############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:InterMineR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings InterMineR_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/InterMineR.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘InterMineR/DESCRIPTION’ ... OK * this is package ‘InterMineR’ version ‘1.26.0’ * 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: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:41: unexpected section header '\arguments' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:42: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:50: unexpected section header '\arguments' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:51: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:59: unexpected section header '\arguments' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:60: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:63: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:66: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:69: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:72: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:80: unexpected section header '\arguments' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:81: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:84: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:87: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:90: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:98: unexpected section header '\arguments' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:99: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:102: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:105: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:108: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:116: unexpected section header '\arguments' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:117: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:120: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:123: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:126: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:134: unexpected section header '\arguments' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:135: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:138: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:141: unknown macro '\item' Warning: /home/biocbuild/bbs-3.19-bioc/meat/InterMineR/man/ListManager-methods.Rd:144: unknown macro '\item' Warning: /home/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’ See ‘/home/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 code 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 loading without being on the library search path ... 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' checkRd: (-1) ListManager-methods.Rd:41-45: Lost braces 41 | \arguments{ | ^ checkRd: (-1) ListManager-methods.Rd:42: Lost braces 42 | \item{list_name}{ | ^ checkRd: (-1) ListManager-methods.Rd:42-44: Lost braces 42 | \item{list_name}{ | ^ checkRd: (-1) ListManager-methods.Rd:50-54: Lost braces 50 | \arguments{ | ^ checkRd: (-1) ListManager-methods.Rd:51: Lost braces 51 | \item{lists}{ | ^ checkRd: (-1) ListManager-methods.Rd:51-53: Lost braces 51 | \item{lists}{ | ^ checkRd: (-1) ListManager-methods.Rd:59-75: Lost braces 59 | \arguments{ | ^ checkRd: (-1) ListManager-methods.Rd:60: Lost braces 60 | \item{content}{ | ^ checkRd: (-1) ListManager-methods.Rd:60-62: Lost braces 60 | \item{content}{ | ^ checkRd: (-1) ListManager-methods.Rd:63: Lost braces 63 | \item{list_type}{ | ^ checkRd: (-1) ListManager-methods.Rd:63-65: Lost braces 63 | \item{list_type}{ | ^ checkRd: (-1) ListManager-methods.Rd:66: Lost braces 66 | \item{name}{ | ^ checkRd: (-1) ListManager-methods.Rd:66-68: Lost braces 66 | \item{name}{ | ^ checkRd: (-1) ListManager-methods.Rd:69: Lost braces 69 | \item{description}{ | ^ checkRd: (-1) ListManager-methods.Rd:69-71: Lost braces 69 | \item{description}{ | ^ checkRd: (-1) ListManager-methods.Rd:72: Lost braces 72 | \item{organism}{ | ^ checkRd: (-1) ListManager-methods.Rd:72-74: Lost braces 72 | \item{organism}{ | ^ checkRd: (-1) ListManager-methods.Rd:80-93: Lost braces 80 | \arguments{ | ^ checkRd: (-1) ListManager-methods.Rd:81: Lost braces 81 | \item{lists}{ | ^ checkRd: (-1) ListManager-methods.Rd:81-83: Lost braces 81 | \item{lists}{ | ^ checkRd: (-1) ListManager-methods.Rd:84: Lost braces 84 | \item{name}{ | ^ checkRd: (-1) ListManager-methods.Rd:84-86: Lost braces 84 | \item{name}{ | ^ checkRd: (-1) ListManager-methods.Rd:87: Lost braces 87 | \item{description}{ | ^ checkRd: (-1) ListManager-methods.Rd:87-89: Lost braces 87 | \item{description}{ | ^ checkRd: (-1) ListManager-methods.Rd:90: Lost braces 90 | \item{tags}{ | ^ checkRd: (-1) ListManager-methods.Rd:90-92: Lost braces 90 | \item{tags}{ | ^ checkRd: (-1) ListManager-methods.Rd:98-111: Lost braces 98 | \arguments{ | ^ checkRd: (-1) ListManager-methods.Rd:99: Lost braces 99 | \item{lists}{ | ^ checkRd: (-1) ListManager-methods.Rd:99-101: Lost braces 99 | \item{lists}{ | ^ checkRd: (-1) ListManager-methods.Rd:102: Lost braces 102 | \item{name}{ | ^ checkRd: (-1) ListManager-methods.Rd:102-104: Lost braces 102 | \item{name}{ | ^ checkRd: (-1) ListManager-methods.Rd:105: Lost braces 105 | \item{description}{ | ^ checkRd: (-1) ListManager-methods.Rd:105-107: Lost braces 105 | \item{description}{ | ^ checkRd: (-1) ListManager-methods.Rd:108: Lost braces 108 | \item{tags}{ | ^ checkRd: (-1) ListManager-methods.Rd:108-110: Lost braces 108 | \item{tags}{ | ^ checkRd: (-1) ListManager-methods.Rd:116-129: Lost braces 116 | \arguments{ | ^ checkRd: (-1) ListManager-methods.Rd:117: Lost braces 117 | \item{lists}{ | ^ checkRd: (-1) ListManager-methods.Rd:117-119: Lost braces 117 | \item{lists}{ | ^ checkRd: (-1) ListManager-methods.Rd:120: Lost braces 120 | \item{name}{ | ^ checkRd: (-1) ListManager-methods.Rd:120-122: Lost braces 120 | \item{name}{ | ^ checkRd: (-1) ListManager-methods.Rd:123: Lost braces 123 | \item{description}{ | ^ checkRd: (-1) ListManager-methods.Rd:123-125: Lost braces 123 | \item{description}{ | ^ checkRd: (-1) ListManager-methods.Rd:126: Lost braces 126 | \item{tags}{ | ^ checkRd: (-1) ListManager-methods.Rd:126-128: Lost braces 126 | \item{tags}{ | ^ checkRd: (-1) ListManager-methods.Rd:134-150: Lost braces 134 | \arguments{ | ^ checkRd: (-1) ListManager-methods.Rd:135: Lost braces 135 | \item{lefts}{ | ^ checkRd: (-1) ListManager-methods.Rd:135-137: Lost braces 135 | \item{lefts}{ | ^ checkRd: (-1) ListManager-methods.Rd:138: Lost braces 138 | \item{rights}{ | ^ checkRd: (-1) ListManager-methods.Rd:138-140: Lost braces 138 | \item{rights}{ | ^ checkRd: (-1) ListManager-methods.Rd:141: Lost braces 141 | \item{name}{ | ^ checkRd: (-1) ListManager-methods.Rd:141-143: Lost braces 141 | \item{name}{ | ^ checkRd: (-1) ListManager-methods.Rd:144: Lost braces 144 | \item{description}{ | ^ checkRd: (-1) ListManager-methods.Rd:144-146: Lost braces 144 | \item{description}{ | ^ checkRd: (-1) ListManager-methods.Rd:147: Lost braces 147 | \item{tags}{ | ^ checkRd: (-1) ListManager-methods.Rd:147-149: Lost braces 147 | \item{tags}{ | ^ checkRd: (-1) initInterMine.Rd:26: Lost braces 26 | /url{http://intermine.readthedocs.io/en/latest/web-services/} | ^ * 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 11.206 0.318 20.290 convertToRangedSummarizedExperiment 2.911 0.278 12.456 runQuery 2.957 0.112 9.164 getGeneIds 0.486 0.036 7.067 * 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 ‘/home/biocbuild/bbs-3.19-bioc/meat/InterMineR.Rcheck/00check.log’ for details.