bioconductor.org/packages/BiocCheck
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One test fails on PPC: Error in checkEqualsNumeric(9, .BiocCheck$getNum("warning")): Mean relative difference: 0.1111111 #188

Open barracuda156 opened 1 year ago

barracuda156 commented 1 year ago 
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: powerpc-apple-darwin10.8.0 (32-bit)

> BiocGenerics:::testPackage("BiocCheck") 
Loading required package: usethis
    * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
      removed
    * ERROR: System files found that should not be Git tracked.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
    * ERROR: Remove whitespace from DESCRIPTION field names.
* Checking for blank lines in DESCRIPTION...
    * ERROR: Remove blank lines from DESCRIPTION.
    * WARNING: Description field in the DESCRIPTION file is too concise
    * NOTE: The Description field in the DESCRIPTION is made up by less
      than 3 sentences. Please consider expanding this field, and
      structure it as a full paragraph
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
    * ERROR: Package directory 'unitTestTempDir' must match Package:
      field (got 'Foo').
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
    * ERROR: No 'Version:' field in DESCRIPTION.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * ERROR: Authors@R must evaluate to 'person' object.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * ERROR: Authors@R field in DESCRIPTION file is malformed.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * ERROR: No Authors@R [cre] field in DESCRIPTION file.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
    * ERROR: Package directory 'unitTestTempDir' must match Package:
      field (got '%s unitTestTempDir').
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
    * ERROR: Use Authors@R field not Author/Maintainer fields. Do not
      use both.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * NOTE: Invalid ORCID iD for Bioconductor Package Maintainer
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * ERROR: Do not use Author/Maintainer fields. Use Authors@R.
    * ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * ERROR: Designated only one maintainer with Authors@R [cre].
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* Checking that provided CITATION file is correctly formatted...
* Checking that provided CITATION file is correctly formatted...
    * NOTE: CITATION file might be not correctly formatted
    * ERROR: Remove 'testpkg.BiocCheck' from the package directory
* Checking that biocViews are present...
    * ERROR: No biocViews terms found.
* 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...
    * WARNING: Invalid BiocViews term(s):
* Checking for recommended 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...
* 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...
    * WARNING: Use biocViews from one category only (one of Software,
      ExperimentData, AnnotationData, Workflow)
    * ERROR: Use 'BiocParallel' instead of 'multicore'. 'multicore' is
      deprecated and does not work on Windows.
    * ERROR: At least 80% of man pages documenting exported objects
      must have runnable examples.
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 67% of man pages use at least one of these tags.
    * NOTE: Use donttest{} instead of dontrun{}.
    Found @ in ./FooBar
    * NOTE: Use accessors; don't access S4 class slots via '@' in
      examples/vignettes.
    Found install() in R/bad_coding.R (line 41, column 18)
    Found install() in vignettes/testpkg0.Rmd
    * WARNING: Avoid the use of 'library' or 'require' in R code
    * NOTE: Auto-generated '%% ~' comments found in Rd man pages.
    Maintainer is registered at support site.
    * ERROR: Maintainer must register at the support site; visit
      https://support.bioconductor.org/accounts/signup/
    Maintainer is registered at support site.
    Package name is in support site watched tags.
    * ERROR: Maintainer must add package name to Watched Tags on the
      support site; Edit your Support Site User Profile to add Watched
      Tags.
    Package name is in support site watched tags.
    Package name is in support site watched tags.

    * ERROR: Version number in tarball filename must match Version
      field in DESCRIPTION. (Tip: create tarball with R CMD build)
    * NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 1 lines
      (0%) are not.
    See https://contributions.bioconductor.org/r-code.html
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking License: for restrictive use...
* Checking License: for restrictive use...
    * ERROR: License 'CC BY-NC-ND 4.0' restricts use
* Checking License: for restrictive use...
    * ERROR: License 'CC BY-NC-ND 4.0 + file LICENSE' restricts use
* Checking License: for restrictive use...
    * NOTE: License 'UNKNOWN' unknown; licenses cannot restrict use
* Checking License: for restrictive use...
    * NOTE: malformed 'License:' field 'NA'
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
    * WARNING: Fix formatting of NEWS.Rd. Malformed package NEWS will
      not be included in Bioconductor release announcements.
    * NOTE: More than 1 NEWS file found. See ?news for recognition
      ordering.
    * WARNING: Fix formatting of NEWS.Rd. Malformed package NEWS will
      not be included in Bioconductor release announcements.
    * WARNING: New package x version starting with non-zero value
      (e.g., 1.y.z, 2.y.z); got '1.99.3'.
    * ERROR: New package 'y' version not 99 (i.e., x.99.z); Package
      version: 0.2.3
    * NOTE: Update R version dependency from 1.0.0 to 4.2.0.
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      https://contributions.bioconductor.org/tests.html
    * NOTE: skip_on_bioc() found in testthat files: a_test.R
$undefined
$undefined$checkLazyDataUsage
$undefined$checkLazyDataUsage[[1]]
[1] "* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed"

$undefined$checkBadFiles
$undefined$checkBadFiles[[1]]
[1] "* ERROR: System files found that should not be Git tracked."

$undefined$checkBadFiles[[2]]
[1] "something.Rproj"

$`* Checking for blank lines in DESCRIPTION...`
list()

$`* Checking if DESCRIPTION is well formatted...`
list()

$`* Checking for proper Description: field...`
list()

$`* Checking for whitespace in DESCRIPTION field names...`
list()

$`* Checking that Package field matches directory/tarball name...`
list()

$`* Checking for Version field...`
list()

$`* Checking for valid maintainer...`
$`* Checking for valid maintainer...`$checkBBScompatibility
$`* Checking for valid maintainer...`$checkBBScompatibility[[1]]
[1] "* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with 'comment=c(ORCID=\"...\")'"

$`* Checking that provided CITATION file is correctly formatted...`
$`* Checking that provided CITATION file is correctly formatted...`$`3`
$`* Checking that provided CITATION file is correctly formatted...`$`3`[[1]]
[1] "* NOTE: CITATION file might be not correctly formatted"

$`* Checking that provided CITATION file is correctly formatted...`$checkBiocCheckOutputFolder
$`* Checking that provided CITATION file is correctly formatted...`$checkBiocCheckOutputFolder[[1]]
[1] "* ERROR: Remove 'testpkg.BiocCheck' from the package directory"

$`* Checking that biocViews are present...`
list()

$`* Checking package type based on biocViews...`
list()

$`* Checking for non-trivial biocViews...`
list()

$`* Checking that biocViews come from the same category...`
$`* Checking that biocViews come from the same category...`$checkBiocViews
$`* Checking that biocViews come from the same category...`$checkBiocViews[[1]]
[1] "* WARNING: Use biocViews from one category only (one of Software, ExperimentData, AnnotationData, Workflow)"

$`* Checking that biocViews come from the same category...`$checkDeprecatedPackages
$`* Checking that biocViews come from the same category...`$checkDeprecatedPackages[[1]]
[1] "* ERROR: Use 'BiocParallel' instead of 'multicore'. 'multicore' is deprecated and does not work on Windows."

$`* Checking that biocViews come from the same category...`$checkDescriptionNamespaceConsistency
$`* Checking that biocViews come from the same category...`$checkDescriptionNamespaceConsistency[[1]]
[1] "* WARNING: Import devtools in NAMESPACE as well as DESCRIPTION."

$`* Checking that biocViews come from the same category...`$checkDescriptionNamespaceConsistency
$`* Checking that biocViews come from the same category...`$checkDescriptionNamespaceConsistency[[1]]
[1] "* WARNING: Import BiocCheck in NAMESPACE as well as DESCRIPTION."

$`* Checking that biocViews come from the same category...`$checkDescriptionNamespaceConsistency
$`* Checking that biocViews come from the same category...`$checkDescriptionNamespaceConsistency[[1]]
[1] "* WARNING: Import devtools in DESCRIPTION as well as NAMESPACE."

$`* Checking that biocViews come from the same category...`$checkExportsAreDocumented
$`* Checking that biocViews come from the same category...`$checkExportsAreDocumented[[1]]
[1] "* ERROR: At least 80% of man pages documenting exported objects must have runnable examples."

$`* Checking that biocViews come from the same category...`$checkExportsAreDocumented[[2]]
[1] "The following pages do not:"

$`* Checking that biocViews come from the same category...`$checkExportsAreDocumented[[3]]
[1] "baddep.Rd"

$`* Checking that biocViews come from the same category...`$checkUsageOfDont
$`* Checking that biocViews come from the same category...`$checkUsageOfDont[[1]]
[1] "* NOTE: Usage of dontrun{} / donttest{} tags found in man page examples. 67% of man pages use at least one of these tags."

$`* Checking that biocViews come from the same category...`$checkUsageOfDont[[2]]
[1] "Found in files:"

$`* Checking that biocViews come from the same category...`$checkUsageOfDont[[3]]
[1] "a.Rd"      "baddep.Rd"

$`* Checking that biocViews come from the same category...`$checkUsageOfDont
$`* Checking that biocViews come from the same category...`$checkUsageOfDont[[1]]
[1] "* NOTE: Use donttest{} instead of dontrun{}."

$`* Checking that biocViews come from the same category...`$checkUsageOfDont[[2]]
[1] "Found in files:"

$`* Checking that biocViews come from the same category...`$checkUsageOfDont[[3]]
[1] "baddep.Rd"

$`* Checking that biocViews come from the same category...`$checkForDirectSlotAccess
$`* Checking that biocViews come from the same category...`$checkForDirectSlotAccess[[1]]
[1] "* NOTE: Use accessors; don't access S4 class slots via '@' in examples/vignettes."

$`* Checking that biocViews come from the same category...`$checkForLibraryRequire
$`* Checking that biocViews come from the same category...`$checkForLibraryRequire[[1]]
[1] "* WARNING:  Avoid the use of 'library' or 'require' in R code"

$`* Checking that biocViews come from the same category...`$checkForLibraryRequire[[2]]
[1] "Found in files:"

$`* Checking that biocViews come from the same category...`$checkForLibraryRequire[[3]]
 [1] "library() in R/requireme.R (line  3, column 5)"
 [2] "library() in R/requireme.R (line  5, column 5)"
 [3] "library() in R/requireme.R (line  7, column 5)"
 [4] "library() in R/requireme.R (line  8, column 5)"
 [5] "library() in R/requireme.R (line 13, column 5)"
 [6] "require() in R/requireme.R (line  4, column 5)"
 [7] "require() in R/requireme.R (line  6, column 5)"
 [8] "require() in R/requireme.R (line  9, column 5)"
 [9] "require() in R/requireme.R (line 10, column 5)"
[10] "require() in R/requireme.R (line 11, column 5)"
[11] "require() in R/requireme.R (line 12, column 5)"
[12] "require() in R/requireme.R (line 14, column 5)"
[13] "require() in R/requireme.R (line 17, column 5)"
[14] "require() in R/requireme.R (line 18, column 5)"

$`* Checking that biocViews come from the same category...`$checkForPromptComments
$`* Checking that biocViews come from the same category...`$checkForPromptComments[[1]]
[1] "* NOTE: Auto-generated '%% ~' comments found in Rd man pages."

$`* Checking that biocViews come from the same category...`$checkForPromptComments[[2]]
[1] "a.Rd"      "baddep.Rd"

$`* Checking that biocViews come from the same category...`$checkSupportReg
$`* Checking that biocViews come from the same category...`$checkSupportReg[[1]]
[1] "* ERROR: Maintainer must register at the support site; visit https://support.bioconductor.org/accounts/signup/"

$`* Checking that biocViews come from the same category...`$checkWatchedTag
$`* Checking that biocViews come from the same category...`$checkWatchedTag[[1]]
[1] "* ERROR: Maintainer must add package name to Watched Tags on the support site; Edit your Support Site User Profile to add Watched Tags."

$`* Checking that biocViews come from the same category...`$checkForVersionNumberMismatch
$`* Checking that biocViews come from the same category...`$checkForVersionNumberMismatch[[1]]
[1] "* ERROR: Version number in tarball filename must match Version field in DESCRIPTION. (Tip: create tarball with R CMD build)"

$`* Checking that biocViews come from the same category...`$checkFormatting
$`* Checking that biocViews come from the same category...`$checkFormatting[[1]]
[1] "* NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters long."

$`* Checking that biocViews come from the same category...`$checkFormatting[[2]]
[1] "First few lines:"

$`* Checking that biocViews come from the same category...`$checkFormatting[[3]]
[1] "R/morebadcode.R#L2 # this is a really long line with many c..."

$`* Checking that biocViews come from the same category...`$checkFormatting
$`* Checking that biocViews come from the same category...`$checkFormatting[[1]]
[1] "* NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs."

$`* Checking that biocViews come from the same category...`$checkFormatting[[2]]
[1] "First few lines:"

$`* Checking that biocViews come from the same category...`$checkFormatting[[3]]
[1] "man/a.Rd#L48 ##--\tor do  help(data=index)  for the st..."     
[2] "man/baddep.Rd#L41 ##--\tor do  help(data=index)  for the st..."

$`* Checking that biocViews come from the same category...`$checkFormatting
$`* Checking that biocViews come from the same category...`$checkFormatting[[1]]
[1] "* NOTE: Consider multiples of 4 spaces for line indents; 1 lines (0%) are not."

$`* Checking that biocViews come from the same category...`$checkFormatting[[2]]
[1] "First few lines:"

$`* Checking that biocViews come from the same category...`$checkFormatting[[3]]
[1] "R/morebadcode.R#L6      # something other than a multiple o..."

$`* Checking biocViews validity...`
list()

$`* Checking for recommended biocViews...`
list()

$`* Checking License: for restrictive use...`
$`* Checking License: for restrictive use...`$.checkLicenseForRestrictiveUse
$`* Checking License: for restrictive use...`$.checkLicenseForRestrictiveUse[[1]]
[1] "* NOTE: malformed 'License:' field 'NA'"

$`* Checking License: for restrictive use...`$checkNEWS
$`* Checking License: for restrictive use...`$checkNEWS[[1]]
[1] "* NOTE: Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements."

$`* Checking License: for restrictive use...`$`3`
$`* Checking License: for restrictive use...`$`3`[[1]]
[1] "* WARNING: Fix formatting of NEWS.Rd. Malformed package NEWS will not be included in Bioconductor release announcements."

$`* Checking License: for restrictive use...`$checkNEWS
$`* Checking License: for restrictive use...`$checkNEWS[[1]]
[1] "* NOTE: More than 1  NEWS file found. See ?news for recognition ordering."

$`* Checking License: for restrictive use...`$checkNEWS[[2]]
[1] "Please remove one of the following: "

$`* Checking License: for restrictive use...`$checkNEWS[[3]]
[1] "/inst/NEWS.Rd" "/./NEWS.md"   

$`* Checking License: for restrictive use...`$`3`
$`* Checking License: for restrictive use...`$`3`[[1]]
[1] "* WARNING: Fix formatting of NEWS.Rd. Malformed package NEWS will not be included in Bioconductor release announcements."

$`* Checking License: for restrictive use...`$checkNewPackageVersionNumber
$`* Checking License: for restrictive use...`$checkNewPackageVersionNumber[[1]]
[1] "* WARNING: New package x version starting with non-zero value (e.g., 1.y.z, 2.y.z); got '1.99.3'."

$`* Checking License: for restrictive use...`$checkNewPackageVersionNumber
$`* Checking License: for restrictive use...`$checkNewPackageVersionNumber[[1]]
[1] "* ERROR: New package 'y' version not 99 (i.e., x.99.z); Package version: 0.2.3"

$`* Checking License: for restrictive use...`$checkRVersionDependency
$`* Checking License: for restrictive use...`$checkRVersionDependency[[1]]
[1] "* NOTE: Update R version dependency from 1.0.0 to 4.2.0."

$`* Checking License: for restrictive use...`$checkTFSymbolUsage
$`* Checking License: for restrictive use...`$checkTFSymbolUsage[[1]]
[1] "* WARNING:  Avoid T/F variables; If logical, use TRUE/FALSE"

$`* Checking License: for restrictive use...`$checkTFSymbolUsage[[2]]
[1] "Found in files:"

$`* Checking License: for restrictive use...`$checkTFSymbolUsage[[3]]
[1] "vignettes/testpkg0.Rmd (code line 47, column 5)"

$`* Checking License: for restrictive use...`$checkUnitTests
$`* Checking License: for restrictive use...`$checkUnitTests[[1]]
[1] "* NOTE: Consider adding unit tests. We strongly encourage them. See\n  https://contributions.bioconductor.org/tests.html"

$`* Checking License: for restrictive use...`$checkSkipOnBioc
$`* Checking License: for restrictive use...`$checkSkipOnBioc[[1]]
[1] "* NOTE: skip_on_bioc() found in testthat files: a_test.R"

$`* Checking License: for restrictive use...`$checkUsageOfDont
$`* Checking License: for restrictive use...`$checkUsageOfDont[[1]]
[1] "* NOTE: Usage of dontrun{} / donttest{} tags found in man page examples. 67% of man pages use at least one of these tags."

$`* Checking License: for restrictive use...`$checkUsageOfDont[[2]]
[1] "Found in files:"

$`* Checking License: for restrictive use...`$checkUsageOfDont[[3]]
[1] "a.Rd"      "baddep.Rd"

$`* Checking License: for restrictive use...`$checkUsageOfDont
$`* Checking License: for restrictive use...`$checkUsageOfDont[[1]]
[1] "* NOTE: Use donttest{} instead of dontrun{}."

$`* Checking License: for restrictive use...`$checkUsageOfDont[[2]]
[1] "Found in files:"

$`* Checking License: for restrictive use...`$checkUsageOfDont[[3]]
[1] "baddep.Rd"

    * ERROR: Invalid package Version, see
      https://contributions.bioconductor.org/versionnum.html
    * ERROR: Invalid package Version, see
      https://contributions.bioconductor.org/versionnum.html
    * WARNING: y of x.y.z version should be even in release
    * WARNING: BiocInstaller code found in vignette(s)
    * ERROR: Installation calls found in vignette(s)
    * NOTE: 'sessionInfo' not found in vignette(s)

    * NOTE: The recommended function length is 50 lines or less. There
      are 1660 functions greater than 50 lines.
    * ERROR: Package must be removed from CRAN.
    * ERROR: 'GenomicRanges' already exists in Bioconductor.
    * ERROR: 'GO.db' already exists in Bioconductor.
    * ERROR: 'TENxBrainData' already exists in Bioconductor.
    * ERROR: 'annotation' already exists in Bioconductor.
    * ERROR: Package dependencies must be on CRAN or Bioconductor.
      Remove 'Remotes:' from DESCRIPTION
    * ERROR: No vignette sources in vignettes/ directory.
    * WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette
      Title}'.
    * NOTE: 'sessionInfo' not found in vignette(s)
    * NOTE: 'sessionInfo' not found in vignette(s)
    * WARNING: Remove vignette sources from inst/doc; they belong in
      vignettes/.
    * WARNING: Remove vignette sources from inst/doc; they belong in
      vignettes/.
    * ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
      'VignetteEngine' in any vignettes:
    * WARNING: Package listed as VignetteEngine or VignetteBuilder but
      not currently Suggested.
    * NOTE: 'sessionInfo' not found in vignette(s)
    * NOTE: 'sessionInfo' not found in vignette(s)
    * WARNING: Package listed as VignetteEngine or VignetteBuilder but
      not currently Suggested.
    * NOTE: 'sessionInfo' not found in vignette(s)
    * ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
      'VignetteEngine' in any vignettes:
    * WARNING: Vignette(s) missing Vignette metadata. See
      http://r-pkgs.had.co.nz/vignettes.html
    * ERROR: No 'VignetteEngine' specified in vignette or DESCRIPTION.
    * WARNING: Package listed as VignetteEngine or VignetteBuilder but
      not currently Suggested.
    * WARNING: Vignette(s) still using 'VignetteIndexEntry{Vignette
      Title}'
    * WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette
      Title}'.
    * WARNING: Evaluate more vignette chunks.
        7 code chunks / 14 total = 50% percent unevaluated
        0 non-exec code chunks (e.g., '``` r')
    * WARNING: BiocInstaller code found in vignette(s)
    * ERROR: Installation calls found in vignette(s)
    * WARNING: Avoid class membership checks with class() / is() and ==
      / !=; Use is(x, 'class') for S4 classes
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
    * NOTE: 'sessionInfo' not found in vignette(s)
Timing stopped at: 3.129 0.189 3.439
Error in checkEqualsNumeric(9, .BiocCheck$getNum("warning")) : 
  Mean relative difference: 0.1111111

RUNIT TEST PROTOCOL -- Tue Apr  4 08:42:41 2023 
*********************************************** 
Number of test functions: 51 
Number of errors: 0 
Number of failures: 1 

1 Test Suite : 
BiocCheck RUnit Tests - 51 test functions, 0 errors, 1 failure
FAILURE in test_vignettes0: Error in checkEqualsNumeric(9, .BiocCheck$getNum("warning")) : 
  Mean relative difference: 0.1111111

Test files with failing tests

   test_BiocCheck.R 
     test_vignettes0 

Error in BiocGenerics:::testPackage("BiocCheck") : 
  unit tests failed for package BiocCheck
Execution halted
LiNk-NY commented 1 year ago

Hi @barracuda156 I am unable to reproduce on Linux. Make sure that BiocManager::valid() == TRUE and include more information. -Marcel

barracuda156 commented 4 months ago

@LiNk-NY Sorry for a delay. The error is still there with 3.19. And, well, I do not particularly understand what is it doing:


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: powerpc-apple-darwin10.0.0d2 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> pkgname <- "BiocCheck"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> library('BiocCheck')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
> nameEx("BiocCheck-class")
> ### * BiocCheck-class
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: BiocCheck-class
> ### Title: A class for composing BiocCheck reports.
> ### Aliases: BiocCheck-class
> ### Keywords: internal
> 
> ### ** Examples
> 
> 
> bc <- BiocCheck:::.BiocCheck
> 
> bc$verbose
[1] FALSE
> 
> 
> 
> 
> cleanEx()
> nameEx("BiocCheck")
> ### * BiocCheck
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: BiocCheck
> ### Title: Check a package's adherence with the Bioconductor Package
> ###   Guidelines
> ### Aliases: BiocCheck
> 
> ### ** Examples
> 
> 
> packageDir <- system.file("testpackages", "testpkg0", package="BiocCheck")
> BiocCheck(packageDir, `quit-with-status`=FALSE)
─ BiocCheckVersion: 1.40.0
─ BiocVersion: 3.19
─ Package: testpkg0
─ PackageVersion: 0.1
─ sourceDir: /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-BiocCheck/R-BiocCheck/work/BiocCheck/BiocCheck.Rcheck/BiocCheck/testpackages/testpkg0
─ installDir: /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-BiocCheck/R-BiocCheck/work/.tmp/Rtmp4fj7G4/filed3887dad1836
─ BiocCheckDir: /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-BiocCheck/R-BiocCheck/work/BiocCheck/BiocCheck.Rcheck/BiocCheck/testpackages/testpkg0.BiocCheck
─ platform: unix
─ isTarBall: FALSE

* Installing package...
* Checking for deprecated package usage...
adding rname 'https://bioconductor.org/checkResults/3.19/bioc-LATEST/meat-index.dcf'
adding rname 'https://bioconductor.org/checkResults/3.20/bioc-LATEST/meat-index.dcf'
* Checking for remote package usage...
    * ERROR: Package dependencies must be on CRAN or Bioconductor.
      Remove 'Remotes:' from DESCRIPTION
* Checking for 'LazyData: true' usage...
    * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
      removed
* Checking version number...
* Checking version number validity...
    * ERROR: Invalid package Version, see
      https://contributions.bioconductor.org/versionnum.html
* Checking R version dependency...
    * NOTE: Update R version dependency from 3.1.0 to 4.4.0.
* Checking package size...
    Skipped... only checked on source tarball
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
    * ERROR: No biocViews terms found.
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * WARNING: Description field in the DESCRIPTION file is too concise
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
    * ERROR: Do not use Author/Maintainer fields. Use Authors@R.
    * ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
    * 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 .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking vignette directory...
    * ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
      'VignetteEngine' in any vignettes:
    * WARNING: Vignette(s) missing Vignette metadata. See
      http://r-pkgs.had.co.nz/vignettes.html
    * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
    * ERROR: No 'VignetteEngine' specified in vignette or DESCRIPTION.
    * WARNING: Package listed as VignetteEngine or VignetteBuilder but
      not currently Suggested.
    * WARNING: Vignette(s) still using 'VignetteIndexEntry{Vignette
      Title}'
    * WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette
      Title}'.
    * ERROR: Vignette(s) found with duplicate chunk labels
    * WARNING: BiocInstaller code found in vignette(s)
    * ERROR: Installation calls found in vignette(s)
    * WARNING: Avoid class membership checks with class() / is() and ==
      / !=; Use is(x, 'class') for S4 classes
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
    * NOTE: 'sessionInfo' not found in vignette(s)
* Checking package installation calls in R code...
    * NOTE: Avoid using install, biocLite, install.packages, or
      update.packages
* Checking for library/require of testpkg0...
    * WARNING: Avoid the use of 'library' or 'require' in R code
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
invalid UTF-8 input in readChar()
invalid UTF-8 input in readChar()
invalid UTF-8 input in readChar()
invalid UTF-8 input in readChar()
invalid UTF-8 input in readChar()
invalid UTF-8 input in readChar()
    * ERROR: Use double colon for qualified imports: 'pkg::foo()'
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
    * NOTE: Avoid using '=' for assignment and use '<-' instead
    * NOTE: Avoid the use of 'paste' in condition signals
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
    * WARNING: Avoid class membership checks with class() / is() and ==
      / !=; Use is(x, 'class') for S4 classes
    * ERROR: Avoid references to external hosting platforms
    * ERROR: Avoid downloads in '.onAttach' or '.onLoad' functions
    * WARNING: .Deprecated / .Defunct usage (found 2 times)
* Checking parsed R code in R directory, examples, vignettes...
    * WARNING: Remove browser() statements (found 1 times)
    * ERROR: Remove install() calls (found 2 times)
    * NOTE: Avoid '<<-' if possible (found 1 times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      is 1 function greater than 50 lines.
* Checking man page documentation...
    * NOTE: Auto-generated '%% ~' comments found in Rd man pages.
    * WARNING: Empty or missing \value sections found in man page(s).
    * ERROR: At least 80% of man pages documenting exported objects
      must have runnable examples.
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 67% of man pages use at least one of these tags.
    * NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* Checking unit tests...
    * ERROR: Add a .R or .Rin file in tests/ directory or unit tests
      will not be run by R CMD check. See
      https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
    * NOTE: skip_on_bioc() found in testthat files: a_test.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 52 lines
      (9%) are not.
    See https://contributions.bioconductor.org/r-code.html
    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...
    * 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 results ──
16 ERRORS | 16 WARNINGS | 21 NOTES

See the testpkg0.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.
> 
> 
> 
> 
> cleanEx()
> nameEx("BiocCheckGitClone")
> ### * BiocCheckGitClone
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: BiocCheckGitClone
> ### Title: Checks specific to a Git clone of a package repository
> ### Aliases: BiocCheckGitClone
> 
> ### ** Examples
> 
> 
> packageDir <- system.file("testpackages", "testpkg0", package="BiocCheck")
> BiocCheckGitClone(packageDir, `quit-with-status`=FALSE)
─ BiocCheckVersion: 1.40.0
─ BiocVersion: 3.19
─ Package: testpkg0
─ PackageVersion: 0.1
─ sourceDir: /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-BiocCheck/R-BiocCheck/work/BiocCheck/BiocCheck.Rcheck/BiocCheck/testpackages/testpkg0
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
    * ERROR: Do not use Author/Maintainer fields. Use Authors@R.
* Checking CITATION...
    * NOTE: (Optional) CITATION file not found. Only include a CITATION
      file if there is a preprint or publication for this Bioconductor
      package. Note that Bioconductor packages are not required to have
      a CITATION file but it is useful both for users and for tracking
      Bioconductor project-wide metrics. When including a CITATION
      file, add the publication using the 'doi' argument of
      'bibentry()'.

─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 1 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  20.236 6.077 81.765 30.902 11.068 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: powerpc-apple-darwin10.0.0d2 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("BiocCheck") 
Loading required package: usethis
    * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
      removed
* Checking License: for restrictive use...
    * NOTE: License 'GPL-3.0' unknown; refer to
      $R_HOME/share/licenses/license.db
      and https://choosealicense.com/appendix/ for more info.
* Checking License: for restrictive use...
    * ERROR: System files found that should not be Git tracked.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
    * ERROR: Remove whitespace from DESCRIPTION field names.
* Checking for blank lines in DESCRIPTION...
    * ERROR: Remove blank lines from DESCRIPTION.
    * WARNING: Description field in the DESCRIPTION file is too concise
    * NOTE: The Description field in the DESCRIPTION is made up of less
      than 3 sentences. Provide a more detailed description of the
      package.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
    * ERROR: Package directory 'unitTestTempDir' must match Package:
      field (got 'Foo').
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
    * ERROR: No 'Version:' field in DESCRIPTION.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
    * ERROR: Authors@R must evaluate to 'person' object.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
    * ERROR: Authors@R field in DESCRIPTION file is malformed.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
    * ERROR: No Authors@R [cre] field in DESCRIPTION file.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
    * ERROR: Package directory 'unitTestTempDir' must match Package:
      field (got '%s unitTestTempDir').
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
    * ERROR: Use Authors@R field not Author/Maintainer fields. Do not
      use both.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
    * NOTE: Invalid ORCID iD for Bioconductor Package Maintainer
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
    * ERROR: Do not use Author/Maintainer fields. Use Authors@R.
    * ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
    * ERROR: Designated only one maintainer with Authors@R [cre].
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* Checking that provided CITATION file is correctly formatted...
    * WARNING: The 'doi' argument is missing or empty in the CITATION's
      'bibentry()'. Only include a CITATION file if there is a preprint
      or publication associated with this Bioconductor package.
* Checking that provided CITATION file is correctly formatted...
    * WARNING: Unable to read CITATION file with
      'utils::readCitationFile()'
    * ERROR: Remove 'testpkg.BiocCheck' from the package directory
* Checking that biocViews are present...
    * ERROR: No biocViews terms found.
* 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...
    * WARNING: Invalid BiocViews term(s):
* Checking for recommended biocViews...
No man pages found.
No vignettes found.
* 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...
No man pages found.
No vignettes found.
* 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...
    * WARNING: Use biocViews from one category only (one of Software,
      ExperimentData, AnnotationData, Workflow)
* Checking for recommended DESCRIPTION fields...
    * NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for recommended DESCRIPTION fields...
    * NOTE: Provide 'URL' field(s) in DESCRIPTION
* 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 Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (100%).
* Checking for pinned package versions in DESCRIPTION...
    * ERROR: Dependencies in the DESCRIPTION file contain '=='
    * ERROR: Use 'BiocParallel' instead of 'multicore'. 'multicore' is
      deprecated and does not work on Windows.
    * ERROR: Vignette(s) found with duplicate chunk labels
    * ERROR: At least 80% of man pages documenting exported objects
      must have runnable examples.
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 67% of man pages use at least one of these tags.
    * NOTE: Use donttest{} instead of dontrun{}.
    Found @ in ./FooBar
    * NOTE: Use accessors; don't access S4 class slots via '@' in
      examples/vignettes.
    Found install() in R/bad_coding.R (line 41, column 18)
    Found install() in vignettes/testpkg0.Rmd
    * WARNING: Avoid the use of 'library' or 'require' in R code
    * NOTE: Auto-generated '%% ~' comments found in Rd man pages.
    Maintainer is registered at support site.
    * ERROR: Unable to find your email in the Support Site: HTTP 404
      Not Found.
    Maintainer is registered at support site.
    Package is in the Support Site Watched Tags.
    * ERROR: Add package to Watched Tags in your Support Site profile;
      visit https://support.bioconductor.org/accounts/edit/profile
    Package is in the Support Site Watched Tags.
    Package is in the Support Site Watched Tags.
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-BiocCheck/R-BiocCheck/work/.tmp/Rtmpo0Fa9T/filed552718bdb6f/filed55214f38ea6/DESCRIPTION’ ... OK
* preparing ‘filed55214f38ea6’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Removed empty directory ‘filed55214f38ea6/R’
* building ‘filed55214f38ea6_0.0.1.tar.gz’

    * ERROR: Version number in tarball filename must match Version
      field in DESCRIPTION. (Tip: create tarball with R CMD build)
    * NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 52 lines
      (9%) are not.
    See https://contributions.bioconductor.org/r-code.html
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
    * WARNING: Package files exceed the 5MB size limit.
    * WARNING: Data files exceed the 5MB size limit.
    * ERROR: Remove 'inst/doc' folder from the package source
* Checking License: for restrictive use...
    * NOTE: License 'GPL-3.0' unknown; refer to
      $R_HOME/share/licenses/license.db
      and https://choosealicense.com/appendix/ for more info.
* Checking License: for restrictive use...
    * ERROR: License 'CC BY-NC-ND 4.0' restricts use
* Checking License: for restrictive use...
    * ERROR: License 'CC BY-NC-ND 4.0 + file LICENSE' restricts use
* Checking License: for restrictive use...
    * NOTE: License 'UNKNOWN' unknown; refer to
      $R_HOME/share/licenses/license.db
      and https://choosealicense.com/appendix/ for more info.
* Checking License: for restrictive use...
    * NOTE: malformed 'License:' field 'NA'
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
    * WARNING: Fix formatting of NEWS.Rd. Malformed package NEWS will
      not be included in Bioconductor release announcements.
    * NOTE: More than 1 NEWS file found. See ?news for recognition
      ordering.
    * WARNING: Fix formatting of NEWS.Rd. Malformed package NEWS will
      not be included in Bioconductor release announcements.
    * WARNING: New package x version starting with non-zero value
      (e.g., 1.y.z, 2.y.z); got '1.99.3'.
    * ERROR: New package 'y' version not 99 (i.e., x.99.z); Package
      version: 0.2.3
    * NOTE: Update R version dependency from 1.0.0 to 4.4.0.
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      https://contributions.bioconductor.org/tests.html
    * NOTE: skip_on_bioc() found in testthat files: a_test.R
$undefined
$undefined$checkLazyDataUsage
$undefined$checkLazyDataUsage[[1]]
[1] "* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed"

$`* Checking License: for restrictive use...`
$`* Checking License: for restrictive use...`$.checkLicenseForRestrictiveUse
$`* Checking License: for restrictive use...`$.checkLicenseForRestrictiveUse[[1]]
[1] "* NOTE: malformed 'License:' field 'NA'"

$`* Checking License: for restrictive use...`$checkNEWS
$`* Checking License: for restrictive use...`$checkNEWS[[1]]
[1] "* NOTE: Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements."

$`* Checking License: for restrictive use...`$`3`
$`* Checking License: for restrictive use...`$`3`[[1]]
[1] "* WARNING: Fix formatting of NEWS.Rd. Malformed package NEWS will not be included in Bioconductor release announcements."

$`* Checking License: for restrictive use...`$checkNEWS
$`* Checking License: for restrictive use...`$checkNEWS[[1]]
[1] "* NOTE: More than 1  NEWS file found. See ?news for recognition ordering."

$`* Checking License: for restrictive use...`$checkNEWS[[2]]
[1] "Please remove one of the following: "

$`* Checking License: for restrictive use...`$checkNEWS[[3]]
[1] "/inst/NEWS.Rd" "/./NEWS.md"   

$`* Checking License: for restrictive use...`$`3`
$`* Checking License: for restrictive use...`$`3`[[1]]
[1] "* WARNING: Fix formatting of NEWS.Rd. Malformed package NEWS will not be included in Bioconductor release announcements."

$`* Checking License: for restrictive use...`$checkNewPackageVersionNumber
$`* Checking License: for restrictive use...`$checkNewPackageVersionNumber[[1]]
[1] "* WARNING: New package x version starting with non-zero value (e.g., 1.y.z, 2.y.z); got '1.99.3'."

$`* Checking License: for restrictive use...`$checkNewPackageVersionNumber
$`* Checking License: for restrictive use...`$checkNewPackageVersionNumber[[1]]
[1] "* ERROR: New package 'y' version not 99 (i.e., x.99.z); Package version: 0.2.3"

$`* Checking License: for restrictive use...`$checkRVersionDependency
$`* Checking License: for restrictive use...`$checkRVersionDependency[[1]]
[1] "* NOTE: Update R version dependency from 1.0.0 to 4.4.0."

$`* Checking License: for restrictive use...`$checkTFSymbolUsage
$`* Checking License: for restrictive use...`$checkTFSymbolUsage[[1]]
[1] "* WARNING:  Avoid T/F variables; If logical, use TRUE/FALSE"

$`* Checking License: for restrictive use...`$checkTFSymbolUsage[[2]]
[1] "Found in files:"

$`* Checking License: for restrictive use...`$checkTFSymbolUsage[[3]]
[1] "vignettes/testpkg0.Rmd (code line 47, column 5)"

$`* Checking License: for restrictive use...`$checkUnitTests
$`* Checking License: for restrictive use...`$checkUnitTests[[1]]
[1] "* NOTE: Consider adding unit tests. We strongly encourage them. See\n  https://contributions.bioconductor.org/tests.html"

$`* Checking License: for restrictive use...`$checkSkipOnBioc
$`* Checking License: for restrictive use...`$checkSkipOnBioc[[1]]
[1] "* NOTE: skip_on_bioc() found in testthat files: a_test.R"

$`* Checking License: for restrictive use...`$checkUsageOfDont
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[1] "* NOTE: Usage of dontrun{} / donttest{} tags found in man page examples. 67% of man pages use at least one of these tags."

$`* Checking License: for restrictive use...`$checkUsageOfDont[[2]]
[1] "Found in files:"

$`* Checking License: for restrictive use...`$checkUsageOfDont[[3]]
[1] "a.Rd"      "baddep.Rd"

$`* Checking License: for restrictive use...`$checkUsageOfDont
$`* Checking License: for restrictive use...`$checkUsageOfDont[[1]]
[1] "* NOTE: Use donttest{} instead of dontrun{}."

$`* Checking License: for restrictive use...`$checkUsageOfDont[[2]]
[1] "Found in files:"

$`* Checking License: for restrictive use...`$checkUsageOfDont[[3]]
[1] "baddep.Rd"

$`* Checking for blank lines in DESCRIPTION...`
list()

$`* Checking if DESCRIPTION is well formatted...`
list()

$`* Checking for proper Description: field...`
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$`* Checking for whitespace in DESCRIPTION field names...`
list()

$`* Checking that Package field matches directory/tarball name...`
list()

$`* Checking for Version: field...`
list()

$`* Checking for valid maintainer...`
$`* Checking for valid maintainer...`$checkBBScompatibility
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[1] "* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with 'comment=c(ORCID=\"...\")'"

$`* Checking that provided CITATION file is correctly formatted...`
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[1] "* WARNING: Unable to read CITATION file with 'utils::readCitationFile()'"

$`* Checking that provided CITATION file is correctly formatted...`$checkBiocCheckOutputFolder
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[1] "* ERROR: Remove 'testpkg.BiocCheck' from the package directory"

$`* Checking that biocViews are present...`
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[1] "* WARNING: Use biocViews from one category only (one of Software, ExperimentData, AnnotationData, Workflow)"

$`* Checking biocViews validity...`
list()

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$`* Checking for recommended DESCRIPTION fields...`
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$`* Checking for Bioconductor software dependencies...`
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$`* Checking for pinned package versions in DESCRIPTION...`
$`* Checking for pinned package versions in DESCRIPTION...`$.checkPinnedDeps
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[1] "* ERROR: Dependencies in the DESCRIPTION file contain '=='"

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[1] "* ERROR: Use 'BiocParallel' instead of 'multicore'. 'multicore' is deprecated and does not work on Windows."

$`* Checking for pinned package versions in DESCRIPTION...`$checkDupChunkLabels
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[1] "* ERROR:  Vignette(s) found with duplicate chunk labels"

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[1] "Found in files:"

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[1] "dupChunks.Rmd"

$`* Checking for pinned package versions in DESCRIPTION...`$checkExportsAreDocumented
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[1] "* ERROR: At least 80% of man pages documenting exported objects must have runnable examples."

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[1] "The following pages do not:"

$`* Checking for pinned package versions in DESCRIPTION...`$checkExportsAreDocumented[[3]]
[1] "baddep.Rd"

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[1] "* NOTE: Usage of dontrun{} / donttest{} tags found in man page examples. 67% of man pages use at least one of these tags."

$`* Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[2]]
[1] "Found in files:"

$`* Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[3]]
[1] "a.Rd"      "baddep.Rd"

$`* Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont
$`* Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[1]]
[1] "* NOTE: Use donttest{} instead of dontrun{}."

$`* Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[2]]
[1] "Found in files:"

$`* Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[3]]
[1] "baddep.Rd"

$`* Checking for pinned package versions in DESCRIPTION...`$checkForDirectSlotAccess
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[1] "* NOTE: Use accessors; don't access S4 class slots via '@' in examples/vignettes."

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[1] "* WARNING:  Avoid the use of 'library' or 'require' in R code"

$`* Checking for pinned package versions in DESCRIPTION...`$checkForLibraryRequire[[2]]
[1] "Found in files:"

$`* Checking for pinned package versions in DESCRIPTION...`$checkForLibraryRequire[[3]]
 [1] "library() in R/requireme.R (line 3, column 5)" 
 [2] "library() in R/requireme.R (line 5, column 5)" 
 [3] "library() in R/requireme.R (line 7, column 5)" 
 [4] "library() in R/requireme.R (line 8, column 5)" 
 [5] "library() in R/requireme.R (line 13, column 5)"
 [6] "require() in R/requireme.R (line 4, column 5)" 
 [7] "require() in R/requireme.R (line 6, column 5)" 
 [8] "require() in R/requireme.R (line 9, column 5)" 
 [9] "require() in R/requireme.R (line 10, column 5)"
[10] "require() in R/requireme.R (line 11, column 5)"
[11] "require() in R/requireme.R (line 12, column 5)"
[12] "require() in R/requireme.R (line 14, column 5)"
[13] "require() in R/requireme.R (line 17, column 5)"
[14] "require() in R/requireme.R (line 18, column 5)"

$`* Checking for pinned package versions in DESCRIPTION...`$checkForPromptComments
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[1] "* NOTE: Auto-generated '%% ~' comments found in Rd man pages."

$`* Checking for pinned package versions in DESCRIPTION...`$checkForPromptComments[[2]]
[1] "a.Rd"      "baddep.Rd"

$`* Checking for pinned package versions in DESCRIPTION...`$checkSupportReg
$`* Checking for pinned package versions in DESCRIPTION...`$checkSupportReg[[1]]
[1] "* ERROR: Unable to find your email in the Support Site:\n  HTTP 404 Not Found."

$`* Checking for pinned package versions in DESCRIPTION...`$checkWatchedTag
$`* Checking for pinned package versions in DESCRIPTION...`$checkWatchedTag[[1]]
[1] "* ERROR: Add package to Watched Tags in your Support Site profile; visit https://support.bioconductor.org/accounts/edit/profile"

$`* Checking for pinned package versions in DESCRIPTION...`$checkForVersionNumberMismatch
$`* Checking for pinned package versions in DESCRIPTION...`$checkForVersionNumberMismatch[[1]]
[1] "* ERROR: Version number in tarball filename must match Version field in DESCRIPTION. (Tip: create tarball with R CMD build)"

$`* Checking for pinned package versions in DESCRIPTION...`$checkFormatting
$`* Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[1]]
[1] "* NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters long."

$`* Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[2]]
[1] "First few lines:"

$`* Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[3]]
[1] "R/morebadcode.R#L2 # this is a really long line with many c ..."

$`* Checking for pinned package versions in DESCRIPTION...`$checkFormatting
$`* Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[1]]
[1] "* NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs."

$`* Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[2]]
[1] "First few lines:"

$`* Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[3]]
[1] "man/a.Rd#L48 ##--\tor do  help(data=index)  for the st ..."     
[2] "man/baddep.Rd#L41 ##--\tor do  help(data=index)  for the st ..."

$`* Checking for pinned package versions in DESCRIPTION...`$checkFormatting
$`* Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[1]]
[1] "* NOTE: Consider multiples of 4 spaces for line indents; 52 lines (9%) are not."

$`* Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[2]]
[1] "First few lines:"

$`* Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[3]]
 [1] "R/bad_coding.R#L82    ..."                                      
 [2] "R/bad_coding.R#L83    ..."                                      
 [3] "R/bad_coding.R#L84    ..."                                      
 [4] "R/bad_coding.R#L85    ..."                                      
 [5] "R/bad_coding.R#L86    ..."                                      
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 [8] "R/bad_coding.R#L89    ..."                                      
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[10] "R/bad_coding.R#L91    ..."                                      
[11] "R/bad_coding.R#L92    ..."                                      
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[14] "R/bad_coding.R#L95    ..."                                      
[15] "R/bad_coding.R#L96    ..."                                      
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[25] "R/bad_coding.R#L106    ..."                                     
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[27] "R/bad_coding.R#L108    ..."                                     
[28] "R/bad_coding.R#L109    ..."                                     
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[35] "R/bad_coding.R#L116    ..."                                     
[36] "R/bad_coding.R#L117    ..."                                     
[37] "R/bad_coding.R#L118    ..."                                     
[38] "R/bad_coding.R#L119    ..."                                     
[39] "R/bad_coding.R#L120    ..."                                     
[40] "R/bad_coding.R#L121    ..."                                     
[41] "R/bad_coding.R#L122    ..."                                     
[42] "R/bad_coding.R#L123    ..."                                     
[43] "R/bad_coding.R#L124    ..."                                     
[44] "R/bad_coding.R#L125    ..."                                     
[45] "R/bad_coding.R#L126    ..."                                     
[46] "R/bad_coding.R#L127    ..."                                     
[47] "R/bad_coding.R#L128    ..."                                     
[48] "R/bad_coding.R#L129    ..."                                     
[49] "R/bad_coding.R#L130    ..."                                     
[50] "R/bad_coding.R#L131    ..."                                     
[51] "R/bad_coding.R#L132   return(TRUE) ..."                         
[52] "R/morebadcode.R#L6      # something other than a multiple o ..."

$`* Checking for pinned package versions in DESCRIPTION...`$checkIndivFileSizes
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[1] "* WARNING: Package files exceed the 5MB size limit."

$`* Checking for pinned package versions in DESCRIPTION...`$checkIndivFileSizes[[2]]
[1] "Files over the limit: "

$`* Checking for pinned package versions in DESCRIPTION...`$checkIndivFileSizes[[3]]
[1] "fileA.rda" "fileB.rds"

$`* Checking for pinned package versions in DESCRIPTION...`$checkDataFileSizes
$`* Checking for pinned package versions in DESCRIPTION...`$checkDataFileSizes[[1]]
[1] "* WARNING: Data files exceed the 5MB size limit."

$`* Checking for pinned package versions in DESCRIPTION...`$checkDataFileSizes[[2]]
[1] "Use 'ExperimentHub' or 'AnnotationHub' for the files: "

$`* Checking for pinned package versions in DESCRIPTION...`$checkDataFileSizes[[3]]
[1] "fileA.rda" "fileB.rds"

$`* Checking for pinned package versions in DESCRIPTION...`$checkInstDocFolder
$`* Checking for pinned package versions in DESCRIPTION...`$checkInstDocFolder[[1]]
[1] "* ERROR: Remove 'inst/doc' folder from the package source"

    * ERROR: Invalid package Version, see
      https://contributions.bioconductor.org/versionnum.html
    * ERROR: Invalid package Version, see
      https://contributions.bioconductor.org/versionnum.html
    * WARNING: y of x.y.z version should be even in release
    * WARNING: BiocInstaller code found in vignette(s)
    * ERROR: Installation calls found in vignette(s)
    * NOTE: 'sessionInfo' not found in vignette(s)
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-BiocCheck/R-BiocCheck/work/.tmp/Rtmpo0Fa9T/filed55276516f16/filed5525c544a09/DESCRIPTION’ ... OK
* preparing ‘filed5525c544a09’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Removed empty directory ‘filed5525c544a09/R’
* building ‘filed5525c544a09_0.99.0.tar.gz’

    * NOTE: The recommended function length is 50 lines or less. There
      are 25 functions greater than 50 lines.
    * NOTE: The recommended function length is 50 lines or less. There
      is 1 function greater than 50 lines.
    * WARNING: The package already exists on CRAN. Packages submitted
      to Bioconductor must be removed from CRAN before the next
      Bioconductor release.
    * ERROR: 'GenomicRanges' already exists in Bioconductor.
    * ERROR: 'gwascatData' already exists in Bioconductor.
    * ERROR: 'TENxBrainData' already exists in Bioconductor.
    * ERROR: 'annotation' already exists in Bioconductor.
    * ERROR: Package dependencies must be on CRAN or Bioconductor.
      Remove 'Remotes:' from DESCRIPTION
    * ERROR: No vignette sources in vignettes/ directory.
    * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
    * WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette
      Title}'.
    * NOTE: 'sessionInfo' not found in vignette(s)
    * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
    * NOTE: 'sessionInfo' not found in vignette(s)
    * WARNING: Remove vignette sources from inst/doc; they belong in
      vignettes/.
    * WARNING: Remove vignette sources from inst/doc; they belong in
      vignettes/.
    * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
    * ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
      'VignetteEngine' in any vignettes:
    * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
    * WARNING: Package listed as VignetteEngine or VignetteBuilder but
      not currently Suggested.
    * NOTE: 'sessionInfo' not found in vignette(s)
    * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
    * NOTE: 'sessionInfo' not found in vignette(s)
    * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
    * WARNING: Package listed as VignetteEngine or VignetteBuilder but
      not currently Suggested.
    * NOTE: 'sessionInfo' not found in vignette(s)
    * ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
      'VignetteEngine' in any vignettes:
    * WARNING: Vignette(s) missing Vignette metadata. See
      http://r-pkgs.had.co.nz/vignettes.html
    * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
    * ERROR: No 'VignetteEngine' specified in vignette or DESCRIPTION.
    * WARNING: Package listed as VignetteEngine or VignetteBuilder but
      not currently Suggested.
    * WARNING: Vignette(s) still using 'VignetteIndexEntry{Vignette
      Title}'
    * WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette
      Title}'.
    * ERROR: Vignette(s) found with duplicate chunk labels
    * WARNING: BiocInstaller code found in vignette(s)
    * ERROR: Installation calls found in vignette(s)
    * WARNING: Avoid class membership checks with class() / is() and ==
      / !=; Use is(x, 'class') for S4 classes
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
    * NOTE: 'sessionInfo' not found in vignette(s)
Timing stopped at: 36.43 18.32 53.88
Error in checkIdentical(.BiocCheck$getNum(c("error", "warning", "note")),  : 
  FALSE 

RUNIT TEST PROTOCOL -- Sat May  4 15:14:02 2024 
*********************************************** 
Number of test functions: 55 
Number of errors: 0 
Number of failures: 1 

1 Test Suite : 
BiocCheck RUnit Tests - 55 test functions, 0 errors, 1 failure
FAILURE in test_vignettes0: Error in checkIdentical(.BiocCheck$getNum(c("error", "warning", "note")),  : 
  FALSE 

Test files with failing tests

   test_BiocCheck.R 
     test_vignettes0 

Error in BiocGenerics:::testPackage("BiocCheck") : 
  unit tests failed for package BiocCheck
Execution halted
lshep commented 4 months ago

@barracuda156 I cannot reproduce this either; are you sure you have the latest version of BiocCheck?

barracuda156 commented 4 months ago

@lshep I do.

Just to be clear, has anyone tested it on any OS on ppc? Say, BSD or Linux.

vjcitn commented 4 months ago

Yes, it is tested on Linux as noted at https://bioconductor.org/checkResults/release/bioc-LATEST/BiocCheck/

I think the issue concerns the 32-bit character of your OS. The test could be softened for that context.

barracuda156 commented 4 months ago

@vjcitn I think on that page all tested archs are 64-bit? ppc is 32-bit, yes.

If the error is due to bitness, then it is of course desirable to have it fixed. (On the other hand if everything works fine on ppc on BSD/Linux, but fails on Darwin, that could be a macOS-specific issue, which may not be worth bothering to fix in upstream.)

vjcitn commented 4 months ago

We don't have a 32-bit PPC. I am trying to recall the context of your testing -- you are repackaging, right? We want to help you as much as possible but without access to the platform it is hard. Can you create a PR that passes on 32-bit ppc but is innocuous for other platforms?

barracuda156 commented 4 months ago

We don't have a 32-bit PPC.

This should be possible via Qemu and alike. You do not need a literally 32-bit cpu. On macOS perhaps via UTM (interface to Qemu, open source).

I am trying to recall the context of your testing -- you are repackaging, right?

We provide packages in Macports for macOS users. CRAN has a rather abysmal macOS support :)

Can you create a PR that passes on 32-bit ppc but is innocuous for other platforms?

Possibly, if someone could help me with pointing out at what is likely to be failing specifically in the source.

LiNk-NY commented 4 months ago

Hi @barracuda156

Possibly, if someone could help me with pointing out at what is likely to be failing specifically in the source.

Thanks for taking a look.

The error comes from the unit test at :

https://github.com/Bioconductor/BiocCheck/blob/5f56c4bffdc8160bdb6da6242de66ac379f78c9d/inst/unitTests/test_BiocCheck.R#L93-L273

You can run it interactively via: 

devtools::load_all(".")
source("inst/unitTests/test_BiocCheck.R")
library(RUnit)
test_vignettes0()