CRAN Package Check Results for Package yCrypticRNAs

Last updated on 2018-05-09 22:49:04 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.99.2 38.90 61.21 100.11 ERROR
r-devel-linux-x86_64-debian-gcc 0.99.2 30.12 47.14 77.26 ERROR
r-devel-linux-x86_64-fedora-clang 0.99.2 122.23 ERROR
r-devel-linux-x86_64-fedora-gcc 0.99.2 116.54 ERROR
r-devel-windows-ix86+x86_64 0.99.2 83.00 120.00 203.00 ERROR
r-patched-linux-x86_64 0.99.2 41.53 51.06 92.59 ERROR
r-patched-solaris-x86 0.99.2 137.20 ERROR
r-release-linux-x86_64 0.99.2 41.47 50.92 92.39 ERROR
r-release-windows-ix86+x86_64 0.99.2 83.00 120.00 203.00 ERROR
r-release-osx-x86_64 0.99.2 ERROR
r-oldrel-windows-ix86+x86_64 0.99.2 83.00 300.00 383.00 OK
r-oldrel-osx-x86_64 0.99.2 OK

Check Details

Version: 0.99.2
Check: compiled code
Result: NOTE
    File ‘yCrypticRNAs/libs/yCrypticRNAs.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.99.2
Check: examples
Result: ERROR
    Running examples in ‘yCrypticRNAs-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: bam_to_reads
    > ### Title: Convert BAM files into BED files containing the reads overlaping
    > ### the specified annotations.
    > ### Aliases: bam_to_reads
    >
    > ### ** Examples
    >
    > bamfile <- system.file("extdata", "wt_rep1.bam", package = "yCrypticRNAs")
    > data(annotations)
    > bam_to_reads(bamfile, annotations)
    Error in FUN(X[[i]], ...) : failed to build index
     file: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
    Calls: bam_to_reads -> .index_bam
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.99.2
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Quitting from lines 48-60 (yCrypticRNAs.Rmd)
    Error: processing vignette ‘yCrypticRNAs.Rmd’ failed with diagnostics:
    failed to build index
     file: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.99.2
Check: examples
Result: ERROR
    Running examples in ‘yCrypticRNAs-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: bam_to_reads
    > ### Title: Convert BAM files into BED files containing the reads overlaping
    > ### the specified annotations.
    > ### Aliases: bam_to_reads
    >
    > ### ** Examples
    >
    > bamfile <- system.file("extdata", "wt_rep1.bam", package = "yCrypticRNAs")
    > data(annotations)
    > bam_to_reads(bamfile, annotations)
    Error in FUN(X[[i]], ...) : failed to build index
     file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
    Calls: bam_to_reads -> .index_bam
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.99.2
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Quitting from lines 48-60 (yCrypticRNAs.Rmd)
    Error: processing vignette ‘yCrypticRNAs.Rmd’ failed with diagnostics:
    failed to build index
     file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.99.2
Check: examples
Result: ERROR
    Running examples in ‘yCrypticRNAs-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: bam_to_reads
    > ### Title: Convert BAM files into BED files containing the reads overlaping
    > ### the specified annotations.
    > ### Aliases: bam_to_reads
    >
    > ### ** Examples
    >
    > bamfile <- system.file("extdata", "wt_rep1.bam", package = "yCrypticRNAs")
    > data(annotations)
    > bam_to_reads(bamfile, annotations)
    Warning: The RangesList() constructor is deprecated. Please coerce to
     IRangesList instead e.g. do 'as(list(x1, x2), "IRangesList")' instead
     of 'RangesList(x1, x2)'. Alternatively, you can use the IRangesList()
     constructor e.g. 'IRangesList(x1, x2, compress=FALSE)'. See
     '?IRangesList' for more information.
    Error in new(Class) :
     trying to generate an object from a virtual class ("SimpleIntegerRangesList")
    Calls: bam_to_reads ... .bam_to_reads_by_gene -> <Anonymous> -> <Anonymous> -> new
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86

Version: 0.99.2
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Quitting from lines 48-60 (yCrypticRNAs.Rmd)
    Error: processing vignette 'yCrypticRNAs.Rmd' failed with diagnostics:
    trying to generate an object from a virtual class ("SimpleIntegerRangesList")
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64

Version: 0.99.2
Check: running examples for arch ‘i386’
Result: ERROR
    Running examples in 'yCrypticRNAs-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: bam_to_reads
    > ### Title: Convert BAM files into BED files containing the reads overlaping
    > ### the specified annotations.
    > ### Aliases: bam_to_reads
    >
    > ### ** Examples
    >
    > bamfile <- system.file("extdata", "wt_rep1.bam", package = "yCrypticRNAs")
    > data(annotations)
    > bam_to_reads(bamfile, annotations)
    Warning: The RangesList() constructor is deprecated. Please coerce to
     IRangesList instead e.g. do 'as(list(x1, x2), "IRangesList")' instead
     of 'RangesList(x1, x2)'. Alternatively, you can use the IRangesList()
     constructor e.g. 'IRangesList(x1, x2, compress=FALSE)'. See
     '?IRangesList' for more information.
    Error in new(Class) :
     trying to generate an object from a virtual class ("SimpleIntegerRangesList")
    Calls: bam_to_reads ... .bam_to_reads_by_gene -> <Anonymous> -> <Anonymous> -> new
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64

Version: 0.99.2
Check: running examples for arch ‘x64’
Result: ERROR
    Running examples in 'yCrypticRNAs-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: bam_to_reads
    > ### Title: Convert BAM files into BED files containing the reads overlaping
    > ### the specified annotations.
    > ### Aliases: bam_to_reads
    >
    > ### ** Examples
    >
    > bamfile <- system.file("extdata", "wt_rep1.bam", package = "yCrypticRNAs")
    > data(annotations)
    > bam_to_reads(bamfile, annotations)
    Warning: The RangesList() constructor is deprecated. Please coerce to
     IRangesList instead e.g. do 'as(list(x1, x2), "IRangesList")' instead
     of 'RangesList(x1, x2)'. Alternatively, you can use the IRangesList()
     constructor e.g. 'IRangesList(x1, x2, compress=FALSE)'. See
     '?IRangesList' for more information.
    Error in new(Class) :
     trying to generate an object from a virtual class ("SimpleIntegerRangesList")
    Calls: bam_to_reads ... .bam_to_reads_by_gene -> <Anonymous> -> <Anonymous> -> new
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64

Version: 0.99.2
Check: examples
Result: ERROR
    Running examples in ‘yCrypticRNAs-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: bam_to_reads
    > ### Title: Convert BAM files into BED files containing the reads overlaping
    > ### the specified annotations.
    > ### Aliases: bam_to_reads
    >
    > ### ** Examples
    >
    > bamfile <- system.file("extdata", "wt_rep1.bam", package = "yCrypticRNAs")
    > data(annotations)
    > bam_to_reads(bamfile, annotations)
    Error in FUN(X[[i]], ...) : failed to build index
     file: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
    Calls: bam_to_reads -> .index_bam
    Execution halted
Flavor: r-patched-linux-x86_64

Version: 0.99.2
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Quitting from lines 48-60 (yCrypticRNAs.Rmd)
    Error: processing vignette ‘yCrypticRNAs.Rmd’ failed with diagnostics:
    failed to build index
     file: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
    Execution halted
Flavor: r-patched-linux-x86_64

Version: 0.99.2
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Quitting from lines 48-60 (yCrypticRNAs.Rmd)
    Error: processing vignette 'yCrypticRNAs.Rmd' failed with diagnostics:
    trying to generate an object from a virtual class ("SimpleIntegerRangesList")
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.99.2
Check: examples
Result: ERROR
    Running examples in ‘yCrypticRNAs-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: bam_to_reads
    > ### Title: Convert BAM files into BED files containing the reads overlaping
    > ### the specified annotations.
    > ### Aliases: bam_to_reads
    >
    > ### ** Examples
    >
    > bamfile <- system.file("extdata", "wt_rep1.bam", package = "yCrypticRNAs")
    > data(annotations)
    > bam_to_reads(bamfile, annotations)
    Error in FUN(X[[i]], ...) : failed to build index
     file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
    Calls: bam_to_reads -> .index_bam
    Execution halted
Flavor: r-release-linux-x86_64

Version: 0.99.2
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Quitting from lines 48-60 (yCrypticRNAs.Rmd)
    Error: processing vignette ‘yCrypticRNAs.Rmd’ failed with diagnostics:
    failed to build index
     file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
    Execution halted
Flavor: r-release-linux-x86_64

Version: 0.99.2
Check: package dependencies
Result: ERROR
    Package required but not available: ‘Rsamtools’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64