CRAN Package Check Results for Package rbamtools

Last updated on 2017-01-18 18:48:28.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.16.0 12.07 62.41 74.48 ERROR
r-devel-linux-x86_64-debian-gcc 2.16.0 13.51 61.30 74.81 ERROR
r-devel-linux-x86_64-fedora-clang 2.16.0 158.93 ERROR --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 2.16.0 168.03 ERROR --no-stop-on-test-error
r-devel-macos-x86_64-clang 2.16.0 121.58 ERROR --no-stop-on-test-error
r-devel-windows-ix86+x86_64 2.16.0 59.00 135.00 194.00 ERROR
r-patched-linux-x86_64 2.16.0 12.97 56.77 69.74 OK
r-patched-solaris-sparc 2.16.0 849.20 OK
r-patched-solaris-x86 2.16.0 175.10 OK
r-release-linux-x86_64 2.16.0 12.55 56.52 69.07 OK
r-release-osx-x86_64-mavericks 2.16.0 OK
r-release-windows-ix86+x86_64 2.16.0 43.00 182.00 225.00 OK
r-oldrel-windows-ix86+x86_64 2.16.0 46.00 193.00 239.00 OK

Check Details

Version: 2.16.0
Check: files in ‘vignettes’
Result: WARN
    Files in the 'vignettes' directory newer than all files in 'inst/doc':
     ‘rbamtools.Rnw’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64

Version: 2.16.0
Check: tests
Result: ERROR
     Running ‘test-all.R’ [2s/2s]
     Running ‘test_bam_align.r’ [0s/0s]
    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
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 2.16.0
Flags: --no-stop-on-test-error
Check: files in ‘vignettes’
Result: WARN
    Files in the 'vignettes' directory newer than all files in 'inst/doc':
     ‘rbamtools.Rnw’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 2.16.0
Flags: --no-stop-on-test-error
Check: tests
Result: ERROR
     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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 2.16.0
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'test-all.R' [3s]
     Running 'test_bam_align.r' [0s]
    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
Flavor: r-devel-windows-ix86+x86_64

Version: 2.16.0
Check: running tests for arch ‘x64’
Result: ERROR
     Running 'test-all.R' [3s]
     Running 'test_bam_align.r' [0s]
    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
Flavor: r-devel-windows-ix86+x86_64