CRAN Package Check Results for Package rbamtools

Last updated on 2014-09-02 13:47:03.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.9.14 5.23 22.83 28.06 NOTE
r-devel-linux-x86_64-debian-gcc 2.9.14 8.76 22.47 31.22 NOTE
r-devel-linux-x86_64-fedora-clang 2.9.14 62.19 NOTE
r-devel-linux-x86_64-fedora-gcc 2.9.14 61.44 NOTE
r-devel-osx-x86_64-clang 2.9.14 56.80 NOTE
r-devel-windows-ix86+x86_64 2.9.14 33.00 49.00 82.00 NOTE
r-patched-linux-x86_64 2.9.14 9.05 23.52 32.57 OK
r-patched-solaris-sparc 2.9.14 404.30 OK
r-patched-solaris-x86 2.9.14 89.80 OK
r-release-linux-ix86 2.9.14 11.60 32.83 44.44 OK
r-release-linux-x86_64 2.9.14 8.93 23.72 32.66 OK
r-release-osx-x86_64-mavericks 2.9.14 NOTE
r-release-osx-x86_64-snowleopard 2.9.14 ERROR
r-release-windows-ix86+x86_64 2.9.14 29.00 50.00 79.00 OK
r-oldrel-windows-ix86+x86_64 2.9.14 30.00 54.00 84.00 OK

Check Details

Version: 2.9.14
Check: compiled code
Result: NOTE
    File ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rbamtools/libs/rbamtools.so’:
     Found ‘rand’, possibly from ‘rand’ (C)
     Objects: ‘samtools/bam_index.o’, ‘samtools/bam_sort.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the C RNG.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.9.14
Check: compiled code
Result: NOTE
    File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rbamtools/libs/rbamtools.so’:
     Found ‘rand’, possibly from ‘rand’ (C)
     Objects: ‘samtools/bam_index.o’, ‘samtools/bam_sort.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the C RNG.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.9.14
Check: compiled code
Result: NOTE
    File ‘/data/gannet/ripley/R/packages/tests-clang/rbamtools.Rcheck/rbamtools/libs/rbamtools.so’:
     Found ‘rand’, possibly from ‘rand’ (C)
     Objects: ‘samtools/bam_index.o’, ‘samtools/bam_sort.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the C RNG.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2.9.14
Check: compiled code
Result: NOTE
    File ‘/data/gannet/ripley/R/packages/tests-devel/rbamtools.Rcheck/rbamtools/libs/rbamtools.so’:
     Found ‘rand’, possibly from ‘rand’ (C)
     Objects: ‘samtools/bam_index.o’, ‘samtools/bam_sort.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the C RNG.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 2.9.14
Check: compiled code
Result: NOTE
    File ‘/Users/ripley/R/packages/tests-devel/rbamtools.Rcheck/rbamtools/libs/rbamtools.so’:
     Found ‘_rand’, possibly from ‘rand’ (C)
     Objects: ‘samtools/bam_index.o’, ‘samtools/bam_sort.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the C RNG.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavor: r-devel-osx-x86_64-clang

Version: 2.9.14
Check: compiled code
Result: NOTE
    File 'd:/Rcompile/CRANpkg/lib/3.2/rbamtools/libs/i386/rbamtools.dll':
     Found 'rand', possibly from 'rand' (C)
     Objects: 'samtools/bam_index.o', 'samtools/bam_sort.o'
    File 'd:/Rcompile/CRANpkg/lib/3.2/rbamtools/libs/x64/rbamtools.dll':
     Found 'rand', possibly from 'rand' (C)
     Objects: 'samtools/bam_index.o', 'samtools/bam_sort.o'
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the C RNG.
    
    See 'Writing portable packages' in the 'Writing R Extensions' manual.
Flavor: r-devel-windows-ix86+x86_64

Version: 2.9.14
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Warning in text.default(xlim[1], 2, transcript, adj = 0, cex = 1.2) :
     font width unknown for character 0x9
    Warning in text.default(xlim[1], 2, transcript, adj = 0, cex = 1.2) :
     font width unknown for character 0x9
    Warning in text.default(xlim[1], 2, transcript, adj = 0, cex = 1.2) :
     font metrics unknown for character 0x9
    Warning in text.default(xlim[1], 2, transcript, adj = 0, cex = 1.2) :
     font metrics unknown for character 0x9
    Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
     Running 'texi2dvi' on 'rbamtools.tex' failed.
    LaTeX errors:
    ! LaTeX Error: File `sectsty.sty' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    
    gn_test/rbamtools/vignettes/rbamtools.tex:25: ==> Fatal error occurred, no out
    put PDF file produced!
    Calls: buildVignettes -> texi2pdf -> texi2dvi
    Execution halted
Flavor: r-release-osx-x86_64-mavericks

Version: 2.9.14
Check: examples
Result: ERROR
    Running examples in ‘rbamtools-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: range2fastq
    > ### Title: range2fastq
    > ### Aliases: range2fastq range2fastq-methods range2fastq,bamRange-method
    > ### Keywords: range2fastq range2fastq
    >
    > ### ** Examples
    >
    > bam<-system.file("extdata","accepted_hits.bam",package="rbamtools")
    > reader<-bamReader(bam,idx=TRUE)
    > coords<-as.integer(c(0,0,249250621))
    > range<-bamRange(reader,coords)
    > range2fastq(range,"range.fq.gz")
    Error in range2fastq(range, "range.fq.gz") :
     [bam_range_write_fastq] File could not be opened!
    Calls: range2fastq -> range2fastq -> .Call
    Execution halted
Flavor: r-release-osx-x86_64-snowleopard