R Development Page

MDP log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2015-03-10-23-04/RF_PKG_CHECK/PKGS/MDP.Rcheck'
* using R version 3.1.3 RC (2015-03-06 r67947)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'MDP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MDP' version '1.1'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Lars Relund Nielsen '
New submission
Vignette sources in 'inst/doc' with no 'vignettes' directory:
  'mdp_examples.Rtex'
A 'vignettes' directory is required as from R 3.1.0
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped
* checking if this is a source package ... WARNING
Subdirectory 'src' contains:
  basicdt.hh hgfreader.hh hmdp.hh hmdpReader.hh htacyclic.hh hypergf.hh
  matalg.hh matrix.hh time.hh
These are unlikely file names for src files.
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'MDP' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  'codeblocks'
* 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
* 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 dependencies in R code ... NOTE
Package in Depends field not imported from: 'XML'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
convertHMP2Binary : setWeights : : no visible global
  function definition for 'xmlAttrs'
convertHMP2Binary : stateCtr: no visible global function definition for
  'xmlChildren'
convertHMP2Binary : process: no visible global function definition for
  'xmlApply'
convertHMP2Binary : stage: no visible global function definition for
  'xmlApply'
convertHMP2Binary : state: no visible global function definition for
  'xmlAttrs'
convertHMP2Binary : state: no visible global function definition for
  'xmlApply'
convertHMP2Binary : action: no visible global function definition for
  'xmlChildren'
convertHMP2Binary : action: no visible global function definition for
  'xmlAttrs'
convertHMP2Binary : action: no visible global function definition for
  'xmlApply'
convertHMP2Binary : action: no visible global function definition for
  'xmlValue'
convertHMP2Binary: no visible global function definition for
  'xmlTreeParse'
convertHMP2Binary: no visible global function definition for 'xmlRoot'
convertHMP2Binary: no visible global function definition for 'free'
hmpMDPWriter : closeWriter: no visible global function definition for
  'saveXML'
hmpMDPWriter: no visible global function definition for 'xmlTree'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'binaryMDPWriter.Rd':
  \examples lines wider than 100 characters:
                                                             w$action(label="A0",weights=c(0,0,1),prob=c(1,0,0.5,1,1,0.5))
                                                             w$action(label="A0",weights=c(0,0,0),prob=c(1,0,1))
                                                             w$action(label="A1",weights=c(1,2,1),prob=c(1,0,0.5,1,1,0.5))
                                                             w$action(label="A0",weights=c(0,0,0),prob=c(1,0,1))
                                                             w$action(label="A1",weights=c(1,2,1),prob=c(1,0,0.5,1,1,0.5))
                                                             w$action(label="A0",weights=c(1,4,0),prob=c(0,0,1))
                                                             w$action(label="A0",weights=c(1,4,0),prob=c(0,0,1))
                                                             w$action(label="A0",weights=c(0,0,1),prob=c(1,0,1))
                                                             w$action(label="A0",weights=c(0,0,0),prob=c(1,0,1))
                                                             w$action(label="A1",weights=c(1,2,1),prob=c(1,0,0.5,1,1,0.5))
                                                             w$action(label="A0",weights=c(1,4,0),prob=c(0,0,1))
                                                             w$action(label="A0",weights=c(1,4,0),prob=c(0,0,1))
                                                             w$action(label="A1",weights=c(0,10,5),prob=c(0,0,0.5,0,1,0.5))
                                                             w$action(label="A0",weights=c(0,0,1),prob=c(1,0,0.5,1,1,0.5))
                                                             w$action(label="A0",weights=c(0,0,0),prob=c(1,0,1))
                                                             w$action(label="A0",weights=c(0,0,0),prob=c(1,0,1))
                                                             w$action(label="A0",weights=c(1,4,0),prob=c(0,0,1))
                                                             w$action(label="A0",weights=c(1,4,0),prob=c(0,0,1))

Rd file 'calcWeights.Rd':
  \examples lines wider than 100 characters:
                             w$action(label="rep", weights=5, prob=c(3,12,1), end=TRUE)     # transition to the node with sId=12 (Dummy)

Rd file 'convertBinary2HMP.Rd':
  \usage lines wider than 90 characters:
         binNames=c("stateIdx.bin","stateIdxLbl.bin","actionIdx.bin","actionIdxLbl.bin","actionWeight.bin","actionWeightLbl.bin","transProb. ... [TRUNCATED]

Rd file 'getActionTransIdS.Rd':
  \examples lines wider than 100 characters:
                             w$action(label="rep", weights=5, prob=c(3,12,1), end=TRUE)     # transition to the node with sId=12 (Dummy)

Rd file 'getActionTransPr.Rd':
  \examples lines wider than 100 characters:
                             w$action(label="rep", weights=5, prob=c(3,12,1), end=TRUE)     # transition to the node with sId=12 (Dummy)

Rd file 'getActionW.Rd':
  \examples lines wider than 100 characters:
                             w$action(label="rep", weights=5, prob=c(3,12,1), end=TRUE)     # transition to the node with sId=12 (Dummy)

Rd file 'getIdS.Rd':
  \examples lines wider than 100 characters:
                             w$action(label="rep", weights=5, prob=c(3,12,1), end=TRUE)     # transition to the node with sId=12 (Dummy)

Rd file 'getIdSStages.Rd':
  \examples lines wider than 100 characters:
                             w$action(label="rep", weights=5, prob=c(3,12,1), end=TRUE)     # transition to the node with sId=12 (Dummy)

Rd file 'getLabel.Rd':
  \examples lines wider than 100 characters:
                             w$action(label="rep", weights=5, prob=c(3,12,1), end=TRUE)     # transition to the node with sId=12 (Dummy)

Rd file 'getPolicy.Rd':
  \examples lines wider than 100 characters:
                             w$action(label="rep", weights=5, prob=c(3,12,1), end=TRUE)     # transition to the node with sId=12 (Dummy)

Rd file 'getPolicyW.Rd':
  \examples lines wider than 100 characters:
                             w$action(label="rep", weights=5, prob=c(3,12,1), end=TRUE)     # transition to the node with sId=12 (Dummy)

Rd file 'getStrIdxS.Rd':
  \examples lines wider than 100 characters:
                             w$action(label="rep", weights=5, prob=c(3,12,1), end=TRUE)     # transition to the node with sId=12 (Dummy)

Rd file 'hmpMDPWriter.Rd':
  \examples lines wider than 100 characters:
                               w$action(label="A1",weights=c(0,10,5),prob=c(0,0,0.5,0,1,0.5), statesNext=0)

Rd file 'hypergf.Rd':
  \examples lines wider than 100 characters:
                             w$action(label="rep", weights=5, prob=c(3,12,1), end=TRUE)     # transition to the node with sId=12 (Dummy)

Rd file 'info.Rd':
  \examples lines wider than 100 characters:
                             w$action(label="rep", weights=5, prob=c(3,12,1), end=TRUE)     # transition to the node with sId=12 (Dummy)

Rd file 'loadMDP.Rd':
  \usage lines wider than 90 characters:
         binNames=c("stateIdx.bin","stateIdxLbl.bin","actionIdx.bin","actionIdxLbl.bin","actionWeight.bin","actionWeightLbl.bin","transProb. ... [TRUNCATED]
  \examples lines wider than 100 characters:
                             w$action(label="rep", weights=5, prob=c(3,12,1), end=TRUE)     # transition to the node with sId=12 (Dummy)

Rd file 'removeAction.Rd':
  \examples lines wider than 100 characters:
                             w$action(label="rep", weights=5, prob=c(3,12,1), end=TRUE)     # transition to the node with sId=12 (Dummy)

Rd file 'resetActions.Rd':
  \examples lines wider than 100 characters:
                             w$action(label="rep", weights=5, prob=c(3,12,1), end=TRUE)     # transition to the node with sId=12 (Dummy)

Rd file 'setActionWeight.Rd':
  \examples lines wider than 100 characters:
                             w$action(label="rep", weights=5, prob=c(3,12,1), end=TRUE)     # transition to the node with sId=12 (Dummy)

Rd file 'setPolicy.Rd':
  \examples lines wider than 100 characters:
                             w$action(label="rep", weights=5, prob=c(3,12,1), end=TRUE)     # transition to the node with sId=12 (Dummy)

Rd file 'valueIte.Rd':
  \examples lines wider than 100 characters:
                             w$action(label="rep", weights=5, prob=c(3,12,1), end=TRUE)     # transition to the node with sId=12 (Dummy)

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'binaryActionWriter'
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 ... 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... WARNING
File 'MDP/libs/i386/MDP.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'hgfreader.o', 'hmdp.o', 'htacyclic.o', 'hypergf.o',
      'rmain.o'
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
    Objects: 'hgfreader.o', 'hmdp.o', 'hypergf.o', 'rmain.o'
  Found 'printf', possibly from 'printf' (C)
    Object: 'hgfreader.o'
File 'MDP/libs/x64/MDP.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'hgfreader.o', 'hmdp.o', 'htacyclic.o', 'hypergf.o',
      'rmain.o'
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
    Objects: 'hgfreader.o', 'hmdp.o', 'hypergf.o', 'rmain.o'
  Found 'printf', possibly from 'printf' (C)
    Object: 'hgfreader.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'mdp_examples.Rtex'
A 'vignettes' directory is required as from R 3.1.0
and these will not be indexed nor checked
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

WARNING: There were 3 warnings.
NOTE: There were 7 notes.
See
  'R:/run/building/build_2015-03-10-23-04/RF_PKG_CHECK/PKGS/MDP.Rcheck/00check.log'
for details.

Run time: 84.23 seconds.