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GWAtoolbox log file (check_x86_64_linux)

Mon May 18 22:25:11 2015: Checking package GWAtoolbox (SVN revision 102) ...
* using log directory ‘/mnt/building/build_2015-05-18-22-23/RF_PKG_CHECK/PKGS/GWAtoolbox.Rcheck’
* using R version 3.2.0 Patched (2015-05-16 r68378)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘GWAtoolbox/DESCRIPTION’ ... OK
* this is package ‘GWAtoolbox’ version ‘2.2.4-10’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Daniel Taliun ’
New submission

CRAN repository db overrides:
  X-CRAN-Comment: Removed on 2014-12-06 for misrepresentation of
    authorship.

Vignette sources in 'inst/doc' with no 'vignettes' directory:
  ‘GWAtoolbox.Rnw’
A 'vignettes' directory is required as from R 3.1.0

No package encoding and non-ASCII characters in the following R files:
  R/ANNOTATE.R
    2: # Copyright  2011 Daniel Taliun, Christian Fuchsberger and Cristian Pattaro. All rights reserved.
  R/DISPERSION_CHECK.R
    2: # Copyright  2011 Daniel Taliun, Christian Fuchsberger and Cristian Pattaro. All rights reserved.
  R/GWASFORMAT.R
    2: # Copyright  2011 Daniel Taliun, Christian Fuchsberger and Cristian Pattaro. All rights reserved.
  R/GWASQC.R
    2: # Copyright  2011 Daniel Taliun, Christian Fuchsberger and Cristian Pattaro. All rights reserved.
  R/HARMONIZE.R
    2: # Copyright  2012 Daniel Taliun, Christian Fuchsberger and Cristian Pattaro. All rights reserved.
  R/HARMONIZE_BY_POS.R
    2: # Copyright  2012 Daniel Taliun, Christian Fuchsberger and Cristian Pattaro. All rights reserved.
  R/INDEPENDENT_SNPS.R
    2: # Copyright  2012 Daniel Taliun, Christian Fuchsberger and Cristian Pattaro. All rights reserved.
  R/KUSK_CHECK.R
    2: # Copyright  2011 Daniel Taliun, Christian Fuchsberger and Cristian Pattaro. All rights reserved.
  R/PANNOTATE.R
    2: # Copyright  2011 Daniel Taliun, Christian Fuchsberger and Cristian Pattaro. All rights reserved.
  R/PGWASFORMAT.R
    2: # Copyright  2011 Daniel Taliun, Christian Fuchsberger and Cristian Pattaro. All rights reserved.
  R/PGWASQC.R
    2: # Copyright  2011 Daniel Taliun, Christian Fuchsberger and Cristian Pattaro. All rights reserved.
  R/PLOT.R
    2: # Copyright  2011 Daniel Taliun, Christian Fuchsberger and Cristian Pattaro. All rights reserved.
  R/PLOT_COMBINED_BOXPLOTS.R
    2: # Copyright  2011 Daniel Taliun, Christian Fuchsberger and Cristian Pattaro. All rights reserved.
  R/RE.R
    2: # Copyright  2011 Daniel Taliun, Christian Fuchsberger and Cristian Pattaro. All rights reserved.
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped
* 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 whether package ‘GWAtoolbox’ can be installed ... [50s/51s] OK
* checking installed package size ... NOTE
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   5.5Mb
* checking package 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 ... NOTE
'library' or 'require' call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
pannotate: no visible global function definition for ‘makeCluster’
pannotate: no visible global function definition for ‘clusterExport’
pannotate: no visible global function definition for ‘clusterEvalQ’
pannotate: no visible global function definition for ‘clusterApply’
pannotate: no visible global function definition for ‘stopCluster’
pgwasformat: no visible global function definition for ‘makeCluster’
pgwasformat: no visible global function definition for ‘clusterExport’
pgwasformat: no visible global function definition for ‘clusterEvalQ’
pgwasformat: no visible global function definition for ‘clusterApply’
pgwasformat: no visible global function definition for ‘stopCluster’
pgwasqc: no visible global function definition for ‘makeCluster’
pgwasqc: no visible global function definition for ‘clusterExport’
pgwasqc: no visible global function definition for ‘clusterEvalQ’
pgwasqc: no visible global function definition for ‘clusterApply’
pgwasqc: no visible global function definition for ‘stopCluster’
* checking Rd files ... NOTE
prepare_Rd: re.Rd:123: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'harmonize.Rd':
  \usage lines wider than 90 characters:
     harmonize(input, output, vcf, chromosome = "chr", id = "markername", alleles = c("ref_allele", "non_ref_allele"), sep = "\t", vcf_allel ... [TRUNCATED]

Rd file 'harmonize_by_pos.Rd':
  \usage lines wider than 90 characters:
     harmonize_by_pos(input, output, vcf, id = "markername", chromosome = "chr", position="position", alleles = c("first_allele", "second_al ... [TRUNCATED]

Rd file 'pgwasformat.Rd':
  \examples lines wider than 100 characters:
             # all input and output files are located in the subdirectory "doc" of the installed GWAtoolbox package

Rd file 'pgwasqc.Rd':
  \examples lines wider than 100 characters:
             # all input and output files are located in the subdirectory "doc" of the installed GWAtoolbox package

These lines will be truncated in the PDF manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ...Warning in grep("^ *#", contents, value = TRUE, invert = TRUE) :
  input string 2 is invalid in this locale
Error in grep("^ *#", contents, value = TRUE, invert = TRUE) : 
  attempt to set index 7/7 in SET_STRING_ELT
Execution halted
Run time: 113.21 seconds.