CRAN Package Check Results for Package TBSSurvival

Last updated on 2016-12-06 12:48:29.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2 2.88 52.20 55.08 WARN --no-tests
r-devel-linux-x86_64-debian-gcc 1.2 3.10 51.48 54.58 WARN --no-tests
r-devel-linux-x86_64-fedora-clang 1.2 1926.32 ERROR --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 1.2 1921.70 ERROR --no-stop-on-test-error
r-devel-macos-x86_64-clang 1.2 1896.92 ERROR --no-stop-on-test-error
r-devel-windows-ix86+x86_64 1.2 8.00 0.00 8.00 WARN
r-patched-linux-x86_64 1.2 2.30 43.95 46.25 NOTE --no-tests
r-patched-solaris-sparc 1.2 581.30 NOTE
r-patched-solaris-x86 1.2 125.90 NOTE
r-release-linux-x86_64 1.2 2.30 43.66 45.97 NOTE --no-tests
r-release-osx-x86_64-mavericks 1.2 NOTE
r-release-windows-ix86+x86_64 1.2 9.00 80.00 89.00 NOTE
r-oldrel-windows-ix86+x86_64 1.2 10.00 94.00 104.00 OK

Check Details

Version: 1.2
Flags: --no-tests
Check: R code for possible problems
Result: NOTE
    .dunif.exp: no visible global function definition for ‘dunif’
    .dunif.exp: no visible global function definition for ‘dexp’
    .logpost: no visible global function definition for ‘dnorm’
    .pt2: no visible global function definition for ‘pbeta’
    .qt2: no visible global function definition for ‘qbeta’
    .rlogis2: no visible global function definition for ‘runif’
    .rt2: no visible global function definition for ‘runif’
    .tbs.survreg: no visible global function definition for ‘model.frame’
    .tbs.survreg: no visible global function definition for ‘model.matrix’
    .tbs.survreg: no visible global function definition for
     ‘model.response’
    .tbs.survreg: no visible global function definition for ‘runif’
    .tbs.survreg: no visible global function definition for ‘optim’
    dist.error : <anonymous>: no visible global function definition for
     ‘dnorm’
    dist.error : <anonymous>: no visible global function definition for
     ‘pnorm’
    dist.error : <anonymous>: no visible global function definition for
     ‘qnorm’
    dist.error : <anonymous>: no visible global function definition for
     ‘rnorm’
    dist.error : <anonymous>: no visible global function definition for
     ‘dcauchy’
    dist.error : <anonymous>: no visible global function definition for
     ‘pcauchy’
    dist.error : <anonymous>: no visible global function definition for
     ‘qcauchy’
    dist.error : <anonymous>: no visible global function definition for
     ‘rcauchy’
    dist.error : <anonymous>: no visible global function definition for
     ‘dlogis’
    dist.error : <anonymous>: no visible global function definition for
     ‘plogis’
    dist.error : <anonymous>: no visible global function definition for
     ‘qlogis’
    dist.error : <anonymous>: no visible global function definition for
     ‘rlogis’
    lines.tbs.survreg.be: no visible global function definition for ‘lines’
    lines.tbs.survreg.be: no visible binding for global variable ‘quantile’
    lines.tbs.survreg.mle: no visible global function definition for
     ‘lines’
    plot.tbs.survreg.be: no visible global function definition for ‘plot’
    plot.tbs.survreg.be: no visible binding for global variable ‘quantile’
    plot.tbs.survreg.be: no visible global function definition for ‘lines’
    plot.tbs.survreg.be: no visible global function definition for ‘hist’
    plot.tbs.survreg.be: no visible global function definition for ‘par’
    plot.tbs.survreg.be: no visible global function definition for ‘acf’
    plot.tbs.survreg.be: no visible global function definition for ‘ts’
    plot.tbs.survreg.mle: no visible global function definition for ‘plot’
    plot.tbs.survreg.mle: no visible global function definition for ‘lines’
    plot.tbs.survreg.mle: no visible global function definition for ‘hist’
    plot.tbs.survreg.mle: no visible global function definition for
     ‘qqplot’
    plot.tbs.survreg.mle: no visible global function definition for
     ‘ppoints’
    plot.tbs.survreg.mle: no visible global function definition for
     ‘qqline’
    summary.tbs.survreg.mle: no visible global function definition for
     ‘pnorm’
    tbs.survreg.be: no visible global function definition for ‘model.frame’
    tbs.survreg.be: no visible global function definition for
     ‘model.matrix’
    tbs.survreg.be: no visible global function definition for
     ‘model.response’
    tbs.survreg.be: no visible global function definition for ‘sd’
    tbs.survreg.be: no visible binding for global variable ‘sd’
    Undefined global functions or variables:
     acf dcauchy dexp dlogis dnorm dunif hist lines model.frame
     model.matrix model.response optim par pbeta pcauchy plogis plot pnorm
     ppoints qbeta qcauchy qlogis qnorm qqline qqplot quantile rcauchy
     rlogis rnorm runif sd ts
    Consider adding
     importFrom("graphics", "hist", "lines", "par", "plot")
     importFrom("stats", "acf", "dcauchy", "dexp", "dlogis", "dnorm",
     "dunif", "model.frame", "model.matrix", "model.response",
     "optim", "pbeta", "pcauchy", "plogis", "pnorm", "ppoints",
     "qbeta", "qcauchy", "qlogis", "qnorm", "qqline", "qqplot",
     "quantile", "rcauchy", "rlogis", "rnorm", "runif", "sd",
     "ts")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.2
Flags: --no-tests
Check: for unstated dependencies in ‘tests’
Result: WARN
    'library' or 'require' calls not declared from:
     ‘R.methodsS3’ ‘R.oo’ ‘ipred’ ‘truncnorm’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.2
Flags: --no-stop-on-test-error
Check: R code for possible problems
Result: NOTE
    .dunif.exp: no visible global function definition for ‘dunif’
    .dunif.exp: no visible global function definition for ‘dexp’
    .logpost: no visible global function definition for ‘dnorm’
    .pt2: no visible global function definition for ‘pbeta’
    .qt2: no visible global function definition for ‘qbeta’
    .rlogis2: no visible global function definition for ‘runif’
    .rt2: no visible global function definition for ‘runif’
    .tbs.survreg: no visible global function definition for ‘model.frame’
    .tbs.survreg: no visible global function definition for ‘model.matrix’
    .tbs.survreg: no visible global function definition for
     ‘model.response’
    .tbs.survreg: no visible global function definition for ‘runif’
    .tbs.survreg: no visible global function definition for ‘optim’
    dist.error : <anonymous>: no visible global function definition for
     ‘dnorm’
    dist.error : <anonymous>: no visible global function definition for
     ‘pnorm’
    dist.error : <anonymous>: no visible global function definition for
     ‘qnorm’
    dist.error : <anonymous>: no visible global function definition for
     ‘rnorm’
    dist.error : <anonymous>: no visible global function definition for
     ‘dcauchy’
    dist.error : <anonymous>: no visible global function definition for
     ‘pcauchy’
    dist.error : <anonymous>: no visible global function definition for
     ‘qcauchy’
    dist.error : <anonymous>: no visible global function definition for
     ‘rcauchy’
    dist.error : <anonymous>: no visible global function definition for
     ‘dlogis’
    dist.error : <anonymous>: no visible global function definition for
     ‘plogis’
    dist.error : <anonymous>: no visible global function definition for
     ‘qlogis’
    dist.error : <anonymous>: no visible global function definition for
     ‘rlogis’
    lines.tbs.survreg.be: no visible global function definition for ‘lines’
    lines.tbs.survreg.be: no visible binding for global variable ‘quantile’
    lines.tbs.survreg.mle: no visible global function definition for
     ‘lines’
    plot.tbs.survreg.be: no visible global function definition for ‘plot’
    plot.tbs.survreg.be: no visible binding for global variable ‘quantile’
    plot.tbs.survreg.be: no visible global function definition for ‘lines’
    plot.tbs.survreg.be: no visible global function definition for ‘hist’
    plot.tbs.survreg.be: no visible global function definition for ‘par’
    plot.tbs.survreg.be: no visible global function definition for ‘acf’
    plot.tbs.survreg.be: no visible global function definition for ‘ts’
    plot.tbs.survreg.mle: no visible global function definition for ‘plot’
    plot.tbs.survreg.mle: no visible global function definition for ‘lines’
    plot.tbs.survreg.mle: no visible global function definition for ‘hist’
    plot.tbs.survreg.mle: no visible global function definition for
     ‘qqplot’
    plot.tbs.survreg.mle: no visible global function definition for
     ‘ppoints’
    plot.tbs.survreg.mle: no visible global function definition for
     ‘qqline’
    summary.tbs.survreg.mle: no visible global function definition for
     ‘pnorm’
    tbs.survreg.be: no visible global function definition for ‘model.frame’
    tbs.survreg.be: no visible global function definition for
     ‘model.matrix’
    tbs.survreg.be: no visible global function definition for
     ‘model.response’
    tbs.survreg.be: no visible global function definition for ‘sd’
    tbs.survreg.be: no visible binding for global variable ‘sd’
    Undefined global functions or variables:
     acf dcauchy dexp dlogis dnorm dunif hist lines model.frame
     model.matrix model.response optim par pbeta pcauchy plogis plot pnorm
     ppoints qbeta qcauchy qlogis qnorm qqline qqplot quantile rcauchy
     rlogis rnorm runif sd ts
    Consider adding
     importFrom("graphics", "hist", "lines", "par", "plot")
     importFrom("stats", "acf", "dcauchy", "dexp", "dlogis", "dnorm",
     "dunif", "model.frame", "model.matrix", "model.response",
     "optim", "pbeta", "pcauchy", "plogis", "pnorm", "ppoints",
     "qbeta", "qcauchy", "qlogis", "qnorm", "qqline", "qqplot",
     "quantile", "rcauchy", "rlogis", "rnorm", "runif", "sd",
     "ts")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 1.2
Flags: --no-stop-on-test-error
Check: for unstated dependencies in ‘tests’
Result: WARN
    'library' or 'require' calls not declared from:
     ‘R.methodsS3’ ‘R.oo’ ‘ipred’ ‘truncnorm’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 1.2
Flags: --no-stop-on-test-error
Check: tests
Result: ERROR
     Running ‘article.r’ [30m/39m]
     Running ‘loadlibs.r’
     Running ‘simple.r’
    Running the tests in ‘tests/article.r’ failed.
    Last 13 lines of output:
     Median time: 167.57
     > cat("95% c.i.: (",round(exp(tbs.mle$norm$beta+qnorm(0.025,0,1)*tbs.mle$norm$beta.se),2),", ",
     + round(exp(tbs.mle$norm$beta+qnorm(0.975,0,1)*tbs.mle$norm$beta.se),2),")\n",sep="")
     95% c.i.: (155.41, 180.68)
     >
     > ###########
     > ## Part of the Bayesian estimation
     > cat("\n"); cat("Bayesian Estimation:\n")
    
     Bayesian Estimation:
     >
     > ## Bayesian Estimation
     > ## We run for each of the five error functions
     > tbs.bayes.norm <- tbs.survreg.be(survival::Surv(alloyT7987$time,alloyT7987$delta) ~ 1,dist=dist.error("norm"),
     + burn=500000,jump=2000,size=1000,scale=0.07)
    Running the tests in ‘tests/loadlibs.r’ failed.
    Last 13 lines of output:
     +
     + } else {
     + library("TBSSurvival")
     + }
     + options("warn" = w[[1]])
     + }
     >
     > ## Load data
     > alloyT7987 <- read.table("../data/alloyT7987.txt",header=TRUE)
     Error in file(file, "rt") : cannot open the connection
     Calls: read.table -> file
     In addition: Warning message:
     In file(file, "rt") :
     cannot open file '../data/alloyT7987.txt': No such file or directory
     Execution halted
    Running the tests in ‘tests/simple.r’ failed.
    Last 13 lines of output:
     > # This program is distributed in the hope that it will be useful,
     > # but WITHOUT ANY WARRANTY; without even the implied warranty of
     > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
     > # GNU General Public License for more details.
     > #
     > # You should have received a copy of the GNU General Public License
     > # along with this program. If not, see <http://www.gnu.org/licenses/>.
     >
     > source("loadlibs.r")
     Error in file(file, "rt") : cannot open the connection
     Calls: source -> withVisible -> eval -> eval -> read.table -> file
     In addition: Warning message:
     In file(file, "rt") :
     cannot open file '../data/alloyT7987.txt': No such file or directory
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.2
Flags: --no-stop-on-test-error
Check: tests
Result: ERROR
     Running ‘article.r’ [30m/32m]
     Running ‘loadlibs.r’
     Running ‘simple.r’
    Running the tests in ‘tests/article.r’ failed.
    Last 13 lines of output:
     + round(exp(tbs.mle$norm$beta+qnorm(0.975,0,1)*tbs.mle$norm$beta.se),2),")\n",sep="")
     95% c.i.: (155.41, 180.68)
     >
     > ###########
     > ## Part of the Bayesian estimation
     > cat("\n"); cat("Bayesian Estimation:\n")
    
     Bayesian Estimation:
     >
     > ## Bayesian Estimation
     > ## We run for each of the five error functions
     > tbs.bayes.norm <- tbs.survreg.be(survival::Surv(alloyT7987$time,alloyT7987$delta) ~ 1,dist=dist.error("norm"),
     + burn=500000,jump=2000,size=1000,scale=0.07)
     > tbs.bayes.t <- tbs.survreg.be(survival::Surv(alloyT7987$time,alloyT7987$delta) ~ 1,dist=dist.error("t"),
     + burn=500000,jump=2000,size=1000,scale=0.07)
    Running the tests in ‘tests/loadlibs.r’ failed.
    Last 13 lines of output:
     +
     + } else {
     + library("TBSSurvival")
     + }
     + options("warn" = w[[1]])
     + }
     >
     > ## Load data
     > alloyT7987 <- read.table("../data/alloyT7987.txt",header=TRUE)
     Error in file(file, "rt") : cannot open the connection
     Calls: read.table -> file
     In addition: Warning message:
     In file(file, "rt") :
     cannot open file '../data/alloyT7987.txt': No such file or directory
     Execution halted
    Running the tests in ‘tests/simple.r’ failed.
    Last 13 lines of output:
     > # This program is distributed in the hope that it will be useful,
     > # but WITHOUT ANY WARRANTY; without even the implied warranty of
     > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
     > # GNU General Public License for more details.
     > #
     > # You should have received a copy of the GNU General Public License
     > # along with this program. If not, see <http://www.gnu.org/licenses/>.
     >
     > source("loadlibs.r")
     Error in file(file, "rt") : cannot open the connection
     Calls: source -> withVisible -> eval -> eval -> read.table -> file
     In addition: Warning message:
     In file(file, "rt") :
     cannot open file '../data/alloyT7987.txt': No such file or directory
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.2
Flags: --no-stop-on-test-error
Check: tests
Result: ERROR
     Running ‘article.r’ [30m/33m]
     Running ‘loadlibs.r’
     Running ‘simple.r’
    Running the tests in ‘tests/article.r’ failed.
    Last 13 lines of output:
     > ## Part of the Bayesian estimation
     > cat("\n"); cat("Bayesian Estimation:\n")
    
     Bayesian Estimation:
     >
     > ## Bayesian Estimation
     > ## We run for each of the five error functions
     > tbs.bayes.norm <- tbs.survreg.be(survival::Surv(alloyT7987$time,alloyT7987$delta) ~ 1,dist=dist.error("norm"),
     + burn=500000,jump=2000,size=1000,scale=0.07)
     > tbs.bayes.t <- tbs.survreg.be(survival::Surv(alloyT7987$time,alloyT7987$delta) ~ 1,dist=dist.error("t"),
     + burn=500000,jump=2000,size=1000,scale=0.07)
     > tbs.bayes.cauchy <- tbs.survreg.be(survival::Surv(alloyT7987$time,alloyT7987$delta) ~ 1,dist=dist.error("cauchy"),
     + burn=500000,jump=2000,size=1000,scale=0.07)
     > tbs.bayes.doubexp <- tbs.survreg.be(survival::Surv(alloyT7987$time,alloyT7987$delta) ~ 1,dist=dist.error("doubexp"),
     + burn=500000,jump=2000,size=1000,scale=0.07)
    Running the tests in ‘tests/loadlibs.r’ failed.
    Last 13 lines of output:
     +
     + } else {
     + library("TBSSurvival")
     + }
     + options("warn" = w[[1]])
     + }
     >
     > ## Load data
     > alloyT7987 <- read.table("../data/alloyT7987.txt",header=TRUE)
     Error in file(file, "rt") : cannot open the connection
     Calls: read.table -> file
     In addition: Warning message:
     In file(file, "rt") :
     cannot open file '../data/alloyT7987.txt': No such file or directory
     Execution halted
    Running the tests in ‘tests/simple.r’ failed.
    Last 13 lines of output:
     > # This program is distributed in the hope that it will be useful,
     > # but WITHOUT ANY WARRANTY; without even the implied warranty of
     > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
     > # GNU General Public License for more details.
     > #
     > # You should have received a copy of the GNU General Public License
     > # along with this program. If not, see <http://www.gnu.org/licenses/>.
     >
     > source("loadlibs.r")
     Error in file(file, "rt") : cannot open the connection
     Calls: source -> withVisible -> eval -> eval -> read.table -> file
     In addition: Warning message:
     In file(file, "rt") :
     cannot open file '../data/alloyT7987.txt': No such file or directory
     Execution halted
Flavor: r-devel-macos-x86_64-clang

Version: 1.2
Check: R code for possible problems
Result: NOTE
    .dunif.exp: no visible global function definition for 'dunif'
    .dunif.exp: no visible global function definition for 'dexp'
    .logpost: no visible global function definition for 'dnorm'
    .pt2: no visible global function definition for 'pbeta'
    .qt2: no visible global function definition for 'qbeta'
    .rlogis2: no visible global function definition for 'runif'
    .rt2: no visible global function definition for 'runif'
    .tbs.survreg: no visible global function definition for 'model.frame'
    .tbs.survreg: no visible global function definition for 'model.matrix'
    .tbs.survreg: no visible global function definition for
     'model.response'
    .tbs.survreg: no visible global function definition for 'runif'
    .tbs.survreg: no visible global function definition for 'optim'
    dist.error : <anonymous>: no visible global function definition for
     'dnorm'
    dist.error : <anonymous>: no visible global function definition for
     'pnorm'
    dist.error : <anonymous>: no visible global function definition for
     'qnorm'
    dist.error : <anonymous>: no visible global function definition for
     'rnorm'
    dist.error : <anonymous>: no visible global function definition for
     'dcauchy'
    dist.error : <anonymous>: no visible global function definition for
     'pcauchy'
    dist.error : <anonymous>: no visible global function definition for
     'qcauchy'
    dist.error : <anonymous>: no visible global function definition for
     'rcauchy'
    dist.error : <anonymous>: no visible global function definition for
     'dlogis'
    dist.error : <anonymous>: no visible global function definition for
     'plogis'
    dist.error : <anonymous>: no visible global function definition for
     'qlogis'
    dist.error : <anonymous>: no visible global function definition for
     'rlogis'
    lines.tbs.survreg.be: no visible global function definition for 'lines'
    lines.tbs.survreg.be: no visible binding for global variable 'quantile'
    lines.tbs.survreg.mle: no visible global function definition for
     'lines'
    plot.tbs.survreg.be: no visible global function definition for 'plot'
    plot.tbs.survreg.be: no visible binding for global variable 'quantile'
    plot.tbs.survreg.be: no visible global function definition for 'lines'
    plot.tbs.survreg.be: no visible global function definition for 'hist'
    plot.tbs.survreg.be: no visible global function definition for 'par'
    plot.tbs.survreg.be: no visible global function definition for 'acf'
    plot.tbs.survreg.be: no visible global function definition for 'ts'
    plot.tbs.survreg.mle: no visible global function definition for 'plot'
    plot.tbs.survreg.mle: no visible global function definition for 'lines'
    plot.tbs.survreg.mle: no visible global function definition for 'hist'
    plot.tbs.survreg.mle: no visible global function definition for
     'qqplot'
    plot.tbs.survreg.mle: no visible global function definition for
     'ppoints'
    plot.tbs.survreg.mle: no visible global function definition for
     'qqline'
    summary.tbs.survreg.mle: no visible global function definition for
     'pnorm'
    tbs.survreg.be: no visible global function definition for 'model.frame'
    tbs.survreg.be: no visible global function definition for
     'model.matrix'
    tbs.survreg.be: no visible global function definition for
     'model.response'
    tbs.survreg.be: no visible global function definition for 'sd'
    tbs.survreg.be: no visible binding for global variable 'sd'
    Undefined global functions or variables:
     acf dcauchy dexp dlogis dnorm dunif hist lines model.frame
     model.matrix model.response optim par pbeta pcauchy plogis plot pnorm
     ppoints qbeta qcauchy qlogis qnorm qqline qqplot quantile rcauchy
     rlogis rnorm runif sd ts
    Consider adding
     importFrom("graphics", "hist", "lines", "par", "plot")
     importFrom("stats", "acf", "dcauchy", "dexp", "dlogis", "dnorm",
     "dunif", "model.frame", "model.matrix", "model.response",
     "optim", "pbeta", "pcauchy", "plogis", "pnorm", "ppoints",
     "qbeta", "qcauchy", "qlogis", "qnorm", "qqline", "qqplot",
     "quantile", "rcauchy", "rlogis", "rnorm", "runif", "sd",
     "ts")
    to your NAMESPACE file.
Flavors: r-devel-windows-ix86+x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 1.2
Check: for unstated dependencies in ‘tests’
Result: WARN
    'library' or 'require' calls not declared from:
     'R.methodsS3' 'R.oo' 'ipred' 'truncnorm'
    Check process probably crashed or hung up for 20 minutes ... killed
    Most likely this happened in the example checks (?),
    if not, ignore the following last lines of example output:
    > formula <- survival::Surv(alloyT7987$time,alloyT7987$delta == 1) ~ 1
    > tbs.mle <- tbs.survreg.mle(formula,dist=dist.error("logistic"),method="Nelder-Mead",nstart=3)
    >
    > # Kaplan-Meier estimation
    > km <- survival::survfit(formula)
    >
    > # Plot survival function
    > plot(tbs.mle)
    > lines(km)
    >
    > # Plot hazard function
    > plot(tbs.mle, plot.type="hazard")
    >
    >
    >
    >
    > ### * <FOOTER>
    > ###
    > options(digits = 7L)
    > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
    Time elapsed: 8.3 0.13 8.47 NA NA
    > grDevices::dev.off()
    null device
     1
    > ###
    > ### Local variables: ***
    > ### mode: outline-minor ***
    > ### outline-regexp: "\\(> \\)?### [*]+" ***
    > ### End: ***
    > quit('no')
    ======== End of example output (where/before crash/hang up occured ?) ========
Flavor: r-devel-windows-ix86+x86_64