Running ‘test-all.R’
  Running ‘test_bam_align.r’
  Running ‘test_bam_header.r’
  Running ‘test_bam_range.r’
  Running ‘test_genome_partition.r’
  Running ‘test_range_seg_count.r’
  Running ‘test_vector_segmentation.r’
Running the tests in ‘tests/test_bam_align.r’ failed.
Complete output:
  > 
  > 
  > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
  > # test_bam_align: General
  > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
  > align <- getNextAlign(reader)
  Error in getNextAlign(reader) : could not find function "getNextAlign"
  Execution halted
Running the tests in ‘tests/test_bam_header.r’ failed.
Complete output:
  > 
  > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
  > # test_bam_header: General
  > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
  > header<-getHeader(reader)
  Error in getHeader(reader) : could not find function "getHeader"
  Execution halted
Running the tests in ‘tests/test_bam_range.r’ failed.
Complete output:
  > 
  > coords<-getRefCoords(reader,"chr1")
  Error in getRefCoords(reader, "chr1") : 
    could not find function "getRefCoords"
  Execution halted
Running the tests in ‘tests/test_genome_partition.r’ failed.
Complete output:
  > 
  > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
  > # Create genomePartition object
  > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
  > # Open (indexed) BAM file (done by calling test-all.R)
  > # bam<-system.file("extdata", "accepted_hits.bam", package="rbamtools")
  > # reader<-bamReader(bam,idx=TRUE)
  > 
  > # Provide exon positions
  > id <- 1:13
  > seqid <- "chr1"
  > gene <- "WASH7P"
  > ensg_id <- "ENSG00000227232"
  > start <- c(14411, 15000, 15796, 15904, 16607, 16748, 16858, 17233,
  +            17602, 17915, 18268, 24737, 29534)
  > end <-   c(14502, 15038, 15901, 15947, 16745, 16765, 17055, 17364,
  +            17742, 18061, 18366, 24891, 29806)
  > 
  > ref <- data.frame(id=id, seqid=seqid, begin=start, end=end, gene=gene, ensg=ensg_id)
  > 
  > # Create partition (adds equidistant grid)
  > partition <- genomePartition(reader, ref)
  Error in genomePartition(reader, ref) : 
    could not find function "genomePartition"
  Execution halted
Running the tests in ‘tests/test_range_seg_count.r’ failed.
Complete output:
  > 
  > 
  > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
  > # Count alignments in specified genomic segments
  > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
  > coords <- c(0, 0, 2e4)
  > segments <- seq(14000, 20000, 20)
  > segcount<-rangeSegCount(reader, coords, segments)
  Error in rangeSegCount(reader, coords, segments) : 
    could not find function "rangeSegCount"
  Execution halted
Running the tests in ‘tests/test_vector_segmentation.r’ failed.
Complete output:
  > 
  > ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ##
  > ## Test vector segmentation
  > ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ##
  > 
  > if(any(multSeq(c(1, 4, 7), c(2, 5, 8)) != c(1,2, 4,5, 7,8)))
  +     stop("[test_vector_segmentation] Wrong multSeq value!")
  Error in multSeq(c(1, 4, 7), c(2, 5, 8)) : 
    could not find function "multSeq"
  Execution halted