R Development Page

MultiABEL log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2019-03-12-18-09/RF_PKG_CHECK/PKGS/MultiABEL.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'MultiABEL/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MultiABEL' version '1.1-9'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Xia Shen '

New submission

Package was archived on CRAN

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2018-07-03 as check problems were not
    corrected despite reminders.

Suggests or Enhances not in mainstream repositories:
  GenABEL, DatABEL

The Description field contains
  https://github.com/xiashen/MultiABEL
Please enclose URLs in angle brackets (<...>).

The Date field is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking: 'GenABEL' 'DatABEL'
* 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 serialization versions ... OK
* checking whether package 'MultiABEL' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
MV.cor.test: no visible binding for global variable 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'MV.cor.test.Rd':
  \examples lines wider than 100 characters:
     res.mv.cor <- MV.cor.test(marker = "rs905938", gwa.1 = example.gwa.1, gwa.2 = example.gwa.2, R.1 = example.R.1,
       geom_point(data=df.plot, mapping=aes(x=rank.1, y=rank.2, color=traits, size = se.beta), alpha = 0.2) + 
       stat_smooth(data=df.plot, mapping=aes(x=rank.1, y=rank.2), method = "lm", se=FALSE, color="black", size=0.3, fullrange = TRUE) + 
             legend.background=element_rect(colour='NA', fill='transparent'), legend.key=element_blank(), 
       geom_bar(stat = "identity", aes(fill=traits), width = 0.4) + theme(legend.position="none") + theme(

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  'example.gwa.1' 'example.gwa.2' 'example.R.1' 'example.R.2'
  'example.gwas' 'example.LD' 'example.R.ref' 'example.snp.ref'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'load.summary'
  'data.table'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 'MultiABEL/libs/x64/MultiABEL.dll':
  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 examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 6 NOTEs
See
  'R:/run/building/build_2019-03-12-18-09/RF_PKG_CHECK/PKGS/MultiABEL.Rcheck/00check.log'
for details.


Run time: 64.99 seconds.