1 error | 6 warnings | 3 notes

[swihart]

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

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

• checking for file ‘/Users/swihartbj/github/repeated/DESCRIPTION’ ... OK
• preparing ‘repeated’:
• 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 ‘repeated_1.1.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_CRANINCOMING : FALSE _R_CHECK_FORCESUGGESTS: FALSE Checking repeated ------------------------------------------------------------- '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ \ --no-save --no-restore --quiet CMD check \ '/var/folders/tv/9xflkyxs21j3747s8wd641t1bd7ntf/T//RtmpdVqGpf/repeated_1.1.tar.gz' \ --as-cran --timings --no-manual

• using log directory ‘/Users/swihartbj/github/repeated.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 ‘repeated/DESCRIPTION’ ... OK
• this is package ‘repeated’ version ‘1.1’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... WARNING Subdirectory ‘repeated/src’ contains apparent object files/libraries repeated.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 ‘repeated’ can be installed ... WARNING Found the following significant warnings: Warning: Deleted feature: End expression in DO loop at (1) must be integer Warning: Legacy Extension: REAL array index at (1) Warning: Deleted feature: Start expression in DO loop at (1) must be integer Warning: Extension: Tab character in format at (1) See ‘/Users/swihartbj/github/repeated.Rcheck/00install.out’ for details.
• checking installed package size ... OK
• checking package directory ... OK
• checking DESCRIPTION meta-information ... OK
• 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 ... WARNING Foreign function calls without 'PACKAGE' argument: .C("PurgeSubjectData", ...) .Fortran("logitord", ...) 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") .C("romberg", ..., PACKAGE = "rmutil") Calls with DUP: .Fortran("chidden", x = as.double(p), as.integer(states), iq = as.integer(nosubj), nobs = as.integer(nobs(response)), mobs = as.integer(mobs), s = as.double(if (mdl == 4) y else response$response$y), n = as.integer(response$response$n), times = as.double(response$response$times), l = as.integer(l), pgamma = as.double(pgamma), gamma = double(states states), gamma2 = double(states states), val = double(states), vec = double(states states), invec = double(states states), model = as.integer(mdl), lgam = as.double(lgam), ismu = as.logical(ismu), pmu = as.double(pmu0), pcmu = as.double(pmu1), ptvmu = as.double(pmu2), pshape = as.double(pshape), pfam = as.double(p[np5]), ppar = as.logical(!is.null(par)), par = as.double(exp(p[np])), delta = double(states), nn = as.integer(nob), filter = double(states nob), cf = as.logical(0), a = double(states), b = double(states states), c = double(states), gmod = double(states states), rhs = double(states), pivot = integer(states), qraux = double(states), work = double(2 states), work2 = double(states), work3 = double(states states), like = double(1), DUP = FALSE, PACKAGE = "repeated") .Fortran("chidden", x = as.double(p), as.integer(states), iq = as.integer(nosubj), nobs = as.integer(nobs(response)), mobs = as.integer(mobs), s = as.double(if (mdl == 4) y else response$response$y), n = as.integer(response$response$n), times = as.double(response$response$times), l = as.integer(l), pgamma = as.double(pgamma), gamma = double(states states), gamma2 = double(states states), val = double(states), vec = double(states states), invec = double(states states), model = as.integer(mdl), lgam = as.double(lgam), ismu = as.logical(ismu), pmu = as.double(pmu0), pcmu = as.double(pmu1), ptvmu = as.double(pmu2), pshape = as.double(pshape), pfam = as.double(p[np5]), ppar = as.logical(!is.null(par)), par = as.double(exp(p[np])), delta = double(states), nn = as.integer(nob), filter = double(states nob), cf = as.logical(1), a = double(states), b = double(states states), c = double(states), gmod = double(states states), rhs = double(states), pivot = integer(states), qraux = double(states), work = double(2 states), work2 = double(states), work3 = double(states states), like = double(1), DUP = FALSE, PACKAGE = "repeated") .Fortran("cphidden", x = as.double(p), as.integer(states), iq = as.integer(nosubj), nobs = as.integer(nobs(response)), mobs = as.integer(mobs), s = as.double(if (mdl == 4) y else response$response$y), n = as.integer(response$response$n), times = as.double(response$response$times), l = as.integer(l), pgamma = as.double(pgamma), gamma = double(states states), gamma2 = double(states states), val = double(states), vec = double(states states), invec = double(states states), model = as.integer(mdl), lgam = as.double(lgam), ismu = as.logical(ismu), pmu = as.double(pmu0), pcmu = as.double(pmu1), ptvmu = as.double(pmu2), pshape = as.double(pshape), pfam = as.double(p[np5]), ppar = as.logical(!is.null(par)), par = as.double(exp(p[np])), delta = double(states), nn = as.integer(nob), filter = double(states nob), cf = as.logical(0), a = double(states), b = double(states states), c = double(states), gmod = double(states states), rhs = double(states), pivot = integer(states), qraux = double(states), work = double(2 states), work2 = double(states), work3 = double(states states), like = double(1), DUP = FALSE, PACKAGE = "repeated") .Fortran("cphidden", x = as.double(p), as.integer(states), iq = as.integer(nosubj), nobs = as.integer(nobs(response)), mobs = as.integer(mobs), s = as.double(if (mdl == 4) y else response$response$y), n = as.integer(response$response$n), times = as.double(response$response$times), l = as.integer(l), pgamma = as.double(pgamma), gamma = double(states states), gamma2 = double(states states), val = double(states), vec = double(states states), invec = double(states states), model = as.integer(mdl), lgam = as.double(lgam), ismu = as.logical(ismu), pmu = as.double(pmu0), pcmu = as.double(pmu1), ptvmu = as.double(pmu2), pshape = as.double(pshape), pfam = as.double(p[np5]), ppar = as.logical(!is.null(par)), par = as.double(exp(p[np])), delta = double(states), nn = as.integer(nob), filter = double(states nob), cf = as.logical(1), a = double(states), b = double(states states), c = double(states), gmod = double(states states), rhs = double(states), pivot = integer(states), qraux = double(states), work = double(2 states), work2 = double(states), work3 = double(states states), like = double(1), DUP = FALSE, PACKAGE = "repeated") .C("gar", y = as.double(y), total = as.double(response$response$n), my = as.integer(3 max(y)), nobs = as.integer(nobs(response)), nind = as.integer(nind), times = as.double(response$response$times), censor = as.integer(censor), cens = as.integer(!is.null(response$response$censor)), eta = as.double(eta), tm = as.integer(tm), theta = as.double(theta), dep = as.double(dep), model = as.integer(mdl), thp = as.integer(thp), shape = as.double(shr), sh = as.integer(sh), link = as.integer(lnk), ar = as.integer(ar), order = as.integer(order), parch = as.double(parch), arch = as.integer(archtype), pred = double(n), rpred = double(n), volatility = double(n), like = double(1), DUP = FALSE, PACKAGE = "repeated") .C("gar", y = as.double(y), total = as.double(response$response$n), my = as.integer(3 max(y)), nobs = as.integer(nobs(response)), nind = as.integer(nind), times = as.double(response$response$times), censor = as.integer(censor), cens = as.integer(!is.null(response$response$censor)), eta = as.double(eta), tm = as.integer(tm), theta = as.double(theta), dep = as.double(dep), model = as.integer(mdl), thp = as.integer(thp), shape = as.double(shr), sh = as.integer(sh), link = as.integer(lnk), ar = as.integer(ar), order = as.integer(order), parch = as.double(parch), arch = as.integer(archtype), pred = double(n), rpred = double(n), volatility = double(n), like = double(1), DUP = FALSE, PACKAGE = "repeated") .C("plevy", as.double(q), as.double(m), as.double(s), as.double(1), len = as.integer(len), eps = as.double(1e-06), pts = as.integer(5), max = as.integer(16), err = integer(1), res = double(len), DUP = FALSE, PACKAGE = "rmutil") .Fortran("gcopula", theta = as.double(corr), like = double(1), x = as.double(response$response$times), y = as.double(q), nobs = as.integer(nobs), nest = as.integer(response$response$nest), lnest = as.integer(lnest), nind = as.integer(nind), nld = as.integer(nld), npre = as.integer(npre), npar = as.integer(npar), ar = as.integer(ar), v = double(nld nld), tmp1 = double(nld), tmp2 = double(nld), tmp3 = double(nld), warn = logical(1), DUP = FALSE, PACKAGE = "repeated") .C("ddb", as.integer(y[, 1]), as.integer(nn), as.double(mu1(p, r)), 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, r)), 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, r)), as.double(exp(sh1(p))), as.integer(n), as.double(wt), res = double(n), DUP = FALSE, PACKAGE = "rmutil") .C("dmp", as.integer(y), as.integer(my), as.double(mu1(p, r)), as.double(exp(sh1(p))), as.integer(n), as.double(wt), res = double(n), 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(mu4(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(mu4(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(mu4(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(mu4(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") .Fortran("hidden", x = as.double(p), as.integer(states), iq = as.integer(nosubj), nobs = as.integer(nobs(response)), mobs = as.integer(mobs), s = as.double(if (mdl == 4) y else response$response$y), n = as.integer(response$response$n), l = as.integer(l), pgamma = as.double(pgamma), pos = as.integer(pos), gamma = double(states states), model = as.integer(mdl), lgam = as.double(lgam), ismu = as.logical(ismu), pmu = as.double(pmu0), pcmu = as.double(pmu1), ptvmu = as.double(pmu2), pshape = as.double(pshape), pfam = as.double(p[np5]), ppar = as.logical(!is.null(par)), par = as.double(p[np]), delta = double(states), nn = as.integer(nob), filter = double(states nob), cf = as.logical(0), a = double(states), b = double(states states), c = double(states), gmod = double(states states), rhs = double(states), pivot = integer(states), qraux = double(states), work = double(2 states), work2 = double(states), like = double(1), DUP = FALSE, PACKAGE = "repeated") .Fortran("hidden", x = as.double(p), as.integer(states), iq = as.integer(nosubj), nobs = as.integer(nobs(response)), mobs = as.integer(mobs), s = as.double(if (mdl == 4) y else response$response$y), n = as.integer(response$response$n), l = as.integer(l), pgamma = as.double(pgamma), pos = as.integer(pos), gamma = double(states states), model = as.integer(mdl), lgam = as.double(lgam), ismu = as.logical(ismu), pmu = as.double(pmu0), pcmu = as.double(pmu1), ptvmu = as.double(pmu2), pshape = as.double(pshape), pfam = as.double(p[np5]), ppar = as.logical(!is.null(par)), par = as.double(p[np]), delta = double(states), nn = as.integer(nob), filter = double(states nob), cf = as.logical(1), a = double(states), b = double(states states), c = double(states), gmod = double(states states), rhs = double(states), pivot = integer(states), qraux = double(states), work = double(2 states), work2 = double(states), like = double(1), DUP = FALSE, PACKAGE = "repeated") .C("ddb", as.integer(y[, 1]), as.integer(nn), as.double(m), 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(m), 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(m), as.double(exp(sh1(p))), as.integer(n), as.double(wt), res = double(n), DUP = FALSE, PACKAGE = "rmutil") .C("dmp", as.integer(y), as.integer(my), as.double(m), as.double(exp(sh1(p))), as.integer(n), as.double(wt), res = double(n), DUP = FALSE, PACKAGE = "rmutil") .C("kcountb", p = as.double(p), y = as.double(resp$response$times), origin = as.double(origin), c = as.integer(resp$response$y), x = as.double(resp$ccov$ccov), nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), nccov = as.integer(nccov), model = as.integer(mdl), density = as.integer(density), pfamily = as.integer(!is.null(pfamily)), dep = as.integer(dep), birth = as.integer(birth), tvc = as.integer(tvc), tvcov = as.double(resp$tvcov$tvcov), fit = as.integer(0), pred = double(n), rpred = double(n), rf = as.integer(rf), bb = as.double(b), sf = as.integer(sf), vv = as.double(v), like = double(1), DUP = FALSE, PACKAGE = "repeated") .C("countfb", p = as.double(p), y = as.double(resp$response$times), c = as.integer(resp$response$y), x = as.double(resp$ccov$ccov), nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), nccov = as.integer(nccov), model = as.integer(mdl), density = as.integer(density), tvc = as.integer(tvc), tvcov = as.double(resp$tvcov$tvcov), fit = as.integer(0), pred = double(n), rpred = double(n), rf = as.integer(rf), bb = as.double(b), sf = as.integer(sf), vv = as.double(v), frser = as.integer(frser), like = double(1), DUP = FALSE, PACKAGE = "repeated") .C("countfb", p = as.double(z0$estimate), y = as.double(resp$response$times), c = as.integer(resp$response$y), x = as.double(resp$ccov$ccov), nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), nccov = as.integer(nccov), model = as.integer(mdl), density = as.integer(density), tvc = as.integer(tvc), tvcov = resp$tvcov$tvcov, fit = as.integer(1), pred = double(n), rpred = double(n), rf = as.integer(rf), bb = as.double(b), sf = as.integer(sf), vv = as.double(v), frser = as.integer(frser), like = double(1), DUP = FALSE, PACKAGE = "repeated") .C("kcountb", p = as.double(z0$estimate), y = as.double(resp$response$times), origin = as.double(origin), c = as.integer(resp$response$y), x = as.double(resp$ccov$ccov), nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), nccov = as.integer(nccov), model = as.integer(mdl), density = as.integer(density), pfamily = as.integer(!is.null(pfamily)), dep = as.integer(dep), birth = as.integer(birth), tvc = as.integer(tvc), tvcov = resp$tvcov$tvcov, fit = as.integer(1), pred = double(n), rpred = double(n), rf = as.integer(rf), bb = as.double(b), sf = as.integer(sf), vv = as.double(v), like = double(1), DUP = FALSE, PACKAGE = "repeated") .C("kserie", p = as.double(p), y = as.double(y), t = as.double(times), x = as.double(resp$ccov$ccov), nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), nccov = as.integer(nccov), npv = as.integer(npv), model = as.integer(mdl), link = as.integer(lnk), density = as.integer(density), pfamily = as.integer(!is.null(pfamily)), dep = as.integer(dep), torder = as.integer(torder), inter = as.integer(interaction), tvc = as.integer(tvc), tvcov = resp$tvcov$tvcov, fit = as.integer(0), pred = double(n), rpred = double(n), rf = as.integer(rf), bbb = as.double(b), sf = as.integer(sf), vv = as.double(v), like = double(1), DUP = FALSE, PACKAGE = "repeated") .C("krand", p = as.double(p), y = as.double(y), t = as.double(times), x = as.double(resp$ccov$ccov), nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), nccov = as.integer(nccov), npv = as.integer(npv), model = as.integer(mdl), link = as.integer(lnk), density = as.integer(density), torder = as.integer(torder), inter = as.integer(interaction), tvc = as.integer(tvc), tvcov = resp$tvcov$tvcov, fit = as.integer(0), pred = double(n), rpred = double(n), rf = as.integer(rf), bbb = as.double(b), sf = as.integer(sf), vv = as.double(v), frser = as.integer(frser), like = double(1), DUP = FALSE, PACKAGE = "repeated") .C("krand", p = as.double(p), y = as.double(y), t = as.double(times), x = as.double(resp$ccov$ccov), nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), nccov = as.integer(nccov), npv = as.integer(npv), model = as.integer(mdl), link = as.integer(lnk), density = as.integer(density), torder = as.integer(torder), inter = as.integer(interaction), tvc = as.integer(tvc), tvcov = resp$tvcov$tvcov, fit = as.integer(1), pred = double(n), rpred = double(n), rf = as.integer(rf), bbb = as.double(b), sf = as.integer(sf), vv = as.double(v), frser = as.integer(frser), like = double(1), DUP = FALSE, PACKAGE = "repeated") .C("kserie", p = as.double(p), y = as.double(y), t = as.double(times), x = as.double(resp$ccov$ccov), nind = as.integer(nind), nobs = as.integer(nobs), nbs = as.integer(n), nccov = as.integer(nccov), npv = as.integer(npv), model = as.integer(mdl), link = as.integer(lnk), density = as.integer(density), pfamily = as.integer(!is.null(pfamily)), dep = as.integer(dep), torder = as.integer(torder), inter = as.integer(interaction), tvc = as.integer(tvc), tvcov = resp$tvcov$tvcov, fit = as.integer(1), pred = double(n), rpred = double(n), rf = as.integer(rf), bbb = as.double(b), sf = as.integer(sf), vv = as.double(v), like = double(1), DUP = FALSE, PACKAGE = "repeated") .Fortran("logitord", y = as.double(data), upk = as.integer(binom.mix), eps = as.double(eps), fcalls = as.integer(fcalls), iout = as.integer(print.level), cg = as.integer(cg), total1 = as.integer(total1), total2a = as.integer(total2a), total2b = as.integer(total2b), nobs = as.integer(nobs), p = as.double(p), x = double(total), ster = double(total), hess = double(total total), hessinv = double(total * total), nflag = integer(1), iter = integer(1), ifun = integer(1), like = double(1), DUP = FALSE) 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

gnlmm: warning in exists(deparse(substitute(y)), env = parent.frame()): partial argument match of 'env' to 'envir' gnlmm3: warning in exists(deparse(substitute(y)), env = parent.frame()): partial argument match of 'env' to 'envir' binnest: no visible global function definition for ‘finterp’ binnest: no visible global function definition for ‘wr’ binnest: no visible global function definition for ‘nobs’ binnest: no visible global function definition for ‘restovec’ binnest: no visible global function definition for ‘tcctomat’ binnest: no visible global function definition for ‘covind’ binnest: no visible global function definition for ‘tvctomat’ biv.betab : like: no visible binding for global variable ‘y’ biv.betab: no visible binding for global variable ‘y’ biv.betab: no visible global function definition for ‘nlm’ biv.binom: no visible global function definition for ‘capply’ biv.binom: no visible global function definition for ‘terms’ biv.binom: no visible global function definition for ‘model.frame’ biv.binom: no visible binding for global variable ‘na.fail’ biv.binom: no visible global function definition for ‘model.matrix’ biv.binom: no visible global function definition for ‘nlm’ catmiss: no visible global function definition for ‘capply’ chidden : likel: no visible global function definition for ‘nobs’ chidden : like: no visible global function definition for ‘nobs’ chidden: no visible global function definition for ‘restovec’ chidden: no visible global function definition for ‘rmna’ chidden: no visible global function definition for ‘nobs’ chidden: no visible global function definition for ‘finterp’ chidden: no visible global function definition for ‘fnenvir’ chidden: no visible global function definition for ‘nlm’ cmcre: no visible global function definition for ‘nlm’ cphidden : likel: no visible global function definition for ‘nobs’ cphidden : like: no visible global function definition for ‘nobs’ cphidden: no visible global function definition for ‘restovec’ cphidden: no visible global function definition for ‘rmna’ cphidden: no visible global function definition for ‘nobs’ cphidden: no visible global function definition for ‘finterp’ cphidden: no visible global function definition for ‘fnenvir’ cphidden: no visible global function definition for ‘nlm’ gar : likekal: no visible global function definition for ‘nobs’ gar: no visible global function definition for ‘restovec’ gar: no visible global function definition for ‘rmna’ gar: no visible global function definition for ‘nobs’ gar: no visible global function definition for ‘finterp’ gar: no visible global function definition for ‘fnenvir’ gar: no visible global function definition for ‘covind’ gar: no visible global function definition for ‘nlm’ gausscop : pinvgauss: no visible global function definition for ‘pnorm’ gausscop : gcopula: no visible global function definition for ‘pexp’ gausscop : gcopula: no visible global function definition for ‘pgamma’ gausscop : gcopula: no visible global function definition for ‘pweibull’ gausscop : gcopula: no visible global function definition for ‘plogis’ gausscop : gcopula: no visible global function definition for ‘pcauchy’ gausscop : gcopula: no visible global function definition for ‘qnorm’ gausscop : gcopula: no visible global function definition for ‘dexp’ gausscop : gcopula: no visible global function definition for ‘dgamma’ gausscop : gcopula: no visible global function definition for ‘dweibull’ gausscop : gcopula: no visible global function definition for ‘dlogis’ gausscop : gcopula: no visible global function definition for ‘dcauchy’ gausscop: no visible global function definition for ‘rmna’ gausscop: no visible global function definition for ‘finterp’ gausscop: no visible global function definition for ‘fnenvir’ gausscop: no visible global function definition for ‘covind’ gausscop: no visible global function definition for ‘nlm’ glmm: no visible binding for global variable ‘gaussian’ glmm: no visible global function definition for ‘glm.control’ glmm: no visible global function definition for ‘model.frame’ glmm: no visible global function definition for ‘terms’ glmm: no visible binding for global variable ‘na.fail’ glmm: no visible global function definition for ‘as.formula’ glmm: no visible global function definition for ‘gauss.hermite’ glmm: no visible global function definition for ‘update.formula’ glmm: no visible global function definition for ‘glm’ gnlmix: no visible global function definition for ‘finterp’ gnlmix: no visible global function definition for ‘fnenvir’ gnlmix: no visible global function definition for ‘wr’ gnlmix: no visible global function definition for ‘nobs’ gnlmix: no visible global function definition for ‘covind’ gnlmix: no visible global function definition for ‘response’ gnlmix : : no visible global function definition for ‘dbinom’ gnlmix : : no visible global function definition for ‘dpois’ gnlmix : : no visible global function definition for ‘dnbinom’ gnlmix : : no visible global function definition for ‘pgamma’ gnlmix : : no visible global function definition for ‘dnorm’ gnlmix : : no visible global function definition for ‘dlogis’ gnlmix : : no visible global function definition for ‘dcauchy’ gnlmix : : no visible global function definition for ‘dexp’ gnlmix : : no visible global function definition for ‘dgamma’ gnlmix : : no visible global function definition for ‘dweibull’ gnlmix : : no visible global function definition for ‘dbeta’ gnlmix : : no visible global function definition for ‘ppois’ gnlmix : : no visible global function definition for ‘pnbinom’ gnlmix : : no visible global function definition for ‘pgeom’ gnlmix : : no visible global function definition for ‘pnorm’ gnlmix : : no visible global function definition for ‘plogis’ gnlmix : : no visible global function definition for ‘pcauchy’ gnlmix : : no visible global function definition for ‘pexp’ gnlmix : : no visible global function definition for ‘pweibull’ gnlmix : like : fn: no visible global function definition for ‘capply’ gnlmix: no visible global function definition for ‘nlm’ gnlmm : pinvgauss: no visible global function definition for ‘pnorm’ gnlmm: no visible global function definition for ‘nobs’ gnlmm: no visible global function definition for ‘finterp’ gnlmm: no visible global function definition for ‘fnenvir’ gnlmm: no visible global function definition for ‘wr’ gnlmm: no visible global function definition for ‘covind’ gnlmm: no visible global function definition for ‘response’ gnlmm: no visible global function definition for ‘gauss.hermite’ gnlmm : fcn: no visible global function definition for ‘pgamma’ gnlmm : fcn: no visible global function definition for ‘pnorm’ gnlmm : fcn: no visible global function definition for ‘plogis’ gnlmm : fcn: no visible global function definition for ‘pcauchy’ gnlmm : fcn: no visible global function definition for ‘pweibull’ gnlmm : fcn: no visible global function definition for ‘pbeta’ gnlmm : fcn: no visible global function definition for ‘dbeta’ gnlmm : fcn: no visible global function definition for ‘ppois’ gnlmm : fcn: no visible global function definition for ‘pnbinom’ gnlmm : fcn: no visible global function definition for ‘pgeom’ gnlmm: no visible global function definition for ‘nlm’ gnlmm3: no visible global function definition for ‘nobs’ gnlmm3: no visible global function definition for ‘finterp’ gnlmm3: no visible global function definition for ‘fnenvir’ gnlmm3: no visible global function definition for ‘wr’ gnlmm3: no visible global function definition for ‘response’ gnlmm3: no visible global function definition for ‘gauss.hermite’ gnlmm3 : fcn: no visible global function definition for ‘pnorm’ gnlmm3 : fcn: no visible global function definition for ‘dnorm’ gnlmm3 : fcn: no visible global function definition for ‘pgamma’ gnlmm3 : fcn: no visible global function definition for ‘pt’ gnlmm3 : fcn: no visible global function definition for ‘dt’ gnlmm3 : fcn: no visible global function definition for ‘pweibull’ gnlmm3: no visible global function definition for ‘nlm’ hidden : likel: no visible global function definition for ‘nobs’ hidden : like: no visible global function definition for ‘nobs’ hidden: no visible global function definition for ‘restovec’ hidden: no visible global function definition for ‘rmna’ hidden: no visible global function definition for ‘nobs’ hidden: no visible global function definition for ‘finterp’ hidden: no visible global function definition for ‘fnenvir’ hidden: no visible global function definition for ‘nlm’ hnlmix: no visible global function definition for ‘finterp’ hnlmix: no visible global function definition for ‘fnenvir’ hnlmix: no visible global function definition for ‘wr’ hnlmix: no visible global function definition for ‘nobs’ hnlmix: no visible global function definition for ‘covind’ hnlmix: no visible global function definition for ‘response’ hnlmix : : no visible global function definition for ‘dbinom’ hnlmix : : no visible global function definition for ‘dpois’ hnlmix : : no visible global function definition for ‘dnbinom’ hnlmix : : no visible global function definition for ‘pgamma’ hnlmix : : no visible global function definition for ‘dnorm’ hnlmix : : no visible global function definition for ‘dlogis’ hnlmix : : no visible global function definition for ‘dcauchy’ hnlmix : : no visible global function definition for ‘dexp’ hnlmix : : no visible global function definition for ‘dgamma’ hnlmix : : no visible global function definition for ‘dweibull’ hnlmix : : no visible global function definition for ‘dbeta’ hnlmix : : no visible global function definition for ‘ppois’ hnlmix : : no visible global function definition for ‘pnbinom’ hnlmix : : no visible global function definition for ‘pgeom’ hnlmix : : no visible global function definition for ‘pnorm’ hnlmix : : no visible global function definition for ‘plogis’ hnlmix : : no visible global function definition for ‘pcauchy’ hnlmix : : no visible global function definition for ‘pexp’ hnlmix : : no visible global function definition for ‘pweibull’ hnlmix : : no visible binding for global variable ‘s’ hnlmix : : no visible global function definition for ‘uniroot’ hnlmix: no visible global function definition for ‘nlm’ hnlmix: no visible global function definition for ‘uniroot’ kalcount: no visible global function definition for ‘rmna’ kalcount: no visible global function definition for ‘terms’ kalcount: no visible global function definition for ‘wr’ kalcount: no visible global function definition for ‘restovec’ kalcount: no visible global function definition for ‘tcctomat’ kalcount: no visible global function definition for ‘tvctomat’ kalcount: no visible global function definition for ‘finterp’ kalcount: no visible global function definition for ‘fnenvir’ kalcount: no visible global function definition for ‘covind’ kalcount : sh1: no visible binding for global variable ‘npl1’ kalcount: no visible global function definition for ‘nlm’ kalseries: no visible global function definition for ‘rmna’ kalseries: no visible global function definition for ‘terms’ kalseries: no visible global function definition for ‘wr’ kalseries: no visible global function definition for ‘restovec’ kalseries: no visible global function definition for ‘tcctomat’ kalseries: no visible global function definition for ‘tvctomat’ kalseries: no visible global function definition for ‘finterp’ kalseries: no visible global function definition for ‘fnenvir’ kalseries: no visible global function definition for ‘covind’ kalseries : sh1: no visible binding for global variable ‘npl1’ kalseries: no visible global function definition for ‘nlm’ logitord: no visible global function definition for ‘terms’ logitord: no visible global function definition for ‘model.matrix’ logitord: no visible global function definition for ‘model.frame’ logitord: no visible binding for global variable ‘na.fail’ marg.hom: no visible global function definition for ‘glm’ marg.hom: no visible global function definition for ‘dpois’ nbkal : likekal: no visible global function definition for ‘nobs’ nbkal : likepred: no visible global function definition for ‘nobs’ nbkal: no visible global function definition for ‘restovec’ nbkal: no visible global function definition for ‘rmna’ nbkal: no visible global function definition for ‘nobs’ nbkal: no visible global function definition for ‘nlm’ plot.hidden: no visible global function definition for ‘nobs’ plot.hidden: no visible global function definition for ‘covind’ plot.hidden: no visible global function definition for ‘par’ plot.hidden: no visible global function definition for ‘plot’ print.gar: no visible global function definition for ‘nobs’ print.gausscop: no visible global function definition for ‘nobs’ print.glmm: no visible global function definition for ‘print.glm’ print.hidden: no visible global function definition for ‘nobs’ print.kalcount: no visible global function definition for ‘nobs’ print.kalseries: no visible global function definition for ‘nobs’ print.nbkal: no visible global function definition for ‘nobs’ summary.glmm: no visible global function definition for ‘summary.glm’ volatility.gar: no visible global function definition for ‘nobs’ volatility.gar: no visible global function definition for ‘covind’ Undefined global functions or variables: as.formula capply covind dbeta dbinom dcauchy dexp dgamma dlogis dnbinom dnorm dpois dt dweibull finterp fnenvir gauss.hermite gaussian glm glm.control model.frame model.matrix na.fail nlm nobs npl1 par pbeta pcauchy pexp pgamma pgeom plogis plot pnbinom pnorm ppois print.glm pt pweibull qnorm response restovec rmna s summary.glm tcctomat terms tvctomat uniroot update.formula wr y Consider adding importFrom("graphics", "par", "plot") importFrom("stats", "as.formula", "dbeta", "dbinom", "dcauchy", "dexp", "dgamma", "dlogis", "dnbinom", "dnorm", "dpois", "dt", "dweibull", "gaussian", "glm", "glm.control", "model.frame", "model.matrix", "na.fail", "nlm", "nobs", "pbeta", "pcauchy", "pexp", "pgamma", "pgeom", "plogis", "pnbinom", "pnorm", "ppois", "pt", "pweibull", "qnorm", "summary.glm", "terms", "uniroot", "update.formula") 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 packages ‘growth’, ‘event’ 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 'biv.betab' ‘print.level’ ‘typsize’ ‘ndigit’ ‘gradtol’ ‘stepmax’ ‘steptol’ ‘iterlim’ ‘fscale’ Documented arguments not in \usage in documentation object 'biv.betab': ‘other’

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

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

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

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

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

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

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

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

Undocumented arguments in documentation object 'gnlmm3' ‘print.level’ ‘typsize’ ‘ndigit’ ‘gradtol’ ‘stepmax’ ‘steptol’ ‘iterlim’ ‘fscale’ Documented arguments not in \usage in documentation object 'gnlmm3': ‘others’

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

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

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

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

Undocumented arguments in documentation object 'nbkal' ‘print.level’ ‘ndigit’ ‘gradtol’ ‘steptol’ ‘fscale’ ‘iterlim’ ‘typsize’ ‘stepmax’ Documented arguments not in \usage in documentation object 'nbkal': ‘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 ... WARNING 'library' or 'require' calls not declared from: ‘gnlm’ ‘growth’
• 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 File ‘/Users/swihartbj/github/repeated.Rcheck/repeated/libs/repeated.so’: Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’ (Fortran) Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)

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. The detected symbols are linked into the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.

• checking examples ... ERROR Running examples in ‘repeated-Ex.R’ failed The error most likely occurred in:

base::assign(".ptime", proc.time(), pos = "CheckExEnv")

Name: binnest

Title: Binary Random Effects Models with Two Levels of Nesting

Aliases: binnest

Keywords: models

** Examples

y <- rbind(matrix(rbinom(20,1,0.6), ncol=4),

matrix(rbinom(20,1,0.4), ncol=4))

y <- matrix(c(1,1,0,1,1,1,1,0,1,1,1,1,1,1,1,1,0,1,1,0,0,1,0,1,1,0,1,0,

• 1,1,1,1,1,1,1,1,0,1,1,0),nrow=10,ncol=4,byrow=TRUE) resp <- restovec(y, nest=1:4, times=FALSE) ccov <- tcctomat(c(rep(0,5),rep(1,5)), name="treatment") reps <- rmna(resp, ccov=ccov)

  two random effects

  binnest(reps, mu=~treatment, preg=c(1,0), pre1=1, pre2=1) Error in .Fortran("binnest", Fvalue = double(1), res = integer(3), x = double(total), : "binnest" not available for .Fortran() for package "repeated" Calls: binnest -> .Fortran Execution halted

• DONE Status: 1 ERROR, 6 WARNINGs, 3 NOTEs

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

checking examples ... ERROR Running examples in ‘repeated-Ex.R’ failed The error most likely occurred in:

base::assign(".ptime", proc.time(), pos = "CheckExEnv")

Name: binnest

Title: Binary Random Effects Models with Two Levels of Nesting

Aliases: binnest

Keywords: models

... 6 lines ... y <- matrix(c(1,1,0,1,1,1,1,0,1,1,1,1,1,1,1,1,0,1,1,0,0,1,0,1,1,0,1,0,

• 1,1,1,1,1,1,1,1,0,1,1,0),nrow=10,ncol=4,byrow=TRUE) resp <- restovec(y, nest=1:4, times=FALSE) ccov <- tcctomat(c(rep(0,5),rep(1,5)), name="treatment") reps <- rmna(resp, ccov=ccov)

  two random effects

  binnest(reps, mu=~treatment, preg=c(1,0), pre1=1, pre2=1) Error in .Fortran("binnest", Fvalue = double(1), res = integer(3), x = double(total), : "binnest" not available for .Fortran() for package "repeated" Calls: binnest -> .Fortran Execution halted

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

checking whether package ‘repeated’ can be installed ... WARNING Found the following significant warnings: Warning: Deleted feature: End expression in DO loop at (1) must be integer Warning: Legacy Extension: REAL array index at (1) Warning: Deleted feature: Start expression in DO loop at (1) must be integer Warning: Extension: Tab character in format at (1) See ‘/Users/swihartbj/github/repeated.Rcheck/00install.out’ for details.

checking foreign function calls ... WARNING Foreign function calls without 'PACKAGE' argument: .C("PurgeSubjectData", ...) .Fortran("logitord", ...) 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") ... 264 lines ... pred = double(n), rpred = double(n), rf = as.integer(rf), bbb = as.double(b), sf = as.integer(sf), vv = as.double(v), like = double(1), DUP = FALSE, PACKAGE = "repeated") .Fortran("logitord", y = as.double(data), upk = as.integer(binom.mix), eps = as.double(eps), fcalls = as.integer(fcalls), iout = as.integer(print.level), cg = as.integer(cg), total1 = as.integer(total1), total2a = as.integer(total2a), total2b = as.integer(total2b), nobs = as.integer(nobs), p = as.double(p), x = double(total), ster = double(total), hess = double(total total), hessinv = double(total total), nflag = integer(1), iter = integer(1), ifun = integer(1), like = double(1), DUP = FALSE) DUP is no longer supported and will be ignored.

checking Rd cross-references ... WARNING Obsolete package ‘nls’ in Rd xrefs Unknown packages ‘growth’, ‘event’ in Rd xrefs

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

Undocumented arguments in documentation object 'biv.binom' ‘print.level’ ‘typsize’ ‘ndigit’ ‘gradtol’ ‘stepmax’ ‘steptol’ ‘iterlim’ ‘fscale’ ... 76 lines ... Undocumented arguments in documentation object 'nbkal' ‘print.level’ ‘ndigit’ ‘gradtol’ ‘steptol’ ‘fscale’ ‘iterlim’ ‘typsize’ ‘stepmax’ Documented arguments not in \usage in documentation object 'nbkal': ‘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 for unstated dependencies in examples ... WARNING 'library' or 'require' calls not declared from: ‘gnlm’ ‘growth’

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

gnlmm: warning in exists(deparse(substitute(y)), env = parent.frame()): partial argument match of 'env' to 'envir' gnlmm3: warning in exists(deparse(substitute(y)), env = parent.frame()): partial argument match of 'env' to 'envir' binnest: no visible global function definition for ‘finterp’ binnest: no visible global function definition for ‘wr’ binnest: no visible global function definition for ‘nobs’ ... 241 lines ... summary.glm tcctomat terms tvctomat uniroot update.formula wr y Consider adding importFrom("graphics", "par", "plot") importFrom("stats", "as.formula", "dbeta", "dbinom", "dcauchy", "dexp", "dgamma", "dlogis", "dnbinom", "dnorm", "dpois", "dt", "dweibull", "gaussian", "glm", "glm.control", "model.frame", "model.matrix", "na.fail", "nlm", "nobs", "pbeta", "pcauchy", "pexp", "pgamma", "pgeom", "plogis", "pnbinom", "pnorm", "ppois", "pt", "pweibull", "qnorm", "summary.glm", "terms", "uniroot", "update.formula") to your NAMESPACE file.

checking compiled code ... NOTE Note: information on .o files is not available File ‘/Users/swihartbj/github/repeated.Rcheck/repeated/libs/repeated.so’: Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’ (Fortran) Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)

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. The detected symbols are linked into the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. R CMD check results 1 error | 6 warnings | 3 notes

R CMD check succeeded

[swihart]

Can I eliminate this:

Consider adding importFrom("graphics", "par", "plot") importFrom("stats", "as.formula", "dbeta", "dbinom", "dcauchy", "dexp", "dgamma", "dlogis", "dnbinom", "dnorm", "dpois", "dt", "dweibull", "gaussian", "glm", "glm.control", "model.frame", "model.matrix", "na.fail", "nlm", "nobs", "pbeta", "pcauchy", "pexp", "pgamma", "pgeom", "plogis", "pnbinom", "pnorm", "ppois", "pt", "pweibull", "qnorm", "summary.glm", "terms", "uniroot", "update.formula") to your NAMESPACE file.

If I add graphics and stats to Imports in the DESCRIPTION?

[swihart]

Well, just adding graphics and stats to Imports in the DESCRIPTION didn't do it. and running devtools::document() didn't update the NAMESPACE file which isn't suppose to be edited by hand.

[swihart]

Went ahead and put:

' @importFrom graphics par plot

' @importFrom stats as.formula dbeta dbinom dcauchy dexp dgamma dlogis dnbinom dnorm dpois dt dweibull gaussian glm glm.control model.frame model.matrix na.fail nlm nobs pbeta pcauchy pexp pgamma pgeom plogis pnbinom pnorm ppois pt pweibull qnorm summary.glm terms uniroot update.formula

under

' @export gnlmix

in gnlmix.R

and re-ran devtools::document() and then shift-cmd-E.

It eliminated that from suggested fixes but did not take away from ERROR-Warning-Notes count.

[swihart]

delete INDEX delete src/Makefile

• down one warning! 1 error | 5 warnings | 3 notes

[swihart]

• Problem: NOTE: ""

• Solution: http://stackoverflow.com/q/23519939/2727349; add @ Import to gnlmix.r

• Result: We removed a NOTE!

1 error | 5 warnings | 2 notes

[swihart]

"Calls with DUP: ouput eliminated by commenting out DUP"

Result: removed a warning but introduced note !?!

R CMD check results 1 error | 4 warnings | 3 notes

R CMD check succeeded

[swihart]

• Problem:

• 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") .C("romberg", ..., PACKAGE = "rmutil")

  • Solution: change "rmutil" -> "repeated"

  • Result: Checking Foreign calls ... OK

R CMD check results 1 error | 4 warnings | 2 notes

I also transferred the dist.c and the romberg.c from rmutil/src to repeated/src (judging by dates, I somehow edited dist.c to make rmutil work).

[swihart]

• Problem: NOTE:NB: .First.lib is obsolete and will not be used in R >= 3.0.0

• Solution:
  step 1: comment out .First.lib line(s) in kalseries.R:

  # .First.lib <- function(lib, pkg)
  #   library.dynam("repeated", pkg, lib)
  # require(rmutil)

  step 2: add LazyLoad: true in DESCRIPTION (previously completed)

  step 3: (didn't do this to later, cycling back to put here now): Add ##' @useDynLib repeated to line 159 of gnlmix.R then do a devtools::document() to update NAMESPACE.

• Result: That particular line of note eliminated; but more lines still remain and thus note persists.

[swihart]

• Problem:

kalcount : sh1: no visible binding for global variable ‘npl1’ kalseries : sh1: no visible binding for global variable ‘npl1’

• I hunted down where else npl1 is used and found it used in

> find ./R -type f -print0 | xargs -0 grep -l 'npl1'
./R/gnlmix.r
./R/gnlmm.r
./R/gnlmm3.r
./R/hnlmix.r
./R/kalcount.r
./R/kalseries.r

In gnlmix.r, line 360 has it defined:

npl1 <- if(common&&!inherits(shape,"formula")) 1 else nlp+1

In gnlmm.r, line 487:

npl1 <- if(common&&!inherits(lin2,"formula")) 1 else nlp+2

In gnlmm3.r, line 552:

npl1 <- if(common&&!inherits(lin2,"formula")) 1 else nlp+2

In hnlmix.r, line 352:

npl1 <- if(common&&!inherits(shape,"formula")) 1 else nlp+1

As one can see, they are all not the same. I'm not sure what npl1 is supposed to be in kalcount and kalseries. It appears the assignment is nlp+2 if there is a lin2 argument and nlp+1 if there is a shape argument. Since kalcount and kalseries have only shape, we will go with

In kalcount.r, line 509 and kalseries.r, line 596:

common <- FALSE
npl1 <- if(common&&!inherits(shape,"formula")) 1 else nlp+1

which means npl1 will always be nlp+1.

[swihart]

Did the following to line 273 of glmm.R to fix the print.glm complaint.

print.glm(z,...)

class(z) <- "glm" print(z)

• Results: R CMD check results 1 error | 4 warnings | 1 note

[swihart]

You know you are resurrecting an out-dated package when:

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

Solution: http://tolstoy.newcastle.edu.au/R/e17/help/12/03/6200.html

Change \code{\link[nls]{nls}} to \code{\link[stats]{nls}} in

./R/glmm.r
./R/gnlmix.r
./R/gnlmm.r
./R/gnlmm3.r
./R/hnlmix.r

[swihart]

• Complaint: Xrefs in Rd for growth and event

• Solution:

  install.packages("http://www.commanster.eu/rcode/event.tgz", repos=NULL, type="source")
  install.packages("http://www.commanster.eu/rcode/growth.tgz", repos=NULL, type="source")

  This may bite me later when tested in the wild where growth and event aren't (yet)

[swihart]

Add ##' @useDynLib repeated to line 159 of gnlmix.R then do a devtools::document() to update NAMESPACE.

( I wish I figured this out before doing the \dontrun to every example due to .C and .Fortran not available complaints!)

[swihart]

Fixed usage/argument complaints straightforwardly.

[swihart]

Still had warnings from compiling. I would delete all the .o and .so files in src and then re-run devtools::document() to get the specific complaints in the R console of Rstudio.

When I did that, I marched through making edits to .f and .c files.

1. delete space between 1 and D and replaced with 1 space on line 1913 of binnest.f
2. delete all of dEval3 line 234 in calcs3.c

and then hidden.f had a bunch; see next comment.

[swihart]

After adding some "C" to .f files that contained print or write and eliminating unused variables from some .c files, I'm left with this:

R CMD check results 0 errors | 1 warning | 0 notes

R CMD check succeeded

The biggest culprit right now is hidden.f and the svec integer/real debate, as well as nobs being over-imported.

I'm not sure how to solve these...I've tried a couple of things but the rabbit hole got real rabbity holey real-quick.

UPDATE: just put int(svec) where complaints UPDATE2: and when a line goes over 130 characters, which it did on line 541 of hidden.f when you put int(svec) in, just break it up likes this:

            pi=1/(1.+dexp(-mu(nm,j,int(svec+1))))
     +           -1/(1.+dexp(-mu(nm,j,int(svec))))

source: http://stackoverflow.com/a/20585942/2727349

I have corrected all the following:

hidden.f:412.17:

      do 1 j = 1, svec                                                  
                 1
Warning: Deleted feature: End expression in DO loop at (1) must be integer
hidden.f:435.29:

            multpr = mu(nm,j,svec)-dlog(denom)                          
                             1
Warning: Legacy Extension: REAL array index at (1)
hidden.f:444.44:

            multpr = cmu(i,j,svec)+tvmu(k,j,svec)-dlog(denom)           
                                            1
Warning: Legacy Extension: REAL array index at (1)
hidden.f:444.29:

            multpr = cmu(i,j,svec)+tvmu(k,j,svec)-dlog(denom)           
                             1
Warning: Legacy Extension: REAL array index at (1)
hidden.f:497.35:

            pi=1./(1.+dexp(mu(nm,j,svec)))                              
                                   1
Warning: Legacy Extension: REAL array index at (1)
hidden.f:499.16:

         do 2 n=svec+1,l                                                
                1
Warning: Deleted feature: Start expression in DO loop at (1) must be integer
hidden.f:506.50:

            pi=1./(1.+dexp(cmu(i,j,svec)+tvmu(k,j,svec)))               
                                                  1
Warning: Legacy Extension: REAL array index at (1)
hidden.f:506.35:

            pi=1./(1.+dexp(cmu(i,j,svec)+tvmu(k,j,svec)))               
                                   1
Warning: Legacy Extension: REAL array index at (1)
hidden.f:508.16:

         do 4 n=svec+1,l                                                
                1
Warning: Deleted feature: Start expression in DO loop at (1) must be integer
hidden.f:534.65:

            pi=1/(1.+dexp(-mu(nm,j,svec+1)))-1/(1.+dexp(-mu(nm,j,svec)))
                                                                 1
Warning: Legacy Extension: REAL array index at (1)
hidden.f:534.35:

            pi=1/(1.+dexp(-mu(nm,j,svec+1)))-1/(1.+dexp(-mu(nm,j,svec)))
                                   1
Warning: Legacy Extension: REAL array index at (1)
hidden.f:543.53:

     +           -1/(1.+dexp(-cmu(i,j,svec)-tvmu(k,j,svec)))            
                                                     1
Warning: Legacy Extension: REAL array index at (1)
hidden.f:543.38:

     +           -1/(1.+dexp(-cmu(i,j,svec)-tvmu(k,j,svec)))            
                                      1
Warning: Legacy Extension: REAL array index at (1)
hidden.f:542.52:

            pi=1/(1.+dexp(-cmu(i,j,svec+1)-tvmu(k,j,svec+1)))           
                                                    1
Warning: Legacy Extension: REAL array index at (1)
hidden.f:542.35:

            pi=1/(1.+dexp(-cmu(i,j,svec+1)-tvmu(k,j,svec+1)))           
                                   1
Warning: Legacy Extension: REAL array index at (1)
hidden.f:575.26:

               do 1 j = 1, svec                                         
                          1
Warning: Deleted feature: End expression in DO loop at (1) must be integer
hidden.f:580.26:

               do 2 j = 1, nvec-svec                                    
                          1
Warning: Deleted feature: End expression in DO loop at (1) must be integer
hidden.f:629.20:

         do 1 j = 1, svec                                               
                    1
Warning: Deleted feature: End expression in DO loop at (1) must be integer
hidden.f:634.20:

         do 2 j = 1, nvec-svec                                          
                    1
Warning: Deleted feature: End expression in DO loop at (1) must be integer

[swihart]

cool hack, but unnecessary just put int(svec) where complaints

line 412 in hidden.f

C      do 1 j = 1, svec
C         poispr = poispr+dlog(pvec/dble(j))
C 1    continue
C      return
C      end

      do 1 j = 1, 999999999
         if(j > svec) exit
         poispr = poispr+dlog(pvec/dble(j))
 1    continue
      return
      end

source:
https://en.wikibooks.org/wiki/Fortran/Fortran_control http://stackoverflow.com/a/30708142/2727349

[swihart]

R CMD check results 0 errors | 0 warnings | 0 notes