1 error | 3 warnings | 5 notes

[swihart]

Okay. Here we go with gnlm. We are using roxygen. Initial R CMD check results:

==> devtools::check(document = FALSE)

Setting env vars ---------------------------------------------------------------
CFLAGS  : -Wall -pedantic
CXXFLAGS: -Wall -pedantic
Building gnlm ------------------------------------------------------------------
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD build '/Users/swihartbj/github/gnlm'  \
  --no-resave-data --no-manual 

* checking for file ‘/Users/swihartbj/github/gnlm/DESCRIPTION’ ... OK
* preparing ‘gnlm’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking whether ‘INDEX’ is up-to-date ... NO
* use ‘--force’ to remove the existing ‘INDEX’
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘gnlm_1.0.tar.gz’
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'

Setting env vars ---------------------------------------------------------------
_R_CHECK_CRAN_INCOMING_ : FALSE
_R_CHECK_FORCE_SUGGESTS_: FALSE
Checking gnlm ------------------------------------------------------------------
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD check  \
  '/var/folders/tv/9xflkyxs21j3747s8wd641t1bd7ntf/T//Rtmp4h1DTr/gnlm_1.0.tar.gz'  \
  --as-cran --timings --no-manual 

* using log directory ‘/Users/swihartbj/github/gnlm.Rcheck’
* using R version 3.3.2 (2016-10-31)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using options ‘--no-manual --as-cran’
* checking for file ‘gnlm/DESCRIPTION’ ... OK
* this is package ‘gnlm’ version ‘1.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... WARNING
Subdirectory ‘gnlm/src’ contains apparent object files/libraries
  gnlm.so
Object files/libraries should not be included in a source package.
* 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 ‘gnlm’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  GPL version 2 or later
Standardizable: TRUE
Standardized license specification:
  GPL (>= 2)
* 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
* 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: ‘rmutil’
  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 ... NOTE
Foreign function calls to a different package:
  .C("ddb", ..., PACKAGE = "rmutil")
  .C("ddp", ..., PACKAGE = "rmutil")
  .C("dmb", ..., PACKAGE = "rmutil")
  .C("dmp", ..., PACKAGE = "rmutil")
  .C("dpvfp", ..., PACKAGE = "rmutil")
  .C("pginvgauss", ..., PACKAGE = "rmutil")
  .C("plevy", ..., PACKAGE = "rmutil")
  .C("ppowexp", ..., PACKAGE = "rmutil")
  .C("psimplex", ..., PACKAGE = "rmutil")
Calls with DUP:
   .C("plevy", as.double(y), as.double(m), as.double(s), as.double(1), 
       len = as.integer(n), eps = as.double(1e-06), pts = as.integer(5), 
       max = as.integer(16), err = integer(1), res = double(n), 
       DUP = FALSE, PACKAGE = "rmutil")
   .C("ddb", as.integer(y[, 1]), as.integer(nn), as.double(mu1(p)), 
       as.double(exp(p[np])), as.integer(n), as.double(wt), res = double(n), 
       DUP = FALSE, PACKAGE = "rmutil")
   .C("dmb", as.integer(y[, 1]), as.integer(nn), as.double(mu1(p)), 
       as.double(exp(p[np])), as.integer(n), as.double(wt), res = double(n), 
       DUP = FALSE, PACKAGE = "rmutil")
   .C("ddp", as.integer(y), as.integer(my), as.double(mu1(p)), as.double(exp(p[np])), 
       as.integer(length(y)), as.double(wt), res = double(length(y)), 
       DUP = FALSE, PACKAGE = "rmutil")
   .C("dmp", as.integer(y), as.integer(my), as.double(mu1(p)), as.double(exp(p[np])), 
       as.integer(length(y)), as.double(wt), res = double(length(y)), 
       DUP = FALSE, PACKAGE = "rmutil")
   .C("plevy", as.double(y), as.double(m), as.double(s), as.double(1), 
       len = as.integer(n), eps = as.double(1e-06), pts = as.integer(5), 
       max = as.integer(16), err = integer(1), res = double(n), 
       DUP = FALSE, PACKAGE = "rmutil")
   .C("psimplex", as.double(y), as.double(m), as.double(s), as.double(1), 
       len = as.integer(n), eps = as.double(1e-06), pts = as.integer(5), 
       max = as.integer(16), err = integer(1), res = double(n), 
       DUP = FALSE, PACKAGE = "rmutil")
   .C("ddb", as.integer(y[, 1]), as.integer(nn), as.double(mu1(p)), 
       as.double(exp(sh1(p))), as.integer(n), as.double(wt), res = double(n), 
       DUP = FALSE, PACKAGE = "rmutil")
   .C("dmb", as.integer(y[, 1]), as.integer(nn), as.double(mu1(p)), 
       as.double(exp(sh1(p))), as.integer(n), as.double(wt), res = double(n), 
       DUP = FALSE, PACKAGE = "rmutil")
   .C("ddp", as.integer(y), as.integer(my), as.double(mu1(p)), as.double(exp(sh1(p))), 
       as.integer(length(y)), as.double(wt), res = double(length(y)), 
       DUP = FALSE, PACKAGE = "rmutil")
   .C("dmp", as.integer(y), as.integer(my), as.double(mu1(p)), as.double(exp(sh1(p))), 
       as.integer(length(y)), as.double(wt), res = double(length(y)), 
       DUP = FALSE, PACKAGE = "rmutil")
   .C("pginvgauss", as.double(y), as.double(m), as.double(s), as.double(f), 
       len = as.integer(n), eps = as.double(1e-06), pts = as.integer(5), 
       max = as.integer(16), err = integer(1), res = double(n), 
       DUP = FALSE, PACKAGE = "rmutil")
   .C("ppowexp", as.double(y), as.double(m), as.double(s), as.double(f), 
       len = as.integer(n), eps = as.double(1e-06), pts = as.integer(5), 
       max = as.integer(16), err = integer(1), res = double(n), 
       DUP = FALSE, PACKAGE = "rmutil")
   .C("dpvfp", as.integer(y), as.double(m), as.double(s), as.double(f), 
       as.integer(length(y)), as.double(rep(1, length(y))), res = double(length(y)), 
       DUP = FALSE, PACKAGE = "rmutil")
DUP is no longer supported and will be ignored.
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

bnlr: warning in exists(deparse(substitute(y)), env = parent.frame()):
  partial argument match of 'env' to 'envir'
fmr: warning in exists(deparse(substitute(y)), env = parent.frame()):
  partial argument match of 'env' to 'envir'
gnlr: warning in exists(deparse(substitute(y)), env = parent.frame()):
  partial argument match of 'env' to 'envir'
gnlr3: warning in exists(deparse(substitute(y)), env = parent.frame()):
  partial argument match of 'env' to 'envir'
nlr: warning in exists(deparse(substitute(y)), env = parent.frame()):
  partial argument match of 'env' to 'envir'
nordr: warning in exists(deparse(substitute(y)), env = parent.frame()):
  partial argument match of 'env' to 'envir'
bnlr: no visible global function definition for ‘nobs’
bnlr: no visible global function definition for ‘finterp’
bnlr: no visible global function definition for ‘fnenvir’
bnlr: no visible global function definition for ‘wr’
bnlr: no visible global function definition for ‘response’
bnlr : fcn: no visible global function definition for ‘plogis’
bnlr : fcn: no visible global function definition for ‘pnorm’
bnlr : fcn: no visible global function definition for ‘pcauchy’
bnlr : fcn: no visible global function definition for ‘pt’
bnlr: no visible global function definition for ‘nlm’
bnlr: no visible binding for global variable ‘const’
fit.dist : cum.histo: no visible global function definition for ‘rect’
fit.dist : cum.histo: no visible global function definition for ‘par’
fit.dist: no visible global function definition for ‘weighted.mean’
fit.dist: no visible global function definition for ‘dbinom’
fit.dist: no visible global function definition for ‘nlm’
fit.dist: no visible global function definition for ‘dpois’
fit.dist: no visible global function definition for ‘dnbinom’
fit.dist : fcn: no visible global function definition for ‘dnbinom’
fit.dist: no visible global function definition for ‘dnorm’
fit.dist: no visible global function definition for ‘dlnorm’
fit.dist : fcn: no visible global function definition for ‘dlogis’
fit.dist: no visible global function definition for ‘dlogis’
fit.dist: no visible global function definition for ‘dlaplace’
fit.dist : fcn: no visible global function definition for ‘dcauchy’
fit.dist: no visible global function definition for ‘dcauchy’
fit.dist : fcn: no visible global function definition for ‘dt’
fit.dist: no visible global function definition for ‘dt’
fit.dist: no visible global function definition for ‘dexp’
fit.dist : fcn: no visible global function definition for ‘dgamma’
fit.dist: no visible global function definition for ‘dgamma’
fit.dist : fcn: no visible global function definition for ‘dweibull’
fit.dist: no visible global function definition for ‘dweibull’
fit.dist: no visible global function definition for ‘lines’
fmr : pinvgauss: no visible global function definition for ‘pnorm’
fmr: no visible global function definition for ‘nobs’
fmr: no visible global function definition for ‘finterp’
fmr: no visible global function definition for ‘fnenvir’
fmr: no visible global function definition for ‘wr’
fmr: no visible global function definition for ‘response’
fmr : fcn: no visible global function definition for ‘dbinom’
fmr : fcn: no visible binding for global variable ‘s’
fmr : fcn: no visible global function definition for ‘dpois’
fmr : fcn: no visible global function definition for ‘dnbinom’
fmr : fcn: no visible global function definition for ‘pgamma’
fmr : fcn: no visible global function definition for ‘pnorm’
fmr : fcn: no visible global function definition for ‘dnorm’
fmr : fcn: no visible global function definition for ‘plogis’
fmr : fcn: no visible global function definition for ‘dlogis’
fmr : fcn: no visible global function definition for ‘pt’
fmr : fcn: no visible global function definition for ‘dt’
fmr : fcn: no visible global function definition for ‘pcauchy’
fmr : fcn: no visible global function definition for ‘dcauchy’
fmr : fcn: no visible global function definition for ‘dgamma’
fmr : fcn: no visible global function definition for ‘pweibull’
fmr : fcn: no visible global function definition for ‘dweibull’
fmr: no visible global function definition for ‘nlm’
gnlr : pinvgauss: no visible global function definition for ‘pnorm’
gnlr: no visible global function definition for ‘nobs’
gnlr: no visible global function definition for ‘finterp’
gnlr: no visible global function definition for ‘fnenvir’
gnlr: no visible global function definition for ‘wr’
gnlr: no visible global function definition for ‘response’
gnlr : fcn: no visible global function definition for ‘pgamma’
gnlr : fcn: no visible global function definition for ‘pnorm’
gnlr : fcn: no visible global function definition for ‘plogis’
gnlr : fcn: no visible global function definition for ‘pcauchy’
gnlr : fcn: no visible global function definition for ‘pweibull’
gnlr : fcn: no visible global function definition for ‘pbeta’
gnlr : fcn: no visible global function definition for ‘dbeta’
gnlr : fcn: no visible global function definition for ‘ppois’
gnlr : fcn: no visible global function definition for ‘pnbinom’
gnlr : fcn: no visible global function definition for ‘pgeom’
gnlr: no visible global function definition for ‘nlm’
gnlr3: no visible global function definition for ‘nobs’
gnlr3: no visible global function definition for ‘finterp’
gnlr3: no visible global function definition for ‘fnenvir’
gnlr3: no visible global function definition for ‘wr’
gnlr3: no visible global function definition for ‘response’
gnlr3 : fcn: no visible global function definition for ‘pnorm’
gnlr3 : fcn: no visible global function definition for ‘dnorm’
gnlr3 : fcn: no visible global function definition for ‘pgamma’
gnlr3 : fcn: no visible global function definition for ‘pt’
gnlr3 : fcn: no visible global function definition for ‘dt’
gnlr3 : fcn: no visible global function definition for ‘pweibull’
gnlr3: no visible global function definition for ‘nlm’
nlr: no visible global function definition for ‘finterp’
nlr: no visible global function definition for ‘fnenvir’
nlr: no visible global function definition for ‘nobs’
nlr: no visible global function definition for ‘response’
nlr: no visible global function definition for ‘nlm’
nordr: no visible global function definition for ‘nobs’
nordr: no visible global function definition for ‘finterp’
nordr: no visible global function definition for ‘fnenvir’
nordr: no visible global function definition for ‘wr’
nordr: no visible binding for global variable ‘lin1’
nordr: no visible global function definition for ‘response’
nordr: no visible global function definition for ‘nlm’
ordglm: no visible global function definition for ‘terms’
ordglm: no visible global function definition for ‘model.frame’
ordglm: no visible binding for global variable ‘na.fail’
ordglm: no visible global function definition for ‘model.response’
ordglm: no visible global function definition for ‘model.matrix’
ordglm: no visible global function definition for ‘qnorm’
ordglm: no visible global function definition for ‘dnorm’
ordglm: no visible global function definition for ‘pnorm’
ordglm: no visible global function definition for ‘capply’
print.nordr: no visible binding for global variable ‘linmodel’
print.rs: no visible global function definition for ‘print.glm’
print.summary.rs: no visible global function definition for
  ‘print.summary.glm’
rs2: no visible binding for global variable ‘normal’
rs2: no visible global function definition for ‘glm’
rs3: no visible binding for global variable ‘normal’
rs3: no visible global function definition for ‘glm’
summary.rs: no visible global function definition for ‘summary.glm’
Undefined global functions or variables:
  capply const dbeta dbinom dcauchy dexp dgamma dlaplace dlnorm dlogis
  dnbinom dnorm dpois dt dweibull finterp fnenvir glm lin1 lines
  linmodel model.frame model.matrix model.response na.fail nlm nobs
  normal par pbeta pcauchy pgamma pgeom plogis pnbinom pnorm ppois
  print.glm print.summary.glm pt pweibull qnorm rect response s
  summary.glm terms weighted.mean wr
Consider adding
  importFrom("graphics", "lines", "par", "rect")
  importFrom("stats", "dbeta", "dbinom", "dcauchy", "dexp", "dgamma",
             "dlnorm", "dlogis", "dnbinom", "dnorm", "dpois", "dt",
             "dweibull", "glm", "model.frame", "model.matrix",
             "model.response", "na.fail", "nlm", "nobs", "pbeta",
             "pcauchy", "pgamma", "pgeom", "plogis", "pnbinom", "pnorm",
             "ppois", "pt", "pweibull", "qnorm", "summary.glm", "terms",
             "weighted.mean")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Obsolete package ‘nls’ in Rd xrefs
Unknown package ‘repeated’ in Rd xrefs
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'bnlr'
  ‘print.level’ ‘typsize’ ‘ndigit’ ‘gradtol’ ‘stepmax’ ‘steptol’
  ‘iterlim’ ‘fscale’
Documented arguments not in \usage in documentation object 'bnlr':
  ‘others’

Undocumented arguments in documentation object 'fit.dist'
  ‘xlab’ ‘ylab’ ‘xlim’ ‘main’ ‘...’
Documented arguments not in \usage in documentation object 'fit.dist':
  ‘others’

Undocumented arguments in documentation object 'fmr'
  ‘print.level’ ‘typsize’ ‘ndigit’ ‘gradtol’ ‘stepmax’ ‘steptol’
  ‘iterlim’ ‘fscale’
Documented arguments not in \usage in documentation object 'fmr':
  ‘others’

Undocumented arguments in documentation object 'gnlr'
  ‘print.level’ ‘typsize’ ‘ndigit’ ‘gradtol’ ‘stepmax’ ‘steptol’
  ‘iterlim’ ‘fscale’
Documented arguments not in \usage in documentation object 'gnlr':
  ‘others’

Undocumented arguments in documentation object 'gnlr3'
  ‘print.level’ ‘typsize’ ‘ndigit’ ‘gradtol’ ‘stepmax’ ‘steptol’
  ‘iterlim’ ‘fscale’
Documented arguments not in \usage in documentation object 'gnlr3':
  ‘others’

Undocumented arguments in documentation object 'nlr'
  ‘print.level’ ‘typsize’ ‘ndigit’ ‘gradtol’ ‘stepmax’ ‘steptol’
  ‘iterlim’ ‘fscale’
Documented arguments not in \usage in documentation object 'nlr':
  ‘others’

Undocumented arguments in documentation object 'nordr'
  ‘print.level’ ‘ndigit’ ‘gradtol’ ‘steptol’ ‘fscale’ ‘iterlim’
  ‘typsize’ ‘stepmax’
Documented arguments not in \usage in documentation object 'nordr':
  ‘others’

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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking examples ... ERROR
Running examples in ‘gnlm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bnlr
> ### Title: Binomial Nonlinear Regression Models
> ### Aliases: bnlr
> ### Keywords: models
> 
> ### ** Examples
> 
> 
> # assay to estimate LD50
> y <- c(9,9,10,4,1,0,0)
> y <- cbind(y,10-y)
> dose <- log10(100/c(2.686,2.020,1.520,1.143,0.860,0.647,0.486))
> 
> summary(glm(y~dose, family=binomial))

Call:
glm(formula = y ~ dose, family = binomial)

Deviance Residuals: 
      1        2        3        4        5        6        7  
-1.5575  -0.5150   2.2574  -0.1437  -0.3347  -0.8073  -0.3732  

Coefficients:
            Estimate Std. Error z value Pr(>|z|)    
(Intercept)   24.003      5.540   4.333 1.47e-05 ***
dose         -12.522      2.881  -4.346 1.38e-05 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for binomial family taken to be 1)

    Null deviance: 63.8467  on 6  degrees of freedom
Residual deviance:  8.7105  on 5  degrees of freedom
AIC: 21.166

Number of Fisher Scoring iterations: 5

> bnlr(y, mu=~dose, pmu=c(1,1))

Call:
bnlr(y, mu = ~dose, pmu = c(1, 1))

binomial distribution

Response: y 

Log likelihood function:
{
    m <- plogis(mu1(p))
    -sum(wt * (y[, 1] * log(m) + y[, 2] * log(1 - m)))
}

Location function:
~dose

-Log likelihood    8.583012 
Degrees of freedom 5 
AIC                10.58301 
Iterations         18 

Location parameters:
             estimate     se
(Intercept)     24.00  5.775
dose           -12.52  3.003

Correlations:
        1       2
1  1.0000 -0.9977
2 -0.9977  1.0000
> summary(glm(y~dose, family=binomial(link=probit)))

Call:
glm(formula = y ~ dose, family = binomial(link = probit))

Deviance Residuals: 
       1         2         3         4         5         6         7  
-1.52693  -0.21069   2.55195  -0.08098  -0.48103  -0.81983  -0.28367  

Coefficients:
            Estimate Std. Error z value Pr(>|z|)    
(Intercept)   12.484      2.492   5.010 5.46e-07 ***
dose          -6.542      1.300  -5.034 4.81e-07 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for binomial family taken to be 1)

    Null deviance: 63.8467  on 6  degrees of freedom
Residual deviance:  9.8789  on 5  degrees of freedom
AIC: 22.334

Number of Fisher Scoring iterations: 6

> bnlr(y, link="probit", mu=~dose, pmu=c(1,1))

Call:
bnlr(y, link = "probit", mu = ~dose, pmu = c(1, 1))

binomial distribution

Response: y 

Log likelihood function:
{
    m <- pnorm(mu1(p))
    -sum(wt * (y[, 1] * log(m) + y[, 2] * log(1 - m)))
}

Location function:
~dose

-Log likelihood    9.167176 
Degrees of freedom 5 
AIC                11.16718 
Iterations         14 

Location parameters:
             estimate     se
(Intercept)    12.484  2.428
dose           -6.542  1.275

Correlations:
        1       2
1  1.0000 -0.9961
2 -0.9961  1.0000
> bnlr(y, link="log log", mu=~dose, pmu=c(1,1))
Warning in nlm(fcn, p = p, hessian = TRUE, print.level = print.level, typsize = typsize,  :
  NA/Inf replaced by maximum positive value
Warning in nlm(fcn, p = p, hessian = TRUE, print.level = print.level, typsize = typsize,  :
  NA/Inf replaced by maximum positive value
Warning in nlm(fcn, p = p, hessian = TRUE, print.level = print.level, typsize = typsize,  :
  NA/Inf replaced by maximum positive value
Warning in nlm(fcn, p = p, hessian = TRUE, print.level = print.level, typsize = typsize,  :
  NA/Inf replaced by maximum positive value

Call:
bnlr(y, link = "log log", mu = ~dose, pmu = c(1, 1))

binomial distribution

Response: y 

Log likelihood function:
{
    m <- exp(-exp(mu1(p)))
    -sum(wt * (y[, 1] * log(m) + y[, 2] * log(1 - m)))
}

Location function:
~dose

-Log likelihood    7.462096 
Degrees of freedom 5 
AIC                9.462096 
Iterations         25 

Location parameters:
             estimate     se
(Intercept)   -17.786  4.253
dose            8.999  2.162

Correlations:
        1       2
1  1.0000 -0.9981
2 -0.9981  1.0000
> bnlr(y, link="comp log log", mu=~dose, pmu=c(1,1))
Warning in nlm(fcn, p = p, hessian = TRUE, print.level = print.level, typsize = typsize,  :
  NA/Inf replaced by maximum positive value
Warning in nlm(fcn, p = p, hessian = TRUE, print.level = print.level, typsize = typsize,  :
  NA/Inf replaced by maximum positive value
Warning in nlm(fcn, p = p, hessian = TRUE, print.level = print.level, typsize = typsize,  :
  NA/Inf replaced by maximum positive value

Call:
bnlr(y, link = "comp log log", mu = ~dose, pmu = c(1, 1))

binomial distribution

Response: y 

Log likelihood function:
{
    m <- 1 - exp(-exp(mu1(p)))
    -sum(wt * (y[, 1] * log(m) + y[, 2] * log(1 - m)))
}

Location function:
~dose

-Log likelihood    12.09475 
Degrees of freedom 5 
AIC                14.09475 
Iterations         19 

Location parameters:
             estimate     se
(Intercept)    10.915  1.904
dose           -6.004  1.057

Correlations:
        1       2
1  1.0000 -0.9939
2 -0.9939  1.0000
> bnlr(y, link="Cauchy", mu=~dose, pmu=c(60,-30))

Call:
bnlr(y, link = "Cauchy", mu = ~dose, pmu = c(60, -30))

binomial distribution

Response: y 

Log likelihood function:
{
    m <- pcauchy(mu1(p))
    -sum(wt * (y[, 1] * log(m) + y[, 2] * log(1 - m)))
}

Location function:
~dose

-Log likelihood    6.728422 
Degrees of freedom 5 
AIC                8.728422 
Iterations         6 

Location parameters:
             estimate     se
(Intercept)     58.96  33.36
dose           -30.52  17.20

Correlations:
        1       2
1  1.0000 -0.9999
2 -0.9999  1.0000
> bnlr(y, link="Student", mu=~dose, pmu=c(60,-30), pshape=0.1)
Warning in sqrt(diag(cov)) : NaNs produced

Call:
bnlr(y, link = "Student", mu = ~dose, pmu = c(60, -30), pshape = 0.1)

Warning: no convergence - error 3 

binomial distribution

Response: y 

Log likelihood function:
{
    m <- pt(mu1(p), exp(p[np]))
    -sum(wt * (y[, 1] * log(m) + y[, 2] * log(1 - m)))
}

Location function:
~dose

Log shape function:
p[1] * rep(1, n)

-Log likelihood    6.408154 
Degrees of freedom 4 
AIC                9.408154 
Iterations         59 

Location parameters:
             estimate      se
(Intercept)     18844     NaN
dose            -9704  0.5653

Shape parameters:
      estimate      se
p[1]    -1.368  0.2268

Correlations:
    1       2       3
1 NaN     NaN     NaN
2 NaN 1.00000 0.01471
3 NaN 0.01471 1.00000
> bnlr(y, link="stable", mu=~dose, pmu=c(20,-15), pshape=0, stepmax=1)
Error in .C("pstable", as.integer(length(y)), y = y, skew = rep(0, n),  : 
  "pstable" not available for .C() for package "gnlm"
Calls: bnlr -> fcn -> pstable -> .C
Execution halted

See
  ‘/Users/swihartbj/github/gnlm.Rcheck/00check.log’
for details.

* DONE
Status: 1 ERROR, 3 WARNINGs, 5 NOTEs
checking examples ... ERROR
Running examples in ‘gnlm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bnlr
> ### Title: Binomial Nonlinear Regression Models
> ### Aliases: bnlr
> ### Keywords: models
> 
... 268 lines ...

Correlations:
    1       2       3
1 NaN     NaN     NaN
2 NaN 1.00000 0.01471
3 NaN 0.01471 1.00000
> bnlr(y, link="stable", mu=~dose, pmu=c(20,-15), pshape=0, stepmax=1)
Error in .C("pstable", as.integer(length(y)), y = y, skew = rep(0, n),  : 
  "pstable" not available for .C() for package "gnlm"
Calls: bnlr -> fcn -> pstable -> .C
Execution halted

checking if this is a source package ... WARNING
Subdirectory ‘gnlm/src’ contains apparent object files/libraries
  gnlm.so
Object files/libraries should not be included in a source package.

checking Rd cross-references ... WARNING
Obsolete package ‘nls’ in Rd xrefs
Unknown package ‘repeated’ in Rd xrefs

checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'bnlr'
  ‘print.level’ ‘typsize’ ‘ndigit’ ‘gradtol’ ‘stepmax’ ‘steptol’
  ‘iterlim’ ‘fscale’
Documented arguments not in \usage in documentation object 'bnlr':
  ‘others’

Undocumented arguments in documentation object 'fit.dist'
  ‘xlab’ ‘ylab’ ‘xlim’ ‘main’ ‘...’
Documented arguments not in \usage in documentation object 'fit.dist':
... 27 lines ...
Undocumented arguments in documentation object 'nordr'
  ‘print.level’ ‘ndigit’ ‘gradtol’ ‘steptol’ ‘fscale’ ‘iterlim’
  ‘typsize’ ‘stepmax’
Documented arguments not in \usage in documentation object 'nordr':
  ‘others’

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 DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  GPL version 2 or later
Standardizable: TRUE
Standardized license specification:
  GPL (>= 2)

checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘rmutil’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

checking foreign function calls ... NOTE
Foreign function calls to a different package:
  .C("ddb", ..., PACKAGE = "rmutil")
  .C("ddp", ..., PACKAGE = "rmutil")
  .C("dmb", ..., PACKAGE = "rmutil")
  .C("dmp", ..., PACKAGE = "rmutil")
  .C("dpvfp", ..., PACKAGE = "rmutil")
  .C("pginvgauss", ..., PACKAGE = "rmutil")
  .C("plevy", ..., PACKAGE = "rmutil")
  .C("ppowexp", ..., PACKAGE = "rmutil")
... 40 lines ...
       len = as.integer(n), eps = as.double(1e-06), pts = as.integer(5), 
       max = as.integer(16), err = integer(1), res = double(n), 
       DUP = FALSE, PACKAGE = "rmutil")
   .C("ppowexp", as.double(y), as.double(m), as.double(s), as.double(f), 
       len = as.integer(n), eps = as.double(1e-06), pts = as.integer(5), 
       max = as.integer(16), err = integer(1), res = double(n), 
       DUP = FALSE, PACKAGE = "rmutil")
   .C("dpvfp", as.integer(y), as.double(m), as.double(s), as.double(f), 
       as.integer(length(y)), as.double(rep(1, length(y))), res = double(length(y)), 
       DUP = FALSE, PACKAGE = "rmutil")
DUP is no longer supported and will be ignored.

checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

bnlr: warning in exists(deparse(substitute(y)), env = parent.frame()):
  partial argument match of 'env' to 'envir'
fmr: warning in exists(deparse(substitute(y)), env = parent.frame()):
  partial argument match of 'env' to 'envir'
gnlr: warning in exists(deparse(substitute(y)), env = parent.frame()):
  partial argument match of 'env' to 'envir'
gnlr3: warning in exists(deparse(substitute(y)), env = parent.frame()):
... 128 lines ...
  summary.glm terms weighted.mean wr
Consider adding
  importFrom("graphics", "lines", "par", "rect")
  importFrom("stats", "dbeta", "dbinom", "dcauchy", "dexp", "dgamma",
             "dlnorm", "dlogis", "dnbinom", "dnorm", "dpois", "dt",
             "dweibull", "glm", "model.frame", "model.matrix",
             "model.response", "na.fail", "nlm", "nobs", "pbeta",
             "pcauchy", "pgamma", "pgeom", "plogis", "pnbinom", "pnorm",
             "ppois", "pt", "pweibull", "qnorm", "summary.glm", "terms",
             "weighted.mean")
to your NAMESPACE file.

checking compiled code ... NOTE
Note: information on .o files is not available
R CMD check results
1 error  | 3 warnings | 5 notes

R CMD check succeeded

[swihart]

• Delete INDEX, src/Makefile, src/stable.o, src/gnlm.so
• Insert GPL (>=2) in DESCRIPTION

R CMD check results:

R CMD check results
1 error  | 2 warnings | 3 notes

[swihart]

Focus on:

Consider adding
  importFrom("graphics", "lines", "par", "rect")
  importFrom("stats", "dbeta", "dbinom", "dcauchy", "dexp", "dgamma",
             "dlnorm", "dlogis", "dnbinom", "dnorm", "dpois", "dt",
             "dweibull", "glm", "model.frame", "model.matrix",
             "model.response", "na.fail", "nlm", "nobs", "pbeta",
             "pcauchy", "pgamma", "pgeom", "plogis", "pnbinom", "pnorm",
             "ppois", "pt", "pweibull", "qnorm", "summary.glm", "terms",
             "weighted.mean")
to your NAMESPACE file.

Which involves adding @importFrom pkg fcn1 fnc2 to a function, say line 210 of gnlr.r.
Also, take care of dynlib and importing rmutil:

#' @importFrom graphics lines par rect 
#' @importFrom stats dbeta dbinom dcauchy dexp dgamma dlnorm dlogis dnbinom dnorm dpois dt dweibull glm model.frame model.matrix model.response na.fail nlm nobs pbeta pcauchy pgamma pgeom plogis pnbinom pnorm ppois pt pweibull qnorm summary.glm terms weighted.mean
#' @import rmutil
#' @useDynLib gnlm

Do devtools::document() and rerun check:

[swihart]

Now, change all Foreign function calls PACKAGE = "rmutil" to PACKAGE = "gnlm" and comment out the DUP lines.

Then probably need to get src/dist files from rmutil and put the into gnlm/src/.

re-check:

R CMD check results
1 error  | 2 warnings | 1 note 

[swihart]

All right, I did a bunch of stuff. This is where we are at:

Status: 1 NOTE
checking R code for possible problems ... NOTE
bnlr: no visible binding for global variable ‘const’
fmr : fcn: no visible binding for global variable ‘s’
Undefined global functions or variables:
  const s

See
  ‘/Users/swihartbj/github/gnlm.Rcheck/00check.log’
for details.


R CMD check results
0 errors | 0 warnings | 1 note 

R CMD check succeeded