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synDss log file (check_x86_64_linux)

Fri Dec 13 00:22:51 2013: Checking package synDss (SVN revision 124) ...
* using log directory ‘/mnt/building/build_2013-12-13-00-12/RF_PKG_CHECK/PKGS/synDss.Rcheck’
* using R version 3.0.2 Patched (2013-12-11 r64449)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘synDss/DESCRIPTION’ ... OK
* this is package ‘synDss’ version ‘0.0-1’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Peter Chi ’
New submission
* 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 ‘synDss’ can be installed ... [9s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file found at top level:
  ‘doc’
* 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
conv.evol: no visible binding for global variable ‘codon.map’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file ‘/mnt/building/build_2013-12-13-00-12/RF_PKG_CHECK/PKGS/synDss.Rcheck/00_pkg_src/synDss/man/calc.null.pboot.syn.Rd’:
  \usage lines wider than 90 characters:
     calc.null.pboot.syn(data, B, l, m, syn.matrix, exhaustive=F, codeml="codeml", evolver="evolverNSsites 6")

Rd file ‘/mnt/building/build_2013-12-13-00-12/RF_PKG_CHECK/PKGS/synDss.Rcheck/00_pkg_src/synDss/man/sim.codon.Rd’:
  \usage lines wider than 90 characters:
     sim.codon(n.taxa, n.codons, reps, tree, freqs = c(0.6, 0.3, 0.1), omega = c(0.1, 0.8, 3.2), kap = 2, call="evolverNSsites 6")

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... WARNING
Missing link or links in documentation object ‘/mnt/building/build_2013-12-13-00-12/RF_PKG_CHECK/PKGS/synDss.Rcheck/00_pkg_src/synDss/man/calc.Dss.syn.Rd’:
  ‘regist.synonym’

Missing link or links in documentation object ‘/mnt/building/build_2013-12-13-00-12/RF_PKG_CHECK/PKGS/synDss.Rcheck/00_pkg_src/synDss/man/calc.null.pboot.Rd’:
  ‘calc.Dss.all’

Missing link or links in documentation object ‘/mnt/building/build_2013-12-13-00-12/RF_PKG_CHECK/PKGS/synDss.Rcheck/00_pkg_src/synDss/man/calc.null.pboot.syn.Rd’:
  ‘regist.synonym’

See the information in section ‘Cross-references’ of the ‘Writing R
Extensions’ manual.

* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'calc.null.pboot':
calc.null.pboot
  Code: function(data, B, l, m, exhaustive = F, codeml = "codeml",
                 evolver = "evolverNSsites")
  Docs: function(data, B, l, m, exhaustive = F, codeml = "codeml",
                 evolver = "evolverNSsites 6")
  Mismatches in argument default values:
    Name: 'evolver' Code: "evolverNSsites" Docs: "evolverNSsites 6"

Codoc mismatches from documentation object 'calc.null.pboot.syn':
calc.null.pboot.syn
  Code: function(data, B, l, m, syn.matrix, exhaustive = F, codeml =
                 "codeml", evolver = "evolverNSsites")
  Docs: function(data, B, l, m, syn.matrix, exhaustive = F, codeml =
                 "codeml", evolver = "evolverNSsites 6")
  Mismatches in argument default values:
    Name: 'evolver' Code: "evolverNSsites" Docs: "evolverNSsites 6"

Codoc mismatches from documentation object 'make.dat':
make.dat
  Code: function(n.seq, n.codons, reps, tree, freqs, omega, kap)
  Docs: function(n.seq, n.codons, reps, tree, template.dat, file,
                 freqs, omega, kap)
  Argument names in docs not in code:
    template.dat file
  Mismatches in argument names:
    Position: 5 Code: freqs Docs: template.dat
    Position: 6 Code: omega Docs: file
    Position: 7 Code: kap Docs: freqs

Codoc mismatches from documentation object 'sim.codon':
sim.codon
  Code: function(n.taxa, n.codons, reps, tree, freqs = c(0.6, 0.3,
                 0.1), omega = c(0.1, 0.8, 3.2), kap = 2, call =
                 "evolverNSsites")
  Docs: function(n.taxa, n.codons, reps, tree, freqs = c(0.6, 0.3,
                 0.1), omega = c(0.1, 0.8, 3.2), kap = 2, call =
                 "evolverNSsites 6")
  Mismatches in argument default values:
    Name: 'call' Code: "evolverNSsites" Docs: "evolverNSsites 6"

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'fasta.to.alignment'
  ‘fasta.file.name’

Undocumented arguments in documentation object 'make.dat'
  ‘n.seq’ ‘n.codons’ ‘reps’ ‘tree’ ‘template.dat’ ‘file’ ‘freqs’
  ‘omega’ ‘kap’

Objects in \usage without \alias in documentation object 'make.mj.align':
  ‘read.phylosim’

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 the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... NONE
* checking PDF version of manual ... OK

WARNING: There were 3 warnings.
NOTE: There were 4 notes.
See
  ‘/mnt/building/build_2013-12-13-00-12/RF_PKG_CHECK/PKGS/synDss.Rcheck/00check.log’
for details.

Run time: 148.79 seconds.