- using R version 3.5.0 RC (2018-04-16 r74625)
- using platform: x86_64-pc-linux-gnu (64-bit)
- using session charset: UTF-8
- checking for file ‘yCrypticRNAs/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘yCrypticRNAs’ version ‘0.99.2’
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking serialization versions ... OK
- checking whether package ‘yCrypticRNAs’ can be installed ... OK
- checking package directory ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking loading without being on the library search path ... OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [7s/9s] OK
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compilation flags used ... OK
- checking compiled code ... 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.
- checking sizes of PDF files under ‘inst/doc’ ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... 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
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [1s/2s] OK
Running ‘testthat.R’ [1s/1s]
Running ‘yCrypticRNAs_tests.R’ [0s/1s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in ‘inst/doc’ ... OK
- checking re-building of vignette outputs ... [6s/7s] WARNING
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
- checking PDF version of manual ... OK
- DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE