##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:annmap.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings annmap_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/annmap.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘annmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘annmap’ version ‘1.48.0’
* 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:
  .BBSoptions
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 ‘annmap’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
* 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 ... 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.table
Consider 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 ... NOTE
checkRd: (-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 ... WARNING
Missing link or links in Rd file 'annmap.range.Rd':
  ‘RangedData’

Missing link or links in Rd file 'annmap.utils.Rd':
  ‘RangedData’

Missing link or links in Rd file 'plot.ngs.Rd':
  ‘[IRanges]{Rle}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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
* DONE

Status: 1 WARNING, 6 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/annmap.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL annmap
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘annmap’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
in 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> 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] "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/annmap.Rcheck/tests"

$pathToUnitTests
[1] "/tmp/Rtmp8TFTjw/RLIBS_1efaec6453b0f3/annmap/unitTests"

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The 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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Using /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 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/annmap/unitTests/tabConfig"
[1] "setting conf.dir to /media/volume/teran2_disk/biocbuild/bbs-3.20-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 -- Tue Nov 19 22:49:53 2024 
*********************************************** 
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 
  5.708   0.388   6.184