Issue #36 resolved
Jason Vander Heiden created an issue

From CRAN:

using R version 3.1.3 (2015-03-09)
using platform: x86_64-w64-mingw32 (64-bit)
using session charset: ISO8859-1
checking for file 'alakazam/DESCRIPTION' ... OK
checking extension type ... Package
this is package 'alakazam' version '0.2.2'
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 hidden files and directories ... OK
checking for portable file names ... OK
checking whether package 'alakazam' can be installed ... OK
checking installed package size ... 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 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 ... NOTE
aliphatic: possible error in nchar(gsub("[X\\.\\*-]", "", seq), keepNA
  = TRUE): unused argument (keepNA = TRUE)
aminoAcidProperties: possible error in nchar(region_aa, keepNA = TRUE):
  unused argument (keepNA = TRUE)
aminoAcidProperties: possible error in nchar(gsub("[X\\.\\*-]", "",
  region_aa), keepNA = TRUE): unused argument (keepNA = TRUE)
charge: possible error in nchar(gsub("[X\\.\\*-]", "", seq), keepNA =
  TRUE): unused argument (keepNA = TRUE)
countPatterns: possible error in nchar(region_aa, keepNA = TRUE):
  unused argument (keepNA = TRUE)
checking Rd files ... OK
checking Rd metadata ... 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 R/sysdata.rda ... OK
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 'alakazam-Ex.R' failed
The error most likely occurred in:

> ### Name: aliphatic
> ### Title: Calculates the aliphatic index of amino acid sequences
> ### Aliases: aliphatic
> 
> ### ** Examples
> 
> seq <- c("CARDRSTPWRRGIASTTVRTSW", "XXTQMYVRT")
> aliphatic(seq)
Error in nchar(gsub("[X\\.\\*-]", "", seq), keepNA = TRUE) : 
  unused argument (keepNA = TRUE)
Calls: aliphatic -> nchar
Execution halted
Please either fix or declare

Depends: R (>= 3.2.0)

in your DESCRIPTION file. 

Comments (3)

  1. Jason Vander Heiden reporter

    Due to the use of the keepNA argument to nchar(), which is a new feature. We should be able to check the package using the R-3.1.2 build on louise in /usr/local/cluster/software/installation/R.

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