CRAN Package Check Results for Package orthoDr

Last updated on 2019-09-04 06:50:03 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	0.6.2				ERROR
r-devel-linux-x86_64-debian-gcc	0.6.2	190.87	56.58	247.45	ERROR
r-devel-linux-x86_64-fedora-clang	0.6.2			463.44	ERROR
r-devel-linux-x86_64-fedora-gcc	0.6.2			434.60	ERROR
r-devel-windows-ix86+x86_64	0.6.2	620.00	135.00	755.00	NOTE
r-patched-linux-x86_64	0.6.2	189.32	70.86	260.18	ERROR
r-patched-solaris-x86	0.6.2			28.90	ERROR
r-release-linux-x86_64	0.6.2	202.37	69.84	272.21	ERROR
r-release-windows-ix86+x86_64	0.6.2	552.00	171.00	723.00	NOTE
r-release-osx-x86_64	0.6.2				ERROR
r-oldrel-windows-ix86+x86_64	0.6.2	433.00	185.00	618.00	NOTE
r-oldrel-osx-x86_64	0.6.2				ERROR

Additional issues

valgrind

Check Details

Version: 0.6.2
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.6.2
Check: examples
Result: ERROR
    Running examples in 'orthoDr-Ex.R' failed
    The error most likely occurred in:

    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: predict.orthoDr
    > ### Title: predict.orthoDr
    > ### Aliases: predict.orthoDr
    >
    > ### ** Examples
    >
    > # generate some survival data
    > N = 100; P = 4; dataX = matrix(rnorm(N*P), N, P)
    > Y = exp(-1 + dataX[,1] + rnorm(N))
    > Censor = rbinom(N, 1, 0.8)
    >
    > # fit the model with keep.data = TRUE
    > orthoDr.fit = orthoDr_surv(dataX, Y, Censor, ndr = 1,
    + method = "dm", keep.data = TRUE)
    >
    > #predict 10 new observations
    > predict(orthoDr.fit, matrix(rnorm(10*P), 10, P))
    Prediction for orthoDr Survival: 10 testing subjects at 79 time points
    See 'surv' and 'timepoints'.>
    > # generate some personalized dose scenario
    >
    > exampleset <- function(size,ncov){
    +
    + X = matrix(runif(size*ncov,-1,1),ncol=ncov)
    + A = runif(size,0,2)
    +
    + Edr = as.matrix(c(0.5,-0.5))
    +
    + D_opt = X %*% Edr + 1
    +
    + mu = 2 + 0.5*(X %*% Edr) - 7*abs(D_opt-A)
    +
    + R = rnorm(length(mu),mu,1)
    +
    + R = R - min(R)
    +
    + datainfo = list(X=X,A=A,R=R,D_opt=D_opt,mu=mu)
    + return(datainfo)
    + }
    >
    > # generate data
    >
    > set.seed(123)
    > n = 150
    > p = 2
    > ndr =1
    > train = exampleset(n,p)
    > test = exampleset(500,p)
    >
    > # the direct learning method
    > orthofit = orthoDr_pdose(train$X, train$A, train$R, ndr = ndr, lambda = 0.1,
    + method = "direct", K = sqrt(n), keep.data = TRUE,
    + maxitr = 150, verbose = FALSE)

    error: Mat::elem(): index out of bounds
    Error in pdose_direct_solver(B.initial, X, a, A.dist, cdose, r, lambda, :
     Mat::elem(): index out of bounds
    Calls: orthoDr_pdose -> pdose_direct_solver
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.6.2
Check: examples
Result: ERROR
    Running examples in ‘orthoDr-Ex.R’ failed
    The error most likely occurred in:

    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: orthoDr_pdose
    > ### Title: orthoDr_pdose model
    > ### Aliases: orthoDr_pdose
    >
    > ### ** Examples
    >
    > # generate some personalized dose scenario
    >
    > exampleset <- function(size,ncov){
    +
    + X = matrix(runif(size*ncov,-1,1),ncol=ncov)
    + A = runif(size,0,2)
    +
    + Edr = as.matrix(c(0.5,-0.5))
    +
    + D_opt = X %*% Edr +1
    +
    + mu = 2 + 0.5*(X %*% Edr) - 7*abs(D_opt-A)
    +
    + R = rnorm(length(mu),mu,1)
    +
    + R = R - min(R)
    +
    + datainfo = list(X=X,A=A,R=R,D_opt=D_opt,mu=mu)
    + return(datainfo)
    + }
    >
    > # generate data
    >
    > set.seed(123)
    > n = 150
    > p = 2
    > ndr =1
    > train = exampleset(n,p)
    > test = exampleset(500,p)
    >
    > # the direct learning method
    > orthofit = orthoDr_pdose(train$X,train$A,train$R,ndr = ndr,lambda = 0.1,
    + method = "direct", K = sqrt(n),keep.data = TRUE,
    + maxitr = 150,verbose = FALSE)

    error: Mat::elem(): index out of bounds
    Error in pdose_direct_solver(B.initial, X, a, A.dist, cdose, r, lambda, :
     Mat::elem(): index out of bounds
    Calls: orthoDr_pdose -> pdose_direct_solver
    Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.6.2
Check: installed package size
Result: NOTE
     installed size is 16.5Mb
     sub-directories of 1Mb or more:
     libs 16.2Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.6.2
Check: examples
Result: ERROR
    Running examples in ‘orthoDr-Ex.R’ failed
    The error most likely occurred in:

    > ### Name: orthoDr_pdose
    > ### Title: orthoDr_pdose model
    > ### Aliases: orthoDr_pdose
    >
    > ### ** Examples
    >
    > # generate some personalized dose scenario
    >
    > exampleset <- function(size,ncov){
    +
    + X = matrix(runif(size*ncov,-1,1),ncol=ncov)
    + A = runif(size,0,2)
    +
    + Edr = as.matrix(c(0.5,-0.5))
    +
    + D_opt = X %*% Edr +1
    +
    + mu = 2 + 0.5*(X %*% Edr) - 7*abs(D_opt-A)
    +
    + R = rnorm(length(mu),mu,1)
    +
    + R = R - min(R)
    +
    + datainfo = list(X=X,A=A,R=R,D_opt=D_opt,mu=mu)
    + return(datainfo)
    + }
    >
    > # generate data
    >
    > set.seed(123)
    > n = 150
    > p = 2
    > ndr =1
    > train = exampleset(n,p)
    > test = exampleset(500,p)
    >
    > # the direct learning method
    > orthofit = orthoDr_pdose(train$X,train$A,train$R,ndr = ndr,lambda = 0.1,
    + method = "direct", K = sqrt(n),keep.data = TRUE,
    + maxitr = 150,verbose = FALSE)
    OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
    OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).

    error: Mat::elem(): index out of bounds
    Error in pdose_direct_solver(B.initial, X, a, A.dist, cdose, r, lambda, :
     Mat::elem(): index out of bounds
    Calls: orthoDr_pdose -> pdose_direct_solver
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.6.2
Check: examples
Result: ERROR
    Running examples in ‘orthoDr-Ex.R’ failed
    The error most likely occurred in:

    > ### Name: orthoDr_pdose
    > ### Title: orthoDr_pdose model
    > ### Aliases: orthoDr_pdose
    >
    > ### ** Examples
    >
    > # generate some personalized dose scenario
    >
    > exampleset <- function(size,ncov){
    +
    + X = matrix(runif(size*ncov,-1,1),ncol=ncov)
    + A = runif(size,0,2)
    +
    + Edr = as.matrix(c(0.5,-0.5))
    +
    + D_opt = X %*% Edr +1
    +
    + mu = 2 + 0.5*(X %*% Edr) - 7*abs(D_opt-A)
    +
    + R = rnorm(length(mu),mu,1)
    +
    + R = R - min(R)
    +
    + datainfo = list(X=X,A=A,R=R,D_opt=D_opt,mu=mu)
    + return(datainfo)
    + }
    >
    > # generate data
    >
    > set.seed(123)
    > n = 150
    > p = 2
    > ndr =1
    > train = exampleset(n,p)
    > test = exampleset(500,p)
    >
    > # the direct learning method
    > orthofit = orthoDr_pdose(train$X,train$A,train$R,ndr = ndr,lambda = 0.1,
    + method = "direct", K = sqrt(n),keep.data = TRUE,
    + maxitr = 150,verbose = FALSE)

    error: Mat::elem(): index out of bounds
    Error in pdose_direct_solver(B.initial, X, a, A.dist, cdose, r, lambda, :
     Mat::elem(): index out of bounds
    Calls: orthoDr_pdose -> pdose_direct_solver
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-gcc, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.6.2
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavor: r-patched-solaris-x86

Version: 0.6.2
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.6.2
Check: dependencies in R code
Result: NOTE
No protocol specified
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.6.2
Check: S3 generic/method consistency
Result: WARN
    No protocol specified
    See section ‘Generic functions and methods’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.6.2
Check: replacement functions
Result: WARN
    No protocol specified
    The argument of a replacement function which corresponds to the right
    hand side must be named ‘value’.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.6.2
Check: foreign function calls
Result: NOTE
    No protocol specified
    See chapter ‘System and foreign language interfaces’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.6.2
Check: R code for possible problems
Result: NOTE
No protocol specified
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.6.2
Check: for missing documentation entries
Result: WARN
    No protocol specified
    All user-level objects in a package should have documentation entries.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.6.2
Check: for code/documentation mismatches
Result: WARN
    No protocol specified
    No protocol specified
    No protocol specified
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.6.2
Check: Rd \usage sections
Result: NOTE
    No protocol specified
    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64