Movatterモバイル変換

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:annmap.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings annmap_1.52.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/annmap.Rcheck’* using R version 4.5.2 (2025-10-31)* using platform: x86_64-pc-linux-gnu* R was compiled by    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0* running under: Ubuntu 24.04.3 LTS* using session charset: UTF-8* checking for file ‘annmap/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘annmap’ version ‘1.52.0’* 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 ... NOTEFound the following hidden files and directories:  .BBSoptionsThese were most likely included in error. See section ‘Packagestructure’ in the ‘Writing R Extensions’ manual.* checking for portable file names ... OK* checking for sufficient/correct file permissions ... OK* checking whether package ‘annmap’ can be installed ... OK* checking installed package size ... OK* checking package directory ... OK* checking ‘build’ directory ... OK* checking DESCRIPTION meta-information ... NOTEMalformed Title field: should not end in a period.Malformed Description field: should contain one or more complete sentences.* checking top-level files ... NOTEFile  LICENSEis 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 ... OK* 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 ... NOTE'library' or 'require' call to ‘rjson’ in package code.  Please use :: or requireNamespace() instead.  See section 'Suggested packages' in the 'Writing R Extensions' manual.There are ::: calls to the package's namespace in its code. A package  almost never needs to use ::: for its own objects:  ‘.make.hash’* checking S3 generic/method consistency ... OK* checking replacement functions ... OK* checking foreign function calls ... OK* checking R code for possible problems ... NOTE.get.stats.cache: no visible global function definition for  ‘flush.console’.layout.genes: no visible global function definition for ‘strwidth’.load.and.parse: no visible global function definition for ‘fromJSON’.read.databases: no visible global function definition for ‘read.table’.single.transcript.coords.to.genome: no visible global function  definition for ‘tail’.xmc.connect: no visible global function definition for ‘menu’.xmcws.connect: no visible global function definition for ‘fromJSON’.xmcws.connect: no visible global function definition for ‘menu’annmapAddConnection: no visible global function definition for  ‘write.table’annmapConnect: no visible global function definition for  ‘install.packages’arrayType: no visible global function definition for ‘menu’convertBamToRle: no visible global function definition for ‘RangedData’convertBamToRle : <anonymous>: no visible global function definition  for ‘Rle’geneToGeneRegionTrack : generate: no visible global function definition  for ‘GeneRegionTrack’generateBridgeData: no visible global function definition for ‘rainbow’genomicPlot : <anonymous>: no visible global function definition for  ‘rgb’genomicPlot: no visible global function definition for ‘rgb’ngsTracePlotter : local.draw: no visible global function definition for  ‘runValue’ngsTracePlotter: no visible global function definition for ‘modifyList’ngsTraceScale : <anonymous>: no visible global function definition for  ‘runValue’seqnameMapping: no visible global function definition for ‘seqlevels<-’seqnameMapping: no visible global function definition for ‘seqlevels’Undefined global functions or variables:  GeneRegionTrack RangedData Rle flush.console fromJSON  install.packages menu modifyList rainbow read.table rgb runValue  seqlevels seqlevels<- strwidth tail write.tableConsider adding  importFrom("grDevices", "rainbow", "rgb")  importFrom("graphics", "strwidth")  importFrom("utils", "flush.console", "install.packages", "menu",             "modifyList", "read.table", "tail", "write.table")to your NAMESPACE file.* checking Rd files ... NOTEcheckRd: (-1) NEWS.Rd:5: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:10: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:11: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:16: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:21: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:22: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:27: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:32: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:33: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:38: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:43: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:44: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:49: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:50: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:51: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:56: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:61: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:66: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:67: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:72: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:77: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:78: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:79: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:84: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:85: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:90: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:95: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:100: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:101: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:102: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:107: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:112: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:117: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:122: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:127: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:132: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:133: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:134: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:139: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:140: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:141: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:146: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:151: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:152: Lost braces in \itemize; meant \describe ?checkRd: (-1) NEWS.Rd:153: Lost braces in \itemize; meant \describe ?* checking Rd metadata ... OK* checking Rd cross-references ... WARNINGMissing link(s) in Rd file 'annmap.range.Rd':  ‘RangedData’Missing link(s) in Rd file 'annmap.utils.Rd':  ‘RangedData’Missing link(s) in Rd file 'plot.ngs.Rd':  ‘[IRanges]{Rle}’Non-topic package-anchored link(s) in Rd file 'annmap.to.Rd':  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’See section 'Cross-references' in the 'Writing R Extensions' manual.Found the following Rd file(s) with Rd \link{} targets missing packageanchors:  annmap-package.Rd: GenomicRanges  annmap.all.Rd: GRanges  annmap.details.Rd: GRanges  annmap.range.Rd: GRanges, RangedData  annmap.to.Rd: GRanges  annmap.utils.Rd: RangedDataPlease provide package anchors for all Rd \link{} targets not in thepackage itself and the base packages.* checking for missing documentation entries ... OK* checking for code/documentation mismatches ... OK* checking Rd \usage sections ... OK* checking Rd contents ... OK* checking for unstated dependencies in examples ... OK* checking line endings in Makefiles ... OK* checking for GNU extensions in Makefiles ... OK* checking include directives in Makefiles ... OK* checking files in ‘vignettes’ ... OK* checking examples ... OK* checking for unstated dependencies in ‘tests’ ... OK* checking tests ...  Running ‘doRUnit.R’ OK* checking for unstated dependencies in vignettes ... OK* checking package vignettes ... OK* checking re-building of vignette outputs ... OK* checking PDF version of manual ... OK* DONEStatus: 1 WARNING, 6 NOTEsSee  ‘/home/biocbuild/bbs-3.22-bioc/meat/annmap.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL annmap###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘annmap’ ...** this is package ‘annmap’ version ‘1.52.0’** using staged installation** R** inst** byte-compile and prepare package for lazy loadingin method for ‘probesetInRange’ with signature ‘x="RangedData"’: no definition for class “RangedData”in method for ‘probeInRange’ with signature ‘x="RangedData"’: no definition for class “RangedData”in method for ‘proteinInRange’ with signature ‘x="RangedData"’: no definition for class “RangedData”in method for ‘domainInRange’ with signature ‘x="RangedData"’: no definition for class “RangedData”in method for ‘geneInRange’ with signature ‘x="RangedData"’: no definition for class “RangedData”in method for ‘transcriptInRange’ with signature ‘x="RangedData"’: no definition for class “RangedData”in method for ‘exonInRange’ with signature ‘x="RangedData"’: no definition for class “RangedData”in method for ‘estGeneInRange’ with signature ‘x="RangedData"’: no definition for class “RangedData”in method for ‘estTranscriptInRange’ with signature ‘x="RangedData"’: no definition for class “RangedData”in method for ‘estExonInRange’ with signature ‘x="RangedData"’: no definition for class “RangedData”in method for ‘predictionTranscriptInRange’ with signature ‘x="RangedData"’: no definition for class “RangedData”** help*** installing help indices** building package indices** installing vignettes** testing if installed package can be loaded from temporary location** testing if installed package can be loaded from final location** testing if installed package keeps a record of temporary installation path* DONE (annmap)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: x86_64-pc-linux-gnuR 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.> if( require( "RUnit", quietly=TRUE ) ) {+   pkg <- "annmap"+  +   if( Sys.getenv( "RCMDCHECK" ) == "FALSE" ) {+     path <- file.path( getwd(), "..", "inst", "unitTests" )+   }+   else {+     path <- system.file( package=pkg, "unitTests" )+   }+ +   cat( "\nRunning unit tests\n" )+   print( list( pkg=pkg, getwd=getwd(), pathToUnitTests=path ) )+   library( package=pkg, character.only=TRUE )+ +   annmapClearCache()+ +   # Run the old style RangedData for tim...+   #annmapSetParam( oldstylekey='P0fSpS' )+   annmapSetParam( spacefn=if( annmap:::.usegranges() ) seqnames else space )+   annmapSetParam( defaultclass=if( annmap:::.usegranges() ) 'GRanges' else 'RangedData' )+ +   #Fail on warnings+   options( warn=2 )+ +   # Get the pattern (if there is one?)+   patt = Sys.getenv( "RUNITFILEPATTERN" )+   func = Sys.getenv( 'RUNITFUNCPATTERN' )+   if( is.null( patt ) || nchar( patt ) == 0 ) {+     patt = "^runit.+\\.[rR]$"+   }+   else {+     patt = paste( "^runit\\.", patt, "\\.[rR]$", sep="" )+   }+   if( is.null( func ) || nchar( func ) == 0 ) {+     func = "^test.+"+   }+   else {+     func = paste( "^test\\.", func, ".+", sep="" )+   }+   #testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), testFileRegexp=patt, testFuncRegexp=func, dirs=path )+   testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), testFileRegexp=patt, testFuncRegexp=func, dirs=path, rngKind="Mersenne-Twister" )+   tests <- runTestSuite( testSuite )+  +   pathReport <- file.path( path, "report" )+  +   cat( "------------------- UNIT TEST SUMMARY ---------------------\n\n" )+   printTextProtocol( tests, showDetails=FALSE )+   printTextProtocol( tests, showDetails=FALSE, fileName=paste( pathReport, "Summary.txt", sep="" ) )+   printTextProtocol( tests, showDetails=TRUE,  fileName=paste( pathReport, ".txt", sep="" ) )+  +   printHTMLProtocol( tests, fileName=paste( pathReport, ".html", sep="" ) )+  +   tmp <- getErrors( tests )+   if( tmp$nFail > 0 | tmp$nErr > 0 ) {+     stop( paste( "\n\nunit testing failed (#test failures: ", tmp$nFail, ", #R errors: ",  tmp$nErr, ")\n\n", sep="" ) )+   }+ } else {+   warning( "cannot run unit tests -- package RUnit is not available" )+ }Running unit tests$pkg[1] "annmap"$getwd[1] "/home/biocbuild/bbs-3.22-bioc/meat/annmap.Rcheck/tests"$pathToUnitTests[1] "/tmp/RtmpbQYU9A/RLIBS_23b8ca2c96bc92/annmap/unitTests"Loading required package: GenomicRangesLoading required package: stats4Loading required package: BiocGenericsLoading required package: genericsAttaching package: 'generics'The following objects are masked from 'package:base':    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,    setequal, unionAttaching package: 'BiocGenerics'The following objects are masked from 'package:stats':    IQR, mad, sd, var, xtabsThe following objects are masked from 'package:base':    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,    as.data.frame, basename, cbind, colnames, dirname, do.call,    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,    unsplit, which.max, which.minLoading required package: S4VectorsAttaching package: 'S4Vectors'The following object is masked from 'package:utils':    findMatchesThe following objects are masked from 'package:base':    I, expand.grid, unnameLoading required package: IRangesLoading required package: SeqinfoUsing /home/biocbuild/.annmap as our configuration directory.Executing test function test.template  ...  done successfully.Executing test function test.all.queries  ... [1] "\nSkipping allXXX tests, as not on a PICR machine" done successfully.Executing test function test.gotsomefunctions  ...  done successfully.Executing test function test.cache  ...  done successfully.Executing test function test.ANNMAP112  ... [1] "Cannot find datasource 'hs-test', so skipping these tests." done successfully.Executing test function test.huisun.ANNMAP48  ... [1] "Cannot find datasource 'hs-test', so skipping these tests." done successfully.Executing test function test.chaining  ... [1] "Cannot find datasource 'hs-test' so skipping this test." done successfully.Executing test function test.addConnection  ... Using /home/biocbuild/.annmap as our configuration directory.[1] "Got conf.dir /home/biocbuild/.annmap"Connection a added. Connection b added. Connection a updated. [1] "Resetting conf.dir to /home/biocbuild/.annmap" done successfully.Executing test function test.buildsql  ... Using /home/biocbuild/.annmap as our configuration directory.[1] "Got conf.dir /home/biocbuild/.annmap"[1] "Resetting conf.dir to /home/biocbuild/.annmap" done successfully.Executing test function test.connection  ... Using /home/biocbuild/.annmap as our configuration directory.[1] "Got conf.dir /home/biocbuild/.annmap"[1] "Cannot find datasource 'hs-test', so skipping these tests."[1] "Resetting conf.dir to /home/biocbuild/.annmap" done successfully.Executing test function test.databases.txt  ... Using /home/biocbuild/.annmap as our configuration directory.[1] "Got conf.dir /home/biocbuild/.annmap"[1] "Mocking annmapConnect()"[1] "setting conf.dir to /home/biocbuild/bbs-3.22-bioc/R/site-library/annmap/unitTests/tabConfig"[1] "setting conf.dir to /home/biocbuild/bbs-3.22-bioc/R/site-library/annmap/unitTests/commaConfig"[1] "restoring connect method"[1] "Resetting conf.dir to /home/biocbuild/.annmap" done successfully.Executing test function test.details.queries  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."[1] "Cannot find datasource 'mm-test', so skipping these tests."[1] "Cannot find datasource 'rn-test', so skipping these tests."[1] "Cannot find datasource 'pb-test', so skipping these tests." done successfully.Executing test function test.gotsomefunctions  ...  done successfully.Executing test function test.filters  ... [1] "Cannot find datasource 'hs-test', so skipping these tests." done successfully.Executing test function test.bug.ACBBUTIL33  ... [1] "Cannot find datasource 'mm-test', so skipping this test." done successfully.Executing test function test.bug.ANNMAP40  ... [1] "Cannot find datasource 'hs-test', so skipping this test." done successfully.Executing test function test.bug.ANNMAP44  ... [1] "Cannot find datasource 'hs-test', so skipping this test." done successfully.Executing test function test.gotsomefunctions  ...  done successfully.Executing test function test.multi.queries  ... [1] "Cannot find datasource 'hs-test', so skipping these tests." done successfully.Executing test function test.range.queries  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."[1] "Cannot find datasource 'mm-test', so skipping these tests."[1] "Cannot find datasource 'rn-test', so skipping these tests."[1] "Cannot find datasource 'pb-test', so skipping these tests." done successfully.Executing test function test.expr.query  ... [1] "Cannot find datasource 'hs-test', so skipping these tests." done successfully.Executing test function test.gotsomefunctions  ...  done successfully.Executing test function test.to.queries  ... [1] "Cannot find datasource 'hs-test', so skipping these tests."[1] "Cannot find datasource 'mm-test', so skipping these tests."[1] "Cannot find datasource 'rn-test', so skipping these tests."[1] "Cannot find datasource 'pb-test', so skipping these tests." done successfully.Executing test function test.transcript.to.translatedprobes  ... [1] "Cannot find datasource 'hs-test', so skipping these tests." done successfully.Executing test function test.ANNMAP.109  ... [1] "Cannot find datasource 'hs-test', so skipping these tests." done successfully.Executing test function test.ANNMAP.97  ... [1] "Cannot find datasource 'hs-test', so skipping these tests." done successfully.Executing test function test.ANNMAP.98  ... [1] "Cannot find datasource 'hs-test', so skipping these tests." done successfully.Executing test function test.array.type  ... [1] "Cannot find datasource 'hs-test', so skipping these tests." done successfully.Executing test function test.make.params  ... [1] "Cannot find datasource 'hs-test', so skipping these tests." done successfully.Executing test function test.needs.array  ...  done successfully.Executing test function test.rangeapply  ... [1] "Cannot find datasource 'hs-test', so skipping these tests." done successfully.Executing test function test.reality  ...  done successfully.Executing test function test.seqnames  ... [1] "Cannot find datasource 'hs-test', so skipping these tests." done successfully.Executing test function test.set.get.params  ...  done successfully.Executing test function test.ANNMAP118  ... [1] "Cannot find datasource 'hs-test', so skipping these tests." done successfully.Executing test function test.michal.utr.bug  ... [1] "Cannot find datasource 'hs-test', so skipping these tests." done successfully.Executing test function test.michal.utr.bug.three  ... [1] "Cannot find datasource 'hs-test', so skipping these tests." done successfully.Executing test function test.michal.utr.bug.two  ... [1] "Cannot find datasource 'hs-test', so skipping these tests." done successfully.Executing test function test.utr  ... [1] "Cannot find datasource 'hs-test', so skipping these tests." done successfully.Executing test function test.yaoyong.utr.bug  ... [1] "Cannot find datasource 'hs-test', so skipping these tests." done successfully.------------------- UNIT TEST SUMMARY ---------------------RUNIT TEST PROTOCOL -- Thu Dec 11 22:00:21 2025 *********************************************** Number of test functions: 40 Number of errors: 0 Number of failures: 0  1 Test Suite : annmap unit testing - 40 test functions, 0 errors, 0 failures> > proc.time()   user  system elapsed   6.132   0.314   6.436