CRAN Package Check Results for Package pcalg

Last updated on 2015-07-03 23:47:44.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.2-2 44.67 116.70 161.37 ERROR
r-devel-linux-x86_64-debian-gcc 2.2-2 52.42 116.98 169.40 ERROR
r-devel-linux-x86_64-fedora-clang 2.2-2 336.03 ERROR
r-devel-linux-x86_64-fedora-gcc 2.2-2 317.46 ERROR
r-devel-osx-x86_64-clang 2.2-2 277.01 ERROR
r-devel-windows-ix86+x86_64 2.2-2 193.00 269.00 462.00 ERROR
r-patched-linux-x86_64 2.2-2 50.05 114.41 164.46 ERROR
r-patched-solaris-sparc 2.2-2 1972.60 ERROR
r-patched-solaris-x86 2.2-2 437.00 ERROR
r-release-linux-x86_64 2.2-2 51.60 115.51 167.11 ERROR
r-release-osx-x86_64-mavericks 2.2-2 ERROR
r-release-windows-ix86+x86_64 2.2-2 201.00 251.00 452.00 ERROR
r-oldrel-windows-ix86+x86_64 2.2-2 138.00 149.00 287.00 ERROR

Check Details

Version: 2.2-2
Check: installed package size
Result: NOTE
     installed size is 12.4Mb
     sub-directories of 1Mb or more:
     R 2.4Mb
     data 2.1Mb
     libs 5.9Mb
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-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.2-2
Check: R code for possible problems
Result: NOTE
    beta.special: no visible global function definition for ‘cov2cor’
    beta.special: no visible global function definition for ‘cov’
    beta.special: no visible global function definition for ‘combn’
    beta.special: no visible global function definition for ‘par’
    beta.special.pcObj: no visible global function definition for ‘combn’
    checkEdges: no visible global function definition for ‘combn’
    ci.test: no visible global function definition for ‘fisher.test’
    corGraph: no visible global function definition for ‘cor.test’
    dep.triple: no visible global function definition for ‘combn’
    erDAG: no visible global function definition for ‘rbinom’
    extract.parent.sets : all.locally.valid.parents.undir: no visible
     global function definition for ‘combn’
    findGamma: no visible global function definition for ‘uniroot’
    gSquareBin: no visible global function definition for ‘pchisq’
    gSquareDis: no visible global function definition for ‘pchisq’
    gaussCItest: no visible global function definition for ‘pnorm’
    geoDAG: no visible binding for global variable ‘runif’
    geoDAG: no visible global function definition for ‘runif’
    ida: no visible global function definition for ‘combn’
    idaFast: no visible global function definition for ‘combn’
    mcor: no visible global function definition for ‘cov2cor’
    mcor: no visible global function definition for ‘cor’
    pcAlgo: no visible global function definition for ‘qnorm’
    pcAlgo: no visible global function definition for ‘symnum’
    pcAlgo.Perfect: no visible global function definition for ‘symnum’
    pcSelect: no visible global function definition for ‘qnorm’
    pdsep: no visible global function definition for ‘combn’
    plotSG: no visible global function definition for ‘title’
    prune: no visible global function definition for ‘sd’
    r.gauss.pardag: no visible global function definition for ‘runif’
    r.gauss.pardag: no visible global function definition for ‘rbinom’
    randDAG: no visible binding for global variable ‘runif’
    randomDAG: no visible global function definition for ‘rbinom’
    randomDAG: no visible global function definition for ‘runif’
    rmvDAG : eMat: no visible global function definition for ‘rnorm’
    rmvDAG: no visible global function definition for ‘rnorm’
    rmvDAG: no visible global function definition for ‘rcauchy’
    rmvDAG: no visible global function definition for ‘rt’
    rmvnorm.ivent: no visible global function definition for ‘rnorm’
    sampleQ: no visible global function definition for ‘rbinom’
    sampleZ2: no visible global function definition for ‘rbinom’
    udag2apag: no visible global function definition for ‘combn’
    udag2pag: no visible global function definition for ‘combn’
    udag2pdagRelaxed : rule3: no visible global function definition for
     ‘combn’
    undirunweight.to.dirweight: no visible binding for global variable
     ‘runif’
    unifDAG: no visible binding for global variable ‘runif’
    unifDAG.approx: no visible binding for global variable ‘runif’
    Undefined global functions or variables:
     combn cor cor.test cov cov2cor fisher.test par pchisq pnorm qnorm
     rbinom rcauchy rnorm rt runif sd symnum title uniroot
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 2.2-2
Check: examples
Result: ERROR
    Running examples in ‘pcalg-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: jointIda
    > ### Title: Estimate Multiset of Possible Total Joint Effects
    > ### Aliases: jointIda
    > ### Keywords: multivariate models graphs
    >
    > ### ** Examples
    >
    > ## Create a weighted DAG
    > p <- 6
    > V<-as.character(1:p)
    > edL <- vector("list",length=6)
    > names(edL)<-V
    > edL[[1]] <- list(edges=c(3,4),weights=c(1.1,0.3))
    > edL[[2]] <- list(edges=c(6),weights=c(0.4))
    > edL[[3]] <- list(edges=c(2,4,6),weights=c(0.6,0.8,0.9))
    > edL[[4]] <- list(edges=c(2),weights=c(0.5))
    > edL[[5]] <- list(edges=c(1,4),weights=c(0.2,0.7))
    > myDAG <- new("graphNEL",nodes=V,edgeL=edL,edgemode="directed") ## true DAG
    > myCPDAG <- dag2cpdag(myDAG) ## true CPDAG
    > covTrue <- trueCov(myDAG) ## true covariance matrix
    >
    > ## simulate Gaussian data from the true DAG
    > set.seed(123)
    > if (require(mvtnorm)) {
    + n <- 1000
    + dat <- rmvnorm(n,mean=rep(0,p),sigma=covTrue)
    + }
    Loading required package: mvtnorm
    >
    > ## estimate CPDAG -- see help(pc)
    > suffStat <- list(C = cor(dat), n = n)
    > pc.fit <- pc(suffStat, indepTest = gaussCItest, p = p, alpha = 0.01 ,u2pd="relaxed")
    >
    > if (require(Rgraphviz)) {
    + ## plot the true and estimated graphs
    + par(mfrow = c(1,2))
    + plot(myDAG, main = "True DAG")
    + plot(pc.fit, main = "Estimated CPDAG")
    + }
    Loading required package: Rgraphviz
    Loading required package: graph
    Loading required package: grid
    >
    > ## Suppose that we know the true CPDAG and covariance matrix
    > jointIda(x.pos=c(1,2),y.pos=6,covTrue,graphEst=myCPDAG,technique="RRC")
    Error in parse_op_args(..., what = "a vertex", is_fun = is_igraph_vs, :
     Not a vertex sequence
    Calls: jointIda ... c -> c.igraph.vs -> parse_vs_op_args -> parse_op_args
    Execution halted
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-osx-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks

Version: 2.2-2
Check: tests
Result: ERROR
    Running the tests in ‘tests/test_jointIda.R’ failed.
    Last 13 lines of output:
     >
     > ## estimate CPDAG -- see help(pc)
     > suffStat <- list(C = cor(dat), n = n)
     > pc.fit <- pc(suffStat, indepTest = gaussCItest, p = p, alpha = 0.01 ,u2pd="relaxed")
     >
     > Rnd <- 7
     > ## Suppose that we know the true CPDAG and covariance matrix
     > mTrue <- matrix(c(0.99, 0.4, 0.99, 0.4, 0, 0.4), 2,3)
     > m1 <- round(jointIda(x.pos=c(1,2),y.pos=6,covTrue,graphEst=myCPDAG,technique="RRC"), Rnd)
     Error in parse_op_args(..., what = "a vertex", is_fun = is_igraph_vs, :
     Not a vertex sequence
     Calls: jointIda ... c -> c.igraph.vs -> parse_vs_op_args -> parse_op_args
     Execution halted
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-osx-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks

Version: 2.2-2
Check: R code for possible problems
Result: NOTE
    beta.special: no visible global function definition for ‘cov2cor’
    beta.special: no visible global function definition for ‘cov’
    beta.special: no visible global function definition for ‘combn’
    beta.special: no visible global function definition for ‘par’
    beta.special.pcObj: no visible global function definition for ‘combn’
    checkEdges: no visible global function definition for ‘combn’
    ci.test: no visible global function definition for ‘fisher.test’
    corGraph: no visible global function definition for ‘cor.test’
    dep.triple: no visible global function definition for ‘combn’
    erDAG: no visible global function definition for ‘rbinom’
    extract.parent.sets : all.locally.valid.parents.undir: no visible
     global function definition for ‘combn’
    findGamma: no visible global function definition for ‘uniroot’
    gSquareBin: no visible global function definition for ‘pchisq’
    gSquareDis: no visible global function definition for ‘pchisq’
    gaussCItest: no visible global function definition for ‘pnorm’
    geoDAG: no visible binding for global variable ‘runif’
    geoDAG: no visible global function definition for ‘runif’
    ida: no visible global function definition for ‘combn’
    idaFast: no visible global function definition for ‘combn’
    mcor: no visible global function definition for ‘cov2cor’
    mcor: no visible global function definition for ‘cor’
    pcAlgo: no visible global function definition for ‘qnorm’
    pcAlgo: no visible global function definition for ‘symnum’
    pcAlgo.Perfect: no visible global function definition for ‘symnum’
    pcSelect: no visible global function definition for ‘qnorm’
    pdsep: no visible global function definition for ‘combn’
    plotSG: no visible global function definition for ‘title’
    prune: no visible global function definition for ‘sd’
    r.gauss.pardag: no visible global function definition for ‘runif’
    r.gauss.pardag: no visible global function definition for ‘rbinom’
    randDAG: no visible binding for global variable ‘runif’
    randomDAG: no visible global function definition for ‘rbinom’
    randomDAG: no visible global function definition for ‘runif’
    rmvDAG : eMat: no visible global function definition for ‘rnorm’
    rmvDAG: no visible global function definition for ‘rnorm’
    rmvDAG: no visible global function definition for ‘rcauchy’
    rmvDAG: no visible global function definition for ‘rt’
    rmvnorm.ivent: no visible global function definition for ‘rnorm’
    sampleQ: no visible global function definition for ‘rbinom’
    sampleZ2: no visible global function definition for ‘rbinom’
    udag2apag: no visible global function definition for ‘combn’
    udag2pag: no visible global function definition for ‘combn’
    udag2pdagRelaxed : rule3: no visible global function definition for
     ‘combn’
    undirunweight.to.dirweight: no visible binding for global variable
     ‘runif’
    unifDAG: no visible binding for global variable ‘runif’
    unifDAG.approx: no visible binding for global variable ‘runif’
    plot,pcAlgo-ANY: no visible global function definition for ‘agopen’
    Undefined global functions or variables:
     agopen combn cor cor.test cov cov2cor fisher.test par pchisq pnorm
     qnorm rbinom rcauchy rnorm rt runif sd symnum title uniroot
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64

Version: 2.2-2
Check: running examples for arch ‘i386’
Result: ERROR
    Running examples in 'pcalg-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: jointIda
    > ### Title: Estimate Multiset of Possible Total Joint Effects
    > ### Aliases: jointIda
    > ### Keywords: multivariate models graphs
    >
    > ### ** Examples
    >
    > ## Create a weighted DAG
    > p <- 6
    > V<-as.character(1:p)
    > edL <- vector("list",length=6)
    > names(edL)<-V
    > edL[[1]] <- list(edges=c(3,4),weights=c(1.1,0.3))
    > edL[[2]] <- list(edges=c(6),weights=c(0.4))
    > edL[[3]] <- list(edges=c(2,4,6),weights=c(0.6,0.8,0.9))
    > edL[[4]] <- list(edges=c(2),weights=c(0.5))
    > edL[[5]] <- list(edges=c(1,4),weights=c(0.2,0.7))
    > myDAG <- new("graphNEL",nodes=V,edgeL=edL,edgemode="directed") ## true DAG
    > myCPDAG <- dag2cpdag(myDAG) ## true CPDAG
    > covTrue <- trueCov(myDAG) ## true covariance matrix
    >
    > ## simulate Gaussian data from the true DAG
    > set.seed(123)
    > if (require(mvtnorm)) {
    + n <- 1000
    + dat <- rmvnorm(n,mean=rep(0,p),sigma=covTrue)
    + }
    Loading required package: mvtnorm
    >
    > ## estimate CPDAG -- see help(pc)
    > suffStat <- list(C = cor(dat), n = n)
    > pc.fit <- pc(suffStat, indepTest = gaussCItest, p = p, alpha = 0.01 ,u2pd="relaxed")
    >
    > if (require(Rgraphviz)) {
    + ## plot the true and estimated graphs
    + par(mfrow = c(1,2))
    + plot(myDAG, main = "True DAG")
    + plot(pc.fit, main = "Estimated CPDAG")
    + }
    Loading required package: Rgraphviz
    Loading required package: graph
    Loading required package: grid
    >
    > ## Suppose that we know the true CPDAG and covariance matrix
    > jointIda(x.pos=c(1,2),y.pos=6,covTrue,graphEst=myCPDAG,technique="RRC")
    Error in parse_op_args(..., what = "a vertex", is_fun = is_igraph_vs, :
     Not a vertex sequence
    Calls: jointIda ... c -> c.igraph.vs -> parse_vs_op_args -> parse_op_args
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.2-2
Check: running examples for arch ‘x64’
Result: ERROR
    Running examples in 'pcalg-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: jointIda
    > ### Title: Estimate Multiset of Possible Total Joint Effects
    > ### Aliases: jointIda
    > ### Keywords: multivariate models graphs
    >
    > ### ** Examples
    >
    > ## Create a weighted DAG
    > p <- 6
    > V<-as.character(1:p)
    > edL <- vector("list",length=6)
    > names(edL)<-V
    > edL[[1]] <- list(edges=c(3,4),weights=c(1.1,0.3))
    > edL[[2]] <- list(edges=c(6),weights=c(0.4))
    > edL[[3]] <- list(edges=c(2,4,6),weights=c(0.6,0.8,0.9))
    > edL[[4]] <- list(edges=c(2),weights=c(0.5))
    > edL[[5]] <- list(edges=c(1,4),weights=c(0.2,0.7))
    > myDAG <- new("graphNEL",nodes=V,edgeL=edL,edgemode="directed") ## true DAG
    > myCPDAG <- dag2cpdag(myDAG) ## true CPDAG
    > covTrue <- trueCov(myDAG) ## true covariance matrix
    >
    > ## simulate Gaussian data from the true DAG
    > set.seed(123)
    > if (require(mvtnorm)) {
    + n <- 1000
    + dat <- rmvnorm(n,mean=rep(0,p),sigma=covTrue)
    + }
    Loading required package: mvtnorm
    >
    > ## estimate CPDAG -- see help(pc)
    > suffStat <- list(C = cor(dat), n = n)
    > pc.fit <- pc(suffStat, indepTest = gaussCItest, p = p, alpha = 0.01 ,u2pd="relaxed")
    >
    > if (require(Rgraphviz)) {
    + ## plot the true and estimated graphs
    + par(mfrow = c(1,2))
    + plot(myDAG, main = "True DAG")
    + plot(pc.fit, main = "Estimated CPDAG")
    + }
    Loading required package: Rgraphviz
    Loading required package: graph
    Loading required package: grid
    >
    > ## Suppose that we know the true CPDAG and covariance matrix
    > jointIda(x.pos=c(1,2),y.pos=6,covTrue,graphEst=myCPDAG,technique="RRC")
    Error in parse_op_args(..., what = "a vertex", is_fun = is_igraph_vs, :
     Not a vertex sequence
    Calls: jointIda ... c -> c.igraph.vs -> parse_vs_op_args -> parse_op_args
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.2-2
Check: running tests for arch ‘i386’
Result: ERROR
    Running the tests in 'tests/test_jointIda.R' failed.
    Last 13 lines of output:
     >
     > ## estimate CPDAG -- see help(pc)
     > suffStat <- list(C = cor(dat), n = n)
     > pc.fit <- pc(suffStat, indepTest = gaussCItest, p = p, alpha = 0.01 ,u2pd="relaxed")
     >
     > Rnd <- 7
     > ## Suppose that we know the true CPDAG and covariance matrix
     > mTrue <- matrix(c(0.99, 0.4, 0.99, 0.4, 0, 0.4), 2,3)
     > m1 <- round(jointIda(x.pos=c(1,2),y.pos=6,covTrue,graphEst=myCPDAG,technique="RRC"), Rnd)
     Error in parse_op_args(..., what = "a vertex", is_fun = is_igraph_vs, :
     Not a vertex sequence
     Calls: jointIda ... c -> c.igraph.vs -> parse_vs_op_args -> parse_op_args
     Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64

Version: 2.2-2
Check: running tests for arch ‘x64’
Result: ERROR
    Running the tests in 'tests/test_jointIda.R' failed.
    Last 13 lines of output:
     >
     > ## estimate CPDAG -- see help(pc)
     > suffStat <- list(C = cor(dat), n = n)
     > pc.fit <- pc(suffStat, indepTest = gaussCItest, p = p, alpha = 0.01 ,u2pd="relaxed")
     >
     > Rnd <- 7
     > ## Suppose that we know the true CPDAG and covariance matrix
     > mTrue <- matrix(c(0.99, 0.4, 0.99, 0.4, 0, 0.4), 2,3)
     > m1 <- round(jointIda(x.pos=c(1,2),y.pos=6,covTrue,graphEst=myCPDAG,technique="RRC"), Rnd)
     Error in parse_op_args(..., what = "a vertex", is_fun = is_igraph_vs, :
     Not a vertex sequence
     Calls: jointIda ... c -> c.igraph.vs -> parse_vs_op_args -> parse_op_args
     Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64