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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:InterMineR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings InterMineR_1.25.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/InterMineR.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘InterMineR/DESCRIPTION’ ... OK
* this is package ‘InterMineR’ version ‘1.25.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘InterMineR’ can be installed ... WARNING
Found the following significant warnings:
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:41: unexpected section header '\arguments'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:42: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:50: unexpected section header '\arguments'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:51: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:59: unexpected section header '\arguments'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:60: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:63: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:66: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:69: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:72: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:80: unexpected section header '\arguments'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:81: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:84: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:87: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:90: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:98: unexpected section header '\arguments'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:99: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:102: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:105: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:108: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:116: unexpected section header '\arguments'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:117: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:120: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:123: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:126: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:134: unexpected section header '\arguments'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:135: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:138: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:141: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:144: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:147: unknown macro '\item'
  Warning: multiple methods tables found for ‘union’
  Warning: multiple methods tables found for ‘subtract’
  Warning: multiple methods tables found for ‘intersect’
  Warning: Package 'InterMineR' is deprecated and will be removed from
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/InterMineR.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: multiple methods tables found for ‘union’
Warning: multiple methods tables found for ‘subtract’
Warning: multiple methods tables found for ‘intersect’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
convertToRangedSummarizedExperiment: no visible global function
  definition for ‘reshape’
listDatasets: no visible binding for global variable ‘child_name’
create_list,ListManager: no visible global function definition for
  ‘URLencode’
doEnrichment,Service: no visible global function definition for
  ‘URLencode’
do_operation,ListManager: no visible global function definition for
  ‘URLencode’
runQuery,ANY-InterMineR: no visible global function definition for
  ‘URLencode’
runQuery,ANY-list: no visible global function definition for
  ‘URLencode’
subtract,ListManager: no visible global function definition for
  ‘URLencode’
Undefined global functions or variables:
  URLencode child_name reshape
Consider adding
  importFrom("stats", "reshape")
  importFrom("utils", "URLencode")
to your NAMESPACE file.
* checking Rd files ... WARNING
prepare_Rd: ./man/ListManager-methods.Rd:41: unexpected section header '\arguments'
prepare_Rd: ./man/ListManager-methods.Rd:42: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:50: unexpected section header '\arguments'
prepare_Rd: ./man/ListManager-methods.Rd:51: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:59: unexpected section header '\arguments'
prepare_Rd: ./man/ListManager-methods.Rd:60: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:63: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:66: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:69: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:72: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:80: unexpected section header '\arguments'
prepare_Rd: ./man/ListManager-methods.Rd:81: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:84: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:87: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:90: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:98: unexpected section header '\arguments'
prepare_Rd: ./man/ListManager-methods.Rd:99: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:102: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:105: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:108: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:116: unexpected section header '\arguments'
prepare_Rd: ./man/ListManager-methods.Rd:117: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:120: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:123: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:126: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:134: unexpected section header '\arguments'
prepare_Rd: ./man/ListManager-methods.Rd:135: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:138: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:141: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:144: unknown macro '\item'
prepare_Rd: ./man/ListManager-methods.Rd:147: unknown macro '\item'
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'webservice-methods':
  ‘doEnrichment.Rd’ ‘list_manager.Rd’
* checking Rd cross-references ... NOTE
Unknown package ‘GeneAnswers’ in Rd xrefs
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘GET_api_list’ ‘do_operation’ ‘get_unused_list_name’
Undocumented S4 classes:
  ‘Service’
Undocumented S4 methods:
  generic 'GET_api_list' and siglist 'ListManager'
  generic 'doEnrichment' and siglist 'Service'
  generic 'do_operation' and siglist 'ListManager'
  generic 'get_unused_list_name' and siglist 'ListManager'
  generic 'list_manager' and siglist 'Service'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in Rd file 'convertToGeneAnswers.Rd' but not in code:
  ‘convertToGeneAnswers’

Codoc mismatches from Rd file 'doEnrichment.Rd':
doEnrichment
  Code: function(object, ...)
  Docs: function(- Service class, genelist = NULL, ids = NULL, widget =
                 NULL, population = NULL, maxp = 0.05, correction =
                 "Benjamini Hochberg", filter = NULL, organism = NULL)
  Argument names in code not in docs:
    object ...
  Argument names in docs not in code:
    - Service class genelist ids widget population maxp correction
    filter organism
  Mismatches in argument names:
    Position: 1 Code: object Docs: - Service class
    Position: 2 Code: ... Docs: genelist

Codoc mismatches from Rd file 'list_manager.Rd':
list_manager
  Code: function(object, ...)
  Docs: function(- Service class)
  Argument names in code not in docs:
    object ...
  Argument names in docs not in code:
    - Service class
  Mismatches in argument names:
    Position: 1 Code: object Docs: - Service class

S4 class codoc mismatches from Rd file 'ListManager-class.Rd':
Slots for class 'ListManager'
  Code: DEFAULT_DESCRIPTION DEFAULT_LIST_NAME DIFFERENCE_PATH
        INTERSECTION_PATH LIST_PATH SUBTRACTION_PATH UNION_PATH mine
        token
  Docs: DEFAULT_DESCRIPTION DEFAULT_LIST_NAME DIFFERENCE_PATH
        INTERSECTION_PATH LIST_PATH SUBTRACTION_PATH UNION_PATH mine
        name token

* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'doEnrichment.Rd'
  ‘Service - class’
Documented arguments not in \usage in Rd file 'doEnrichment.Rd':
  ‘Service-class’

Undocumented arguments in Rd file 'list_manager.Rd'
  ‘Service - class’
Documented arguments not in \usage in Rd file 'list_manager.Rd':
  ‘Service-class’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                      user system elapsed
simplifyResult                      19.018  0.375  24.917
runQuery                             5.468  0.052   7.921
convertToRangedSummarizedExperiment  4.853  0.177  11.557
InterMineR-methods                   0.108  0.029   6.560
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 6 WARNINGs, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/InterMineR.Rcheck/00check.log’
for details.