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swihart / growth

Multivariate normal and elliptically-contoured repeated measurements models
GNU General Public License v2.0
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R CMD check results: 1 error | 2 warnings | 5 notes #1

Closed swihart closed 7 years ago

swihart commented 7 years ago 
==> devtools::check(document = FALSE)

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

* checking for file ‘/Users/swihartbj/github/growth/DESCRIPTION’ ... OK
* preparing ‘growth’:
* 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 ‘growth_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 growth ----------------------------------------------------------------
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD check  \
  '/var/folders/tv/9xflkyxs21j3747s8wd641t1bd7ntf/T//RtmpiujiWI/growth_1.0.tar.gz'  \
  --as-cran --timings --no-manual 

* using log directory ‘/Users/swihartbj/github/growth.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 ‘growth/DESCRIPTION’ ... OK
* this is package ‘growth’ version ‘1.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... WARNING
Subdirectory ‘growth/src’ contains apparent object files/libraries
  growth.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 ‘growth’ 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
Calls with DUP:
   .Fortran("kalman", np = as.integer(length(p)), par = as.double(p), 
       like = double(1), xx = matrix(0, nrow = nlp + 1, ncol = nlp + 
           1), y = as.double(y), sse = double(1), nq = as.integer(nre), 
       nlp = as.integer(nlp), ns = as.integer(ns), nt = as.integer(nt), 
       model = as.integer(arma), t = as.double(times), nobs = as.integer(nobs(response)), 
       nod = as.integer(nod), as.integer(position), cv = as.double(ccov), 
       ncv = as.integer(ncv), nxcv = as.integer(interaction), nx = as.integer(torder), 
       p = double(length(p)), x = double(nlp + 1), state = double(maxre * 
           (nlp + 1)), innov = double(nlp + 1), cstate = complex(maxar * 
           (nlp + 1)), exx = complex(nlp + 1), DUP = FALSE, PACKAGE = "growth")
   .Fortran("kalman", np = as.integer(length(p)), par = as.double(p), 
       like = double(1), xx = matrix(0, nrow = nlp + 1, ncol = nlp + 
           1), y = as.double(y), sse = double(1), nq = as.integer(nre), 
       nlp = as.integer(nlp), ns = as.integer(ns), nt = as.integer(nt), 
       model = as.integer(arma), t = as.double(times), nobs = as.integer(nobs(response)), 
       nod = as.integer(nod), as.integer(position), cv = as.double(ccov), 
       ncv = as.integer(ncv), nxcv = as.integer(interaction), nx = as.integer(torder), 
       p = double(length(p)), x = double(nlp + 1), state = double(maxre * 
           (nlp + 1)), innov = double(nlp + 1), cstate = complex(maxar * 
           (nlp + 1)), exx = complex(nlp + 1), DUP = FALSE, PACKAGE = "growth")
   .Fortran("back", xx = z2$xx, as.integer(nlp), DUP = FALSE, PACKAGE = "growth")
   .Fortran("ttvert", xx = z1$xx, as.integer(nlp), DUP = FALSE, 
       PACKAGE = "growth")
   .Fortran("resid", np = as.integer(length(p)), par = as.double(coef), 
       beta = as.double(beta), ave = as.double(ave), pred = double(nt), 
       sdr = double(nt), res = double(nt), y = as.double(y), sse = as.double(sse), 
       nq = as.integer(nre), nlp = as.integer(nlp), ns = as.integer(ns), 
       nt = as.integer(nt), model = as.integer(arma), t = as.double(times), 
       nobs = as.integer(nobs(response)), nod = as.integer(nod), 
       as.integer(position), cv = as.double(ccov), nxcv = as.integer(interaction), 
       nx = as.integer(torder), ncv = as.integer(ncv), p = double(length(p)), 
       x = double(nlp + 1), DUP = FALSE, PACKAGE = "growth")
   .Fortran("plra", theta = as.double(theta), like = double(1), 
       dist = as.integer(dst), as.double(rxl), x = as.double(times), 
       as.double(y), tvcov = as.double(resp$tvcov$tvcov), ccov = as.double(resp$ccov$ccov), 
       dose = as.double(dose), nobs = as.integer(nobs), nbs = as.integer(n), 
       nest = as.integer(resp$response$nest), lnest = as.integer(lnest), 
       dev = double(nm), nind = as.integer(nind), nld = as.integer(nld), 
       nxrl = as.integer(nxrl), np = as.integer(np), npell = as.integer(npell), 
       npv = as.integer(npv), npvl = as.integer(npvl), nccov = as.integer(nccov), 
       npvar = as.integer(npvar), cvar = as.integer(cvar), ccvar = as.integer(!is.null(covfn)), 
       twins = as.integer(twins), npre = as.integer(npre), npar = as.integer(npar), 
       link = as.integer(lnk), torder = as.integer(torder), inter = as.integer(interaction), 
       model = as.integer(mdl), ar = as.integer(ar), tvc = as.integer(ntvc), 
       beta = double(npv2), betacov = double(npv2 * npv2), v = double(nld * 
           nld), sigsq = double(nld), ey = double(nld), tb = double(npvl), 
       as.double(mu), as.double(varn), as.double(covn), DUP = FALSE, 
       PACKAGE = "growth")
   .Fortran("plra", theta = as.double(theta), like = double(1), 
       dist = as.integer(dst), as.double(rxl), x = as.double(times), 
       as.double(y), tvcov = as.double(resp$tvcov$tvcov), ccov = as.double(resp$ccov$ccov), 
       dose = as.double(dose), nobs = as.integer(nobs), nbs = as.integer(n), 
       nest = as.integer(resp$response$nest), lnest = as.integer(lnest), 
       dev = double(nm), nind = as.integer(nind), nld = as.integer(nld), 
       nxrl = as.integer(nxrl), np = as.integer(np), npell = as.integer(npell), 
       npv = as.integer(npv), npvl = as.integer(npvl), nccov = as.integer(nccov), 
       npvar = as.integer(npvar), cvar = as.integer(cvar), ccvar = as.integer(!is.null(covfn)), 
       twins = as.integer(twins), npre = as.integer(npre), npar = as.integer(npar), 
       link = as.integer(lnk), torder = as.integer(torder), inter = as.integer(interaction), 
       model = as.integer(mdl), ar = as.integer(ar), tvc = as.integer(ntvc), 
       beta = double(npv2), betacov = double(npv2 * npv2), v = double(nld * 
           nld), sigsq = double(nld), ey = double(nld), tb = double(npvl), 
       as.double(mu), as.double(varn), as.double(covn), DUP = FALSE, 
       PACKAGE = "growth")
   .Fortran("resid2", np = as.integer(npar + length(pre)), par = as.double(coef), 
       ave = as.double(ave), pred = as.double(pred), rpred = double(nt), 
       sdr = double(nt), res = double(nt), y = as.double(y), mse = as.double(mse), 
       ns = as.integer(nind), nt = as.integer(nt), model = as.integer(npar), 
       t = as.double(times), nobs = as.integer(nobs(resp)), nod = as.integer(length(pre)), 
       p = double(length(p)), DUP = FALSE, PACKAGE = "growth")
   .Fortran("roots", as.integer(n1), as.double(z$coef[1:n1]), r = complex(n1), 
       DUP = FALSE, PACKAGE = "growth")
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

carma: warning in exists(deparse(substitute(response)), env =
  parent.frame()): partial argument match of 'env' to 'envir'
elliptic: warning in exists(deparse(substitute(response)), env =
  parent.frame()): partial argument match of 'env' to 'envir'
carma : kalman: no visible global function definition for ‘nobs’
carma : kalmanl: no visible global function definition for ‘nobs’
carma: no visible global function definition for ‘terms’
carma: no visible global function definition for ‘wr’
carma: no visible global function definition for ‘restovec’
carma: no visible global function definition for ‘tcctomat’
carma: no visible global function definition for ‘rmna’
carma: no visible global function definition for ‘nobs’
carma: no visible binding for global variable ‘resp’
carma: no visible global function definition for ‘nlm’
corgram: no visible global function definition for ‘lines’
corgram: no visible global function definition for ‘plot’
corgram: no visible global function definition for ‘abline’
elliptic: no visible global function definition for ‘var’
elliptic: no visible global function definition for ‘terms’
elliptic: no visible global function definition for ‘wr’
elliptic: no visible global function definition for ‘rmna’
elliptic: no visible global function definition for ‘restovec’
elliptic: no visible global function definition for ‘tcctomat’
elliptic: no visible global function definition for ‘tvctomat’
elliptic: no visible global function definition for ‘finterp’
elliptic: no visible global function definition for ‘fnenvir’
elliptic: no visible global function definition for ‘covind’
elliptic: no visible global function definition for ‘asb’
elliptic: no visible global function definition for ‘nlm’
pergram: no visible global function definition for ‘fft’
plot.cum.pergram: no visible global function definition for ‘plot’
plot.cum.pergram: no visible global function definition for ‘lines’
plot.pergram: no visible global function definition for ‘lines’
plot.pergram: no visible global function definition for ‘plot’
potthoff: no visible global function definition for ‘terms’
potthoff: no visible global function definition for ‘model.frame’
potthoff: no visible binding for global variable ‘na.fail’
potthoff: no visible global function definition for ‘model.matrix’
potthoff: no visible global function definition for ‘contr.poly’
print.carma: no visible global function definition for ‘nobs’
print.elliptic: no visible global function definition for ‘nobs’
rmaov: no visible binding for global variable ‘b’
rmaov: no visible binding for global variable ‘res’
Undefined global functions or variables:
  abline asb b contr.poly covind fft finterp fnenvir lines model.frame
  model.matrix na.fail nlm nobs plot res resp restovec rmna tcctomat
  terms tvctomat var wr
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "contr.poly", "fft", "model.frame", "model.matrix",
             "na.fail", "nlm", "nobs", "terms", "var")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'carma'
  ‘print.level’ ‘typsize’ ‘ndigit’ ‘gradtol’ ‘steptol’ ‘iterlim’
  ‘fscale’ ‘stepmax’
Documented arguments not in \usage in documentation object 'carma':
  ‘others’ ‘z’ ‘plotse’ ‘recursive’

Undocumented arguments in documentation object 'corgram'
  ‘lty’ ‘xlim’ ‘ylim’ ‘xlab’ ‘ylab’ ‘main’ ‘...’
Documented arguments not in \usage in documentation object 'corgram':
  ‘others’

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

Documented arguments not in \usage in documentation object 'pergram':
  ‘add’ ‘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 ‘growth-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: carma
> ### Title: Continuous ARMA for Unequally Spaced Repeated Measurements
> ### Aliases: carma fitted.carma mprofile.carma residuals.carma
> ### Keywords: models
> 
> ### ** Examples
> 
> 
> y <- matrix(rnorm(40),ncol=5)
> x1 <- gl(2,4)
> x2 <- gl(2,1,8)
> # independence with time trend
> carma(y, ccov=~x1, torder=2)
Error in .Fortran("kalman", np = as.integer(length(p)), par = as.double(p),  : 
  "kalman" not available for .Fortran() for package "growth"
Calls: carma -> kalman -> .Fortran
Execution halted
* DONE
Status: 1 ERROR, 2 WARNINGs, 5 NOTEs
checking examples ... ERROR
Running examples in ‘growth-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: carma
> ### Title: Continuous ARMA for Unequally Spaced Repeated Measurements
> ### Aliases: carma fitted.carma mprofile.carma residuals.carma
> ### Keywords: models
> 
> ### ** Examples
> 
> 
> y <- matrix(rnorm(40),ncol=5)
> x1 <- gl(2,4)
> x2 <- gl(2,1,8)
> # independence with time trend
> carma(y, ccov=~x1, torder=2)
Error in .Fortran("kalman", np = as.integer(length(p)), par = as.double(p),  : 
  "kalman" not available for .Fortran() for package "growth"
Calls: carma -> kalman -> .Fortran
Execution halted

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

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

Undocumented arguments in documentation object 'corgram'
  ‘lty’ ‘xlim’ ‘ylim’ ‘xlab’ ‘ylab’ ‘main’ ‘...’
Documented arguments not in \usage in documentation object 'corgram':
... 6 lines ...
Documented arguments not in \usage in documentation object 'elliptic':
  ‘others’ ‘z’ ‘recursive’

Documented arguments not in \usage in documentation object 'pergram':
  ‘add’ ‘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
Calls with DUP:
   .Fortran("kalman", np = as.integer(length(p)), par = as.double(p), 
       like = double(1), xx = matrix(0, nrow = nlp + 1, ncol = nlp + 
           1), y = as.double(y), sse = double(1), nq = as.integer(nre), 
       nlp = as.integer(nlp), ns = as.integer(ns), nt = as.integer(nt), 
       model = as.integer(arma), t = as.double(times), nobs = as.integer(nobs(response)), 
       nod = as.integer(nod), as.integer(position), cv = as.double(ccov), 
       ncv = as.integer(ncv), nxcv = as.integer(interaction), nx = as.integer(torder), 
       p = double(length(p)), x = double(nlp + 1), state = double(maxre * 
... 55 lines ...
       as.double(mu), as.double(varn), as.double(covn), DUP = FALSE, 
       PACKAGE = "growth")
   .Fortran("resid2", np = as.integer(npar + length(pre)), par = as.double(coef), 
       ave = as.double(ave), pred = as.double(pred), rpred = double(nt), 
       sdr = double(nt), res = double(nt), y = as.double(y), mse = as.double(mse), 
       ns = as.integer(nind), nt = as.integer(nt), model = as.integer(npar), 
       t = as.double(times), nobs = as.integer(nobs(resp)), nod = as.integer(length(pre)), 
       p = double(length(p)), DUP = FALSE, PACKAGE = "growth")
   .Fortran("roots", as.integer(n1), as.double(z$coef[1:n1]), r = complex(n1), 
       DUP = FALSE, PACKAGE = "growth")
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

carma: warning in exists(deparse(substitute(response)), env =
  parent.frame()): partial argument match of 'env' to 'envir'
elliptic: warning in exists(deparse(substitute(response)), env =
  parent.frame()): partial argument match of 'env' to 'envir'
carma : kalman: no visible global function definition for ‘nobs’
carma : kalmanl: no visible global function definition for ‘nobs’
carma: no visible global function definition for ‘terms’
... 35 lines ...
rmaov: no visible binding for global variable ‘b’
rmaov: no visible binding for global variable ‘res’
Undefined global functions or variables:
  abline asb b contr.poly covind fft finterp fnenvir lines model.frame
  model.matrix na.fail nlm nobs plot res resp restovec rmna tcctomat
  terms tvctomat var wr
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "contr.poly", "fft", "model.frame", "model.matrix",
             "na.fail", "nlm", "nobs", "terms", "var")
to your NAMESPACE file.

checking compiled code ... NOTE
Note: information on .o files is not available

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

R CMD check results
1 error  | 2 warnings | 5 notes

R CMD check succeeded
swihart commented 7 years ago

I mowed these down until I got 0E | 0W | 0N on my local mac and on travis (well, travis complained on Xrefs for gnlm and repeated -- but they are on CRAN!). When I submitted to winbuilder I got an error about elliptic.f and that is detailed in Issue 2 : https://github.com/swihart/growth/issues/2