Running ‘test-all.R’
  Running ‘test_overlap_juncs.r’
  Running ‘test_read_gtf.r’
  Running ‘test_unify_juncs.r’
  Running ‘test_unify_ranges.r’
Running the tests in ‘tests/test_overlap_juncs.r’ failed.
Complete output:
  > 
  > 
  > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
  > # Requires: Initialized objects (as done by test-all.R header)
  > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
  > 
  > 
  > ##                      1       2       3       4       5       6       7 ##
  > qry<-data.frame(id = 1:7, seqid = "1",
  +             lstart = c(10100L, 11800L, 12220L, 12220L, 12220L, 32000L, 40000L),
  +             lend =   c(10100L, 12000L, 12225L, 12227L, 12227L, 32100L, 40100L),
  +             rstart = c(10200L, 12200L, 12057L, 12613L, 12650L, 32200L, 40200L),
  +             rend =   c(10300L, 12250L, 12179L, 12620L, 12700L, 32300L, 40300L))
  > ##                      1       2       3       4       5       6       7 ##
  > 
  > 
  > # C) 
  > res<-overlapJuncs(qry,junc)
  Error in overlapJuncs(qry, junc) : could not find function "overlapJuncs"
  Execution halted
Running the tests in ‘tests/test_read_gtf.r’ failed.
Complete output:
  > 
  > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
  > ## Tests read.gtf features
  > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
  > 
  > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
  > ## hs.ensembl.76.small.gtf
  > ## contains the first 100 lines of file
  > ## ftp://ftp.ensembl.org/pub/release-76/gtf/
  > ##                                  homo_sapiens/Homo_sapiens.GRCh38.76.gtf.gz
  > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
  > 
  > ens76 <- system.file("extdata",
  +             "hs.ensembl.76.small.gtf", package = "refGenome", mustWork=TRUE)
  > 
  > en76 <- ensemblGenome()
  Error in ensemblGenome() : could not find function "ensemblGenome"
  Execution halted
Running the tests in ‘tests/test_unify_juncs.r’ failed.
Complete output:
  > 
  > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
  > # Requires: Initialized objects (as done by test-all.R header)
  > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
  > 
  > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
  > # Artificially added transcript_biotype data from ensembl version 80
  > # For transcript_id's which are not found idn ensembl 80,
  > # the transcript_biotype is manually set to "nonsense_mediated_decay".
  > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
  > # ensfile <- system.file("extdata", "hs.ensembl.62.small.RData",
  > #                                         package = "refGenome", mustWork=TRUE)
  > # ens <- loadGenome(ensfile)
  > # jtn <- ens@ev$gtf$transcript_id
  > # mtc <- match(jtn, en80@ev$gtf$transcript_id)
  > # biot <- en80@ev$gtf$transcript_biotype[mtc]
  > # biot[is.na(biot)] <- "nonsense_mediated_decay"
  > # ens@ev$gtf$transcript_biotype <- biot
  > # saveGenome(ens, 
  > #     file="~/projects/R/refGenome/inst/extdata/hs.ensembl.62.small.RData",
  > #     useBasedir=FALSE)
  > # 
  > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
  > 
  > 
  > uj <- unifyJuncs(junc)
  Error in unifyJuncs(junc) : could not find function "unifyJuncs"
  Execution halted
Running the tests in ‘tests/test_unify_ranges.r’ failed.
Complete output:
  > 
  > 
  > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
  > # Output consistency of unify Ranges:
  > # Consecutive ranges must not ovelap.
  > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
  > 
  > urg <- unifyRanges(enex)
  Error in unifyRanges(enex) : could not find function "unifyRanges"
  Execution halted