fabian-s/biosensors.usc

biosensors.usc's Issues

R CMD check fails

W  checking whether package ‘biosensors.usc’ can be installed (59.2s)
   Found the following significant warnings:
     alglib/ap.cpp:9060:16: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
   See ‘/home/fabians/fda/biosensors.usc.Rcheck/00install.out’ for details.

N  checking installed package size
     installed size is 22.8Mb
     sub-directories of 1Mb or more:
       extdata   4.8Mb
       include   1.3Mb
       libs     16.5Mb

N  checking top-level files ...
   File
     LICENSE
   is not mentioned in the DESCRIPTION file.

   W  checking R files for non-ASCII characters ...
   Found the following file with non-ASCII characters:
     regmod.R
   Portable packages must use only ASCII characters in their R code,
   except perhaps in comments.
   Use \uxxxx escapes for other characters.

N  checking R code for possible problems (6.6s)
   clustering: no visible global function definition for ‘is’
   clustering_prediction: no visible global function definition for ‘is’
   clustering_prediction: no visible global function definition for ‘dist’
   generate_data: no visible global function definition for ‘runif’
   hypothesis_testing: no visible global function definition for ‘is’
   load_density_data: no visible global function definition for
     ‘approxfun’
   nadayara_prediction: no visible global function definition for ‘is’
   nadayara_regression: no visible global function definition for ‘is’
   regmod_regression: no visible global function definition for ‘is’
   regmod_regression: no visible global function definition for
     ‘as.formula’
   regmod_regression: no visible global function definition for ‘lm’
   ridge_regression: no visible global function definition for ‘median’
   wasserstein_regression: no visible global function definition for ‘is’
   Undefined global functions or variables:
     approxfun as.formula dist is lm median runif
   Consider adding
     importFrom("methods", "is")
     importFrom("stats", "approxfun", "as.formula", "dist", "lm", "median",
                "runif")
   to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
   contains 'methods').

✓  checking for missing documentation entries (1.1s)
W  checking for code/documentation mismatches (1.1s)
   Functions or methods with usage in documentation object 'clustering_prediction' but not in code:
     ‘energy_prediction’
   
   Codoc mismatches from documentation object 'nadayara_prediction':
   nadayara_prediction
     Code: function(nadaraya, Qpred, hs = NULL)
     Docs: function(data, response)
     Argument names in code not in docs:
       nadaraya Qpred hs
     Argument names in docs not in code:
       data response
     Mismatches in argument names:
       Position: 1 Code: nadaraya Docs: data
       Position: 2 Code: Qpred Docs: response
   
   Codoc mismatches from documentation object 'regmod_regression':
   regmod_regression
     Code: function(data, predictor)
     Docs: function(data, response)
     Argument names in code not in docs:
       predictor
     Argument names in docs not in code:
       response
     Mismatches in argument names:
       Position: 2 Code: predictor Docs: response
   
   Codoc mismatches from documentation object 'ridge_regression':
   regmod_regression
     Code: function(data, predictor)
     Docs: function(data, response)
     Argument names in code not in docs:
       predictor
     Argument names in docs not in code:
       response
     Mismatches in argument names:
       Position: 2 Code: predictor Docs: response
   
   Codoc mismatches from documentation object 'wasserstein_prediction':
   wasserstein_prediction
     Code: function(reg, xpred)
     Docs: function(regression, xpred)
     Argument names in code not in docs:
       reg
     Argument names in docs not in code:
       regression
     Mismatches in argument names:
       Position: 1 Code: reg Docs: regression

W  checking Rd \usage sections (2.4s)
   Objects in \usage without \alias in documentation object 'clustering_prediction':
     ‘energy_prediction’
   
   Undocumented arguments in documentation object 'nadayara_prediction'
     ‘response’
   Documented arguments not in \usage in documentation object 'nadayara_prediction':
     ‘Qpred’ ‘hs’
   
   Documented arguments not in \usage in documentation object 'ridge_regression':
     ‘w’ ‘method’ ‘type’
   Objects in \usage without \alias in documentation object 'ridge_regression':
     ‘regmod_regression’
   
   Undocumented arguments in documentation object 'wasserstein_prediction'
     ‘regression’
   Documented arguments not in \usage in documentation object 'wasserstein_prediction':
     ‘reg’
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

W  checking compilation flags in Makevars ...
   Non-portable flags in variable 'PKG_CXXFLAGS':
     -Wstrict-aliasing=0 -Wno-unused-but-set-variable -Wno-unused-function -Wno-maybe-uninitialized
W  checking for GNU extensions in Makefiles
   Found the following file(s) containing GNU extensions:
     src/Makevars
   Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
   $(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable
   packages’ in the ‘Writing R Extensions’ manual.

W  checking compilation flags used
   Compilation used the following non-portable flag(s):
     ‘-Wno-maybe-uninitialized’ ‘-Wno-unused-but-set-variable’
     ‘-Wno-unused-function’ ‘-Wstrict-aliasing=0’
   including flag(s) suppressing warnings
W  checking compiled code ...
   File ‘biosensors.usc/libs/biosensors.usc.so’:
     Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
       Object: ‘biosensors.usc.o’
     Found ‘abort’, possibly from ‘abort’ (C)
       Object: ‘alglib/ap.o’
     Found ‘rand’, possibly from ‘rand’ (C)
       Object: ‘alglib/ap.o’
   
   Compiled code should not call entry points which might terminate R nor
   write to stdout/stderr instead of to the console, nor use Fortran I/O
   nor system RNGs.

E  checking examples (2s)
   Running examples in ‘biosensors.usc-Ex.R’ failed
   The error most likely occurred in:
   
   > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
   > ### Name: generate_data
   > ### Title: generate_data
   > ### Aliases: generate_data
   > 
   > ### ** Examples
   > 
   > data = generate_data(n=100, Qp=100, Xp=5)
   > names(data)
   [1] "data"      "densities" "quantiles" "variables"
   > header(data$quantiles)
   Error in header(data$quantiles) : could not find function "header"
   Execution halted