CRAN Package Check Results for Package rbamtools

Last updated on 2016-12-08 06:48:33.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.16.0 11.45 63.03 74.48 ERROR
r-devel-linux-x86_64-debian-gcc 2.16.0 14.16 62.61 76.77 ERROR
r-devel-linux-x86_64-fedora-clang 2.16.0 174.41 ERROR --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 2.16.0 172.30 ERROR --no-stop-on-test-error
r-devel-macos-x86_64-clang 2.16.0 126.38 ERROR --no-stop-on-test-error
r-devel-windows-ix86+x86_64 2.16.0 42.00 184.00 226.00 ERROR
r-patched-linux-x86_64 2.16.0 12.72 56.66 69.38 OK
r-patched-solaris-sparc 2.16.0 820.70 OK
r-patched-solaris-x86 2.16.0 173.40 OK
r-release-linux-x86_64 2.16.0 12.95 57.62 70.57 OK
r-release-osx-x86_64-mavericks 2.16.0 OK
r-release-windows-ix86+x86_64 2.16.0 42.00 124.00 166.00 OK
r-oldrel-windows-ix86+x86_64 2.16.0 61.00 143.00 204.00 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.
    Last 13 lines of output:
     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.
    
     >
     >
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
     > # test_bam_align: General
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
     > align <- getNextAlign(reader)
     Error: 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.
    Last 13 lines of output:
     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.
    
     >
     >
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
     > # test_bam_align: General
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
     > align <- getNextAlign(reader)
     Error: could not find function "getNextAlign"
     Execution halted
    Running the tests in ‘tests/test_bam_header.r’ failed.
    Last 13 lines of output:
     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.
    
     >
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
     > # test_bam_header: General
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
     > header<-getHeader(reader)
     Error: could not find function "getHeader"
     Execution halted
    Running the tests in ‘tests/test_bam_range.r’ failed.
    Last 13 lines of output:
     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.
    
     >
     > coords<-getRefCoords(reader,"chr1")
     Error: could not find function "getRefCoords"
     Execution halted
    Running the tests in ‘tests/test_genome_partition.r’ failed.
    Last 13 lines of output:
     > 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: could not find function "genomePartition"
     Execution halted
    Running the tests in ‘tests/test_range_seg_count.r’ failed.
    Last 13 lines of output:
    
     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.
    
     >
     >
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
     > # Count alignments in specified genomic segments
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
     > coords <- c(0, 0, 2e4)
     > segments <- seq(14000, 20000, 20)
     > segcount<-rangeSegCount(reader, coords, segments)
     Error: could not find function "rangeSegCount"
     Execution halted
    Running the tests in ‘tests/test_vector_segmentation.r’ failed.
    Last 13 lines of output:
     '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.
    
     >
     > ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ##
     > ## 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: 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' [4s]
     Running 'test_bam_align.r' [1s]
    Running the tests in 'tests/test_bam_align.r' failed.
    Last 13 lines of output:
     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.
    
     >
     >
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
     > # test_bam_align: General
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
     > align <- getNextAlign(reader)
     Error: 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' [5s]
     Running 'test_bam_align.r' [1s]
    Running the tests in 'tests/test_bam_align.r' failed.
    Last 13 lines of output:
     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.
    
     >
     >
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
     > # test_bam_align: General
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
     > align <- getNextAlign(reader)
     Error: could not find function "getNextAlign"
     Execution halted
Flavor: r-devel-windows-ix86+x86_64