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 |
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