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LDExplorer log file (check_x86_64_linux)

Mon Nov 25 12:25:48 2013: Checking package LDExplorer (SVN revision 59) ...
* using log directory ‘/mnt/building/build_2013-11-25-12-13/RF_PKG_CHECK/PKGS/LDExplorer.Rcheck’
* using R version 3.0.2 Patched (2013-11-22 r64286)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘LDExplorer/DESCRIPTION’ ... OK
* this is package ‘LDExplorer’ version ‘1.0.3’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Daniel Taliun ’
* 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 whether package ‘LDExplorer’ can be installed ... [23s/57s] OK
* checking installed package size ... OK
* 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file ‘/mnt/building/build_2013-11-25-12-13/RF_PKG_CHECK/PKGS/LDExplorer.Rcheck/00_pkg_src/LDExplorer/man/create_browser_track.Rd’:
  \usage lines wider than 90 characters:
             create_browser_track(input_file, output_file, chromosome, strand, track_name = "", track_desc = "")

Rd file ‘/mnt/building/build_2013-11-25-12-13/RF_PKG_CHECK/PKGS/LDExplorer.Rcheck/00_pkg_src/LDExplorer/man/ld.Rd’:
  \usage lines wider than 90 characters:
             ld(phase_file, snps_file, output_file, window = 500000, coefficient = "dprime", maf = 0.0, gzip = TRUE)

Rd file ‘/mnt/building/build_2013-11-25-12-13/RF_PKG_CHECK/PKGS/LDExplorer.Rcheck/00_pkg_src/LDExplorer/man/mig_multi_chr.Rd’:
  \usage lines wider than 90 characters:
             mig_multi_chr(phase_files, output_files, processes = 1, phase_file_format = "VCF", 

Rd file ‘/mnt/building/build_2013-11-25-12-13/RF_PKG_CHECK/PKGS/LDExplorer.Rcheck/00_pkg_src/LDExplorer/man/mig_multi_regions.Rd’:
  \usage lines wider than 90 characters:
             mig_multi_regions(phase_file, output_files, regions_start, regions_end, processes = 1, 
  \examples lines wider than 100 characters:
          output_file = c("HapMapII_r22_CEU_chr20_31767872_32767871.blocks.txt", "HapMapII_r22_CEU_chr20_32767872_33700401.blocks.txt"),

Rd file ‘/mnt/building/build_2013-11-25-12-13/RF_PKG_CHECK/PKGS/LDExplorer.Rcheck/00_pkg_src/LDExplorer/man/mig_rsq.Rd’:
  \usage lines wider than 90 characters:
             weak_rsq = 0.5, strong_rsq = 0.8, fraction = 0.95, pruning_method = "MIG++", window = NULL)

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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [22s/50s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
mig               15.821  0.224  38.457
mig_multi_regions  4.720  0.132   7.867
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/mnt/building/build_2013-11-25-12-13/RF_PKG_CHECK/PKGS/LDExplorer.Rcheck/00check.log’
for details.

Run time: 193.12 seconds.