• 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