Running 'allinputs.R' [1s]
  Running 'amak.R' [0s]
  Running 'do_admb.R' [162s]
  Running 'is_int.R' [159s]
  Running 'nonstdreport.R' [0s]
  Running 'racecond.R' [158s]
  Running 'skate.R' [0s]
  Running 'stderr_bug.R' [0s]
Running the tests in 'tests/do_admb.R' failed.
Complete output:
  > library(R2admb)
  > 
  > s <- try(setup_admb())
  > if (!identical(aa <- admb_version(),NA)) {
  +     ## run only if we can
  +     file.copy(system.file("tplfiles","ReedfrogSizepred0.tpl",package="R2admb"),"tadpole.tpl")
  +     tadpoledat <-  data.frame(TBL = rep(c(9,12,21,25,37),each=3),
  +                               Kill = c(0,2,1,3,4,5,0,0,0,0,1,0,0,0,0L),
  +                               nexposed=rep(10,15))
  +     par1 <- list(c=0.45,d=13,g=1)
  +     ## getvals(par1,"value",valsOK=TRUE)
  +     m1 <- do_admb("tadpole",
  +                   data=c(list(nobs=15),tadpoledat),
  +                   params=par1,
  +                   bounds=list(c=c(0,1),d=c(0,50),g=c(-1,25)),
  +                   run.opts=run.control(checkparam="write",
  +                   checkdata="write",clean="all"))
  + 
  +     m1P <- do_admb("tadpole",
  +                    data=c(list(nobs=15),tadpoledat),
  +                    params=par1,
  +                    bounds=list(c=c(0,1),d=c(0,50),g=c(-1,25)),
  +                    phase=list(c=1,d=2,g=-1),
  +                    run.opts=run.control(checkparam="write",
  +                    checkdata="write",clean="all"))
  + 
  +     par2 <- list(c=list(0.45,bounds=c(0,1)),
  +                  d=list(13,bounds=c(0,50)),
  +                  g=list(1,bounds=c(-1,25)))
  + 
  +     m2 <- do_admb("tadpole",
  +                   data=c(list(nobs=15),tadpoledat),
  +                   params=par2,
  +                   run.opts=run.control(checkparam="write",
  +                   checkdata="write",clean="all"))
  + 
  +     par2P <- list(c=list(0.45,bounds=c(0,1),phase=1),
  +                  d=list(13,bounds=c(0,50),phase=2),
  +                  g=list(1,bounds=c(-1,25),phase=-1))
  + 
  +     m2P <- do_admb("tadpole",
  +                   data=c(list(nobs=15),tadpoledat),
  +                   params=par2P,
  +                   run.opts=run.control(checkparam="write",
  +                   checkdata="write",clean="all"))
  + 
  +     stopifnot(all.equal(m1,m2))
  +     stopifnot(all.equal(m1P,m2P))
  +     unlink("tadpole.tpl")
  + 
  +     file.copy(system.file("tplfiles","toy1.tpl",package="R2admb"),"toy1.tpl")
  +     ## random effects example??
  +     cbpp <-  structure(list(herd = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 
  +          3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 
  +          7L, 7L, 7L, 7L, 8L, 9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 11L, 
  +          11L, 11L, 11L, 12L, 12L, 12L, 12L, 13L, 13L, 13L, 13L, 14L, 14L, 
  +          14L, 14L, 15L, 15L, 15L, 15L),
  +      .Label = c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15"),
  +                             class = "factor"), 
  +     incidence = c(2, 3, 4, 0, 3, 1, 1, 8, 2, 0, 2, 2, 0, 2, 0, 
  +     5, 0, 0, 1, 3, 0, 0, 1, 8, 1, 3, 0, 12, 2, 0, 0, 0, 1, 1, 
  +     0, 2, 0, 5, 3, 1, 2, 1, 0, 0, 1, 2, 0, 0, 11, 0, 0, 0, 1, 
  +     1, 1, 0), size = c(14, 12, 9, 5, 22, 18, 21, 22, 16, 16, 
  +     20, 10, 10, 9, 6, 18, 25, 24, 4, 17, 17, 18, 20, 16, 10, 
  +     9, 5, 34, 9, 6, 8, 6, 22, 22, 18, 22, 25, 27, 22, 22, 10, 
  +     8, 6, 5, 21, 24, 19, 23, 19, 2, 3, 2, 19, 15, 15, 15), period = structure(c(1L, 
  +     2L, 3L, 4L, 1L, 2L, 3L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 
  +     2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 1L, 2L, 3L, 
  +     4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 
  +     3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L), .Label = c("1", 
  +     "2", "3", "4"), class = "factor")), .Names = c("herd", "incidence", 
  + "size", "period"), row.names = c(NA, 56L), class = "data.frame")
  + 
  +     X <- model.matrix(~period,data=cbpp)
  +     Zherd <- model.matrix(~herd-1,data=cbpp)
  + 
  +     tmpdat <- list(X=X,Zherd=Zherd,
  +                  incidence=cbpp$incidence,size=cbpp$size,
  +                  nobs=nrow(cbpp))
  + 
  +     d1 <- do_admb("toy1",
  +                   data=tmpdat,
  +               params=list(beta=rep(0,ncol(X)),sigma_herd=0.1),
  +               bounds=list(sigma_herd=c(0.0001,20)),
  +               re=list(u_herd=ncol(Zherd)),
  +               run.opts=run.control(checkdata="write",checkparam="write"),
  +               mcmc=TRUE,
  +               mcmc.opts=mcmc.control(mcmc=20,mcmcpars=c("beta","sigma_herd")))
  + 
  +         d2 <- do_admb("toy1",
  +                   data=tmpdat,
  +               params=list(beta=rep(0,ncol(X)),
  +                   sigma_herd=list(0.1,bounds=c(0.0001,20))),
  +               re=list(u_herd=ncol(Zherd)),
  +               run.opts=run.control(checkdata="write",checkparam="write"))
  + 
  +     summary(d2)
  +     unlink("toy1.tpl")
  + }
  > 
  > proc.time()
     user  system elapsed 
     0.26    0.09    0.34 
Running the tests in 'tests/is_int.R' failed.
Complete output:
  > is.int <- function(x,n=NULL,debug=FALSE) {
  +   opt_in <- (!is.null(data_type) && !is.null(n) &&
  +              n %in% names(data_type)[data_type=="integer"])
  +   opt_out <- (!is.null(data_type) && !is.null(n) &&
  +               n %in% names(data_type)[data_type!="integer"])
  +   trunc_test <- all(trunc(x)==x)
  +   mode_test <- storage.mode(x)=="integer"
  +   if (debug) cat("opt_in",opt_in,"opt_out",opt_out,"trunc_test",trunc_test,"mode_test",mode_test,"\n")
  +   opt_in || (!opt_out &&
  +              !intcheck=="none" &&
  +              ((intcheck=="strict" && mode_test) ||
  +               (intcheck=="trunc" && trunc_test)))
  + }
  > 
  > intcheck <- "strict"
  > data_type <- NULL
  > i1 <- 1
  > stopifnot(!is.int(i1))
  > i2 <- 1L
  > stopifnot(is.int(i2))
  > 
  > intcheck <- "trunc"
  > stopifnot(is.int(i1))
  > 
  > data_type <- c(i1="numeric")
  > stopifnot(!is.int(i1,"i1"))
  > 
  > proc.time()
     user  system elapsed 
     0.21    0.07    0.25 
Running the tests in 'tests/racecond.R' failed.
Complete output:
  > library(R2admb)
  > ## I'm not sure whether this problem *really* demonstrates a race condition;
  > ## it might be a separate effect.  I do know that it's a problem.  I don't
  > ## know if it's
  > 
  > load(system.file("admbtests","racecond.RData",package="R2admb"))
  > file.copy(system.file("admbtests","deltavar_prof.tpl",package="R2admb"),"deltavar_prof.tpl")
  [1] TRUE
  > d1 <- try(do_admb("deltavar_prof",
  +               data=list(nt=length(dvar)+1,
  +                         dvar=dvar,max_var_g=10),
  +               profile=TRUE,
  +               run.opts=run.control(compile=FALSE,clean_files=FALSE),
  +               params=svals))
  Error in run_admb(fn, verbose, mcmc, mcmc.opts, profile, extra.args, admb_errors) : 
    executable deltavar_prof.exe not found: did you forget to compile it?
  > file.copy("deltavar_prof.pin","deltavar_prof1.pin",overwrite=TRUE)
  [1] TRUE
  > 
  > ## works
  > d1B <- try(do_admb("deltavar_prof",
  +               data=list(nt=length(dvar)+1,
  +                         dvar=dvar,max_var_g=10),
  +               profile=TRUE,
  +                    extra.args="-crit 1.e-7",
  +                    run.opts=run.control(compile=FALSE,clean_files=FALSE),
  +                    params=svals))
  Error in run_admb(fn, verbose, mcmc, mcmc.opts, profile, extra.args, admb_errors) : 
    executable deltavar_prof.exe not found: did you forget to compile it?
  > file.copy("deltavar_prof.pin","deltavar_prof1.pin",overwrite=TRUE)
  [1] TRUE
  > 
  > svals2 <- list(rho=0.5,var_g=4)
  > 
  > d2 <- try(do_admb("deltavar_prof",
  +               data=list(nt=length(dvar)+1,
  +                         dvar=dvar,max_var_g=10),
  +               profile=TRUE,
  +               run.opts=run.control(compile=FALSE,clean_files=FALSE),
  +               params=svals2))
  Error in run_admb(fn, verbose, mcmc, mcmc.opts, profile, extra.args, admb_errors) : 
    executable deltavar_prof.exe not found: did you forget to compile it?
  > file.copy("deltavar_prof.pin","deltavar_prof2.pin",overwrite=TRUE)
  [1] TRUE
  > 
  > proc.time()
     user  system elapsed 
     0.28    0.15    0.37