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ParallelStructure log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2014-06-24-12-04/RF_PKG_CHECK/PKGS/ParallelStructure.Rcheck'
* using R version 3.1.0 Patched (2014-06-21 r65995)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'ParallelStructure/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ParallelStructure' version '1.0'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'francois besnier '
New submission
Non-FOSS package license (GPL3)
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'ParallelStructure' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
  GPL3
Standardizable: FALSE
* 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 ... WARNING
Found the following files with non-ASCII characters:
  MPI_structure.R
  parallel_structure.R
Portable packages must use only ASCII characters in their R code,
except perhaps in comments.
Use \uxxxx escapes for other characters.
* 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 ... WARNING
'library' or 'require' call not declared from: 'Rmpi'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function calls without 'PACKAGE' argument:
  .Call("mpi_finalize", ...)
  .Call("mpi_finalize", ...)
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* checking R code for possible problems ... NOTE
convert_IDs: warning in write(t(sdat), ncolumn = length(sdat[1, ]),
  file = res_name, append = T): partial argument match of 'ncolumn' to
  'ncolumns'
MPI_structure: no visible binding for global variable 'Mac_path'
MPI_structure: no visible global function definition for
  'mpi.spawn.Rslaves'
MPI_structure : .Last: no visible global function definition for
  'mpi.comm.size'
MPI_structure : .Last: no visible global function definition for
  'mpi.close.Rslaves'
MPI_structure : slave_fun_unix: no visible global function definition
  for 'mpi.send.Robj'
MPI_structure : slave_fun_unix: no visible global function definition
  for 'mpi.recv.Robj'
MPI_structure : slave_fun_unix: no visible global function definition
  for 'mpi.any.source'
MPI_structure : slave_fun_unix: no visible global function definition
  for 'mpi.any.tag'
MPI_structure : slave_fun_unix: no visible global function definition
  for 'mpi.get.sourcetag'
MPI_structure : slave_fun_windows: no visible global function
  definition for 'mpi.send.Robj'
MPI_structure : slave_fun_windows: no visible global function
  definition for 'mpi.recv.Robj'
MPI_structure : slave_fun_windows: no visible global function
  definition for 'mpi.any.source'
MPI_structure : slave_fun_windows: no visible global function
  definition for 'mpi.any.tag'
MPI_structure : slave_fun_windows: no visible global function
  definition for 'mpi.get.sourcetag'
MPI_structure: no visible global function definition for
  'mpi.comm.size'
MPI_structure: no visible global function definition for
  'mpi.bcast.Robj2slave'
MPI_structure: no visible global function definition for
  'mpi.bcast.cmd'
MPI_structure: no visible global function definition for
  'mpi.recv.Robj'
MPI_structure: no visible global function definition for
  'mpi.any.source'
MPI_structure: no visible global function definition for 'mpi.any.tag'
MPI_structure: no visible global function definition for
  'mpi.get.sourcetag'
MPI_structure: no visible global function definition for
  'mpi.send.Robj'
MPI_structure: no visible global function definition for
  'mpi.close.Rslaves'
parallel_structure: no visible binding for global variable 'Mac_path'
parallel_structure: no visible global function definition for
  'mclapply'
* checking Rd files ... OK
* checking Rd metadata ... WARNING
Rd files with duplicated name 'plot_str':
  'convert_output_ID.Rd' 'plot_str.Rd'
Rd files with duplicated alias 'plot_str':
  'convert_output_ID.Rd' 'plot_str.Rd'
* checking Rd line widths ... NOTE
Rd file 'MPI_structure.Rd':
  \usage lines wider than 90 characters:
     MPI_structure(joblist = NULL, n_cpu = NULL, structure_path = Mac_path, infile = NULL, outpath = NULL,get_log=1,
      numinds = NULL, numloci = NULL, plot_output = 1, label = 1, popdata = 1, popflag = 0, locdata = 0, 
      phenotypes = 0, markernames = 0, mapdist = 0, onerowperind = 0, phaseinfo = 0, recessivealleles = 0, 
      phased = 0, extracol = 0, missing = -9, ploidy = 2, noadmix = 0, linkage = 0, usepopinfo = 0, locprior = 0,
       inferalpha = 1, alpha = 1, popalphas = 0, unifprioralpha = 1, alphamax = 10, alphapropsd = 0.025, freqscorr = 1, 
       onefst = 0, fpriormean = 0.01, fpriorsd = 0.05, inferlambda = 0, lambda = 1, computeprob = 1, 
       pfromflagonly = 0, ancestdist = 0, startatpopinfo = 0, metrofreq = 10, updatefreq = 1, printqhat = 0,revert_convert=0,
  \examples lines wider than 100 characters:
     #       MPI_structure(structure_path=NULL,joblist='joblist1.txt',n_cpu=4,infile='example_data.txt',outpath='structure_results/',numinds ... [TRUNCATED]
     #       MPI_structure(structure_path=Mac_path,joblist='joblist1.txt',n_cpu=4,infile='example_data.txt',outpath='structure_results/',num ... [TRUNCATED]
     #       MPI_structure(structure_path=NULL,joblist='joblist1.txt',n_cpu=4,infile='example_data.txt',outpath='structure_results/',numinds ... [TRUNCATED]
     #       MPI_structure(structure_path=Windows_path,joblist='joblist1.txt',n_cpu=4,infile='example_data.txt',outpath='structure_results/' ... [TRUNCATED]

Rd file 'parallel_structure.Rd':
  \usage lines wider than 90 characters:
     MPI_structure(joblist = NULL, n_cpu = NULL, structure_path = Mac_path, infile = NULL, outpath = NULL,
      numinds = NULL, numloci = NULL, plot_output = 1, label = 1, popdata = 1, popflag = 0, locdata = 0, 
      phenotypes = 0, markernames = 0, mapdist = 0, onerowperind = 0, phaseinfo = 0, recessivealleles = 0, 
      phased = 0, extracol = 0, missing = -9, ploidy = 2, noadmix = 0, linkage = 0, usepopinfo = 0, locprior = 0,
       inferalpha = 1, alpha = 1, popalphas = 0, unifprioralpha = 1, alphamax = 10, alphapropsd = 0.025, freqscorr = 1, 
       onefst = 0, fpriormean = 0.01, fpriorsd = 0.05, inferlambda = 0, lambda = 1, computeprob = 1, 
       pfromflagonly = 0, ancestdist = 0, startatpopinfo = 0, metrofreq = 10, updatefreq = 1, printqhat = 0,revert_convert=0,
  \examples lines wider than 100 characters:
     #       parallel_structure(structure_path=NULL,joblist='joblist1.txt',n_cpu=4,infile='example_data.txt',outpath='structure_results/',nu ... [TRUNCATED]
     #       parallel_structure(structure_path=Mac_path,joblist='joblist1.txt',n_cpu=4,infile='example_data.txt',outpath='structure_results/ ... [TRUNCATED]
     #       parallel_structure(structure_path=NULL,joblist='joblist1.txt',n_cpu=4,infile='example_data.txt',outpath='structure_results/',nu ... [TRUNCATED]
     #       parallel_structure(structure_path=Windows_path,joblist='joblist1.txt',n_cpu=4,infile='example_data.txt',outpath='structure_resu ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'convert_IDs'
Undocumented data sets:
  'Mac_path'
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'MPI_structure':
MPI_structure
  Code: function(joblist = NULL, n_cpu = NULL, structure_path =
                 Mac_path, infile = NULL, outpath = NULL, numinds =
                 NULL, numloci = NULL, get_log = 1, plot_output = 1,
                 label = 1, popdata = 1, popflag = 0, locdata = 0,
                 phenotypes = 0, markernames = 0, mapdist = 0,
                 onerowperind = 0, phaseinfo = 0, recessivealleles = 0,
                 phased = 0, extracol = 0, missing = -9, ploidy = 2,
                 noadmix = 0, linkage = 0, usepopinfo = 0, locprior =
                 0, inferalpha = 1, alpha = 1, popalphas = 0,
                 unifprioralpha = 1, alphamax = 10, alphapropsd =
                 0.025, freqscorr = 1, onefst = 0, fpriormean = 0.01,
                 fpriorsd = 0.05, inferlambda = 0, lambda = 1,
                 computeprob = 1, pfromflagonly = 0, ancestdist = 0,
                 startatpopinfo = 0, metrofreq = 10, updatefreq = 1,
                 printqhat = 0, revert_convert = 0, randomize = 1)
  Docs: function(joblist = NULL, n_cpu = NULL, structure_path =
                 Mac_path, infile = NULL, outpath = NULL, get_log = 1,
                 numinds = NULL, numloci = NULL, plot_output = 1, label
                 = 1, popdata = 1, popflag = 0, locdata = 0, phenotypes
                 = 0, markernames = 0, mapdist = 0, onerowperind = 0,
                 phaseinfo = 0, recessivealleles = 0, phased = 0,
                 extracol = 0, missing = -9, ploidy = 2, noadmix = 0,
                 linkage = 0, usepopinfo = 0, locprior = 0, inferalpha
                 = 1, alpha = 1, popalphas = 0, unifprioralpha = 1,
                 alphamax = 10, alphapropsd = 0.025, freqscorr = 1,
                 onefst = 0, fpriormean = 0.01, fpriorsd = 0.05,
                 inferlambda = 0, lambda = 1, computeprob = 1,
                 pfromflagonly = 0, ancestdist = 0, startatpopinfo = 0,
                 metrofreq = 10, updatefreq = 1, printqhat = 0,
                 revert_convert = 0, randomize = 1)
  Mismatches in argument names:
    Position: 6 Code: numinds Docs: get_log
    Position: 7 Code: numloci Docs: numinds
    Position: 8 Code: get_log Docs: numloci

Codoc mismatches from documentation object 'plot_str':
convert_IDs
  Code: function(ID1 = NULL, out_nam = NULL, rev_convert = NULL,
                 printqhat = NULL, k = NULL)
  Docs: function()
  Argument names in code not in docs:
    ID1 out_nam rev_convert printqhat k

Codoc mismatches from documentation object 'parallel_structure':
MPI_structure
  Code: function(joblist = NULL, n_cpu = NULL, structure_path =
                 Mac_path, infile = NULL, outpath = NULL, numinds =
                 NULL, numloci = NULL, get_log = 1, plot_output = 1,
                 label = 1, popdata = 1, popflag = 0, locdata = 0,
                 phenotypes = 0, markernames = 0, mapdist = 0,
                 onerowperind = 0, phaseinfo = 0, recessivealleles = 0,
                 phased = 0, extracol = 0, missing = -9, ploidy = 2,
                 noadmix = 0, linkage = 0, usepopinfo = 0, locprior =
                 0, inferalpha = 1, alpha = 1, popalphas = 0,
                 unifprioralpha = 1, alphamax = 10, alphapropsd =
                 0.025, freqscorr = 1, onefst = 0, fpriormean = 0.01,
                 fpriorsd = 0.05, inferlambda = 0, lambda = 1,
                 computeprob = 1, pfromflagonly = 0, ancestdist = 0,
                 startatpopinfo = 0, metrofreq = 10, updatefreq = 1,
                 printqhat = 0, revert_convert = 0, randomize = 1)
  Docs: function(joblist = NULL, n_cpu = NULL, structure_path =
                 Mac_path, infile = NULL, outpath = NULL, numinds =
                 NULL, numloci = NULL, plot_output = 1, label = 1,
                 popdata = 1, popflag = 0, locdata = 0, phenotypes = 0,
                 markernames = 0, mapdist = 0, onerowperind = 0,
                 phaseinfo = 0, recessivealleles = 0, phased = 0,
                 extracol = 0, missing = -9, ploidy = 2, noadmix = 0,
                 linkage = 0, usepopinfo = 0, locprior = 0, inferalpha
                 = 1, alpha = 1, popalphas = 0, unifprioralpha = 1,
                 alphamax = 10, alphapropsd = 0.025, freqscorr = 1,
                 onefst = 0, fpriormean = 0.01, fpriorsd = 0.05,
                 inferlambda = 0, lambda = 1, computeprob = 1,
                 pfromflagonly = 0, ancestdist = 0, startatpopinfo = 0,
                 metrofreq = 10, updatefreq = 1, printqhat = 0,
                 revert_convert = 0, randomize = 1)
  Argument names in code not in docs:
    get_log
  Mismatches in argument names (first 3):
    Position: 8 Code: get_log Docs: plot_output
    Position: 9 Code: plot_output Docs: label
    Position: 10 Code: label Docs: popdata

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'plot_str':
  '...'

Undocumented arguments in documentation object 'edit_params'
  'LocPar' 'GlobPar'

Objects in \usage without \alias in documentation object 'parallel_structure':
  'MPI_structure'

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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking PDF version of manual ... OK

WARNING: There were 8 warnings.
NOTE: There were 4 notes.
See
  'R:/run/building/build_2014-06-24-12-04/RF_PKG_CHECK/PKGS/ParallelStructure.Rcheck/00check.log'
for details.

Run time: 27.62 seconds.

Additional Logs:   00install.out
Thanks to:
Vienna University of Economics and Business University of Wisconsin - Madison Powered By FusionForge