CRAN Package Check Results for Package haplo.stats

Last updated on 2020-08-03 05:48:49 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.7.9 19.08 172.66 191.74 ERROR
r-devel-linux-x86_64-debian-gcc 1.7.9 15.96 137.90 153.86 ERROR
r-devel-linux-x86_64-fedora-clang 1.7.9 239.20 ERROR
r-devel-linux-x86_64-fedora-gcc 1.7.9 231.21 ERROR
r-devel-windows-ix86+x86_64 1.7.9 61.00 256.00 317.00 ERROR
r-patched-linux-x86_64 1.7.9 17.40 219.68 237.08 OK
r-patched-solaris-x86 1.7.9 551.00 OK
r-release-linux-x86_64 1.7.9 18.98 218.63 237.61 OK
r-release-macos-x86_64 1.7.9 OK
r-release-windows-ix86+x86_64 1.7.9 68.00 478.00 546.00 OK
r-oldrel-macos-x86_64 1.7.9 OK
r-oldrel-windows-ix86+x86_64 1.7.9 38.00 440.00 478.00 OK

Check Details

Version: 1.7.9
Check: examples
Result: ERROR
    Running examples in 'haplo.stats-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: Ginv
    > ### Title: Compute Generalized Inverse of Input Matrix
    > ### Aliases: Ginv
    > ### Keywords: matrix
    >
    > ### ** Examples
    >
    > # for matrix x, extract the generalized inverse and
    > # rank of x as follows
    > x <- matrix(c(1,2,1,2,3,2),ncol=3)
    > save <- Ginv(x)
    Error in svd(x, LINPACK = FALSE) :
     the LINPACK argument has been defunct since R 3.1.0
    Calls: Ginv -> svd
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.7.9
Check: tests
Result: ERROR
     Running 'test.haplo.cc.R' [20s/22s]
     Running 'test.haplo.em.R' [21s/24s]
     Comparing 'test.haplo.em.Rout' to 'test.haplo.em.Rout.save' ... OK
     Running 'test.haplo.power.R' [4s/5s]
     Comparing 'test.haplo.power.Rout' to 'test.haplo.power.Rout.save' ... OK
    Running the tests in 'tests/test.haplo.cc.R' failed.
    Complete output:
     > #$Author: sinnwell $
     > #$Date: 2011/12/05 20:53:27 $
     > #$Header: /projects/genetics/cvs/cvsroot/haplo.stats/test/test.haplo.cc.R,v 1.1 2011/12/05 20:53:27 sinnwell Exp $
     > #$Locker: $
     > #$Log: test.haplo.cc.R,v $
     > #Revision 1.1 2011/12/05 20:53:27 sinnwell
     > #changed from .q to .R, to work with R check
     > #
     > #
     > #library(genetics) or library(haplo.stats) for R
     >
     > ## package: haplo.stats
     > ## test script: haplo.cc
     >
     > ## settings
     > verbose=TRUE
     > options(width=140)
     > require(haplo.stats)
     Loading required package: haplo.stats
     > tmp <- Sys.setlocale("LC_ALL", "C")
     > tmp <- Sys.getlocale()
     >
     >
     > # Jason Sinnwell, created 3/2004, updated 9/2014
     > # Mayo Clinic, Biostatistics
     >
     > if(verbose) cat("setting up data...\n")
     setting up data...
     >
     > label <- c("DQB","DRB","B")
     >
     > if(exists("is.R") && is.function(is.R) && is.R()) data(hla.demo)
     > y.bin <- 1*(hla.demo$resp.cat=="low")
     >
     > geno <- as.matrix(hla.demo[,c(17,18,21:24)])
     >
     > # commented code was to check data that goes into haplo.cc
     > # and gets pasted together in the huge data.frame.
     >
     > # sink(file="results.haplo.cc.txt")
     >
     > seed <- c(17, 53, 1, 40, 37, 0, 62, 56, 5, 52, 12, 1)
     > set.seed(seed)
     >
     > # group.hla <- haplo.group(y.bin, geno, miss.val=0, locus.label=label,
     > # control=haplo.em.control(n.try=1))
     > # set.seed(seed)
     > if(verbose) cat("hla data \n")
     hla data
     > cc.hla <- haplo.cc(y.bin, geno, miss.val=0,locus.label=label,
     + control=haplo.glm.control(haplo.min.count=8,
     + em.c=haplo.em.control()))
     Error in svd(x, LINPACK = FALSE) :
     the LINPACK argument has been defunct since R 3.1.0
     Calls: haplo.cc -> haplo.score -> Ginv -> svd
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.7.9
Check: tests
Result: ERROR
     Running ‘test.haplo.cc.R’ [18s/27s]
     Running ‘test.haplo.em.R’ [19s/29s]
     Comparing ‘test.haplo.em.Rout’ to ‘test.haplo.em.Rout.save’ ... OK
     Running ‘test.haplo.power.R’ [3s/5s]
     Comparing ‘test.haplo.power.Rout’ to ‘test.haplo.power.Rout.save’ ... OK
    Running the tests in ‘tests/test.haplo.cc.R’ failed.
    Complete output:
     > #$Author: sinnwell $
     > #$Date: 2011/12/05 20:53:27 $
     > #$Header: /projects/genetics/cvs/cvsroot/haplo.stats/test/test.haplo.cc.R,v 1.1 2011/12/05 20:53:27 sinnwell Exp $
     > #$Locker: $
     > #$Log: test.haplo.cc.R,v $
     > #Revision 1.1 2011/12/05 20:53:27 sinnwell
     > #changed from .q to .R, to work with R check
     > #
     > #
     > #library(genetics) or library(haplo.stats) for R
     >
     > ## package: haplo.stats
     > ## test script: haplo.cc
     >
     > ## settings
     > verbose=TRUE
     > options(width=140)
     > require(haplo.stats)
     Loading required package: haplo.stats
     > tmp <- Sys.setlocale("LC_ALL", "C")
     > tmp <- Sys.getlocale()
     >
     >
     > # Jason Sinnwell, created 3/2004, updated 9/2014
     > # Mayo Clinic, Biostatistics
     >
     > if(verbose) cat("setting up data...\n")
     setting up data...
     >
     > label <- c("DQB","DRB","B")
     >
     > if(exists("is.R") && is.function(is.R) && is.R()) data(hla.demo)
     > y.bin <- 1*(hla.demo$resp.cat=="low")
     >
     > geno <- as.matrix(hla.demo[,c(17,18,21:24)])
     >
     > # commented code was to check data that goes into haplo.cc
     > # and gets pasted together in the huge data.frame.
     >
     > # sink(file="results.haplo.cc.txt")
     >
     > seed <- c(17, 53, 1, 40, 37, 0, 62, 56, 5, 52, 12, 1)
     > set.seed(seed)
     >
     > # group.hla <- haplo.group(y.bin, geno, miss.val=0, locus.label=label,
     > # control=haplo.em.control(n.try=1))
     > # set.seed(seed)
     > if(verbose) cat("hla data \n")
     hla data
     > cc.hla <- haplo.cc(y.bin, geno, miss.val=0,locus.label=label,
     + control=haplo.glm.control(haplo.min.count=8,
     + em.c=haplo.em.control()))
     Error in svd(x, LINPACK = FALSE) :
     the LINPACK argument has been defunct since R 3.1.0
     Calls: haplo.cc -> haplo.score -> Ginv -> svd
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.7.9
Check: examples
Result: ERROR
    Running examples in ‘haplo.stats-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: Ginv
    > ### Title: Compute Generalized Inverse of Input Matrix
    > ### Aliases: Ginv
    > ### Keywords: matrix
    >
    > ### ** Examples
    >
    > # for matrix x, extract the generalized inverse and
    > # rank of x as follows
    > x <- matrix(c(1,2,1,2,3,2),ncol=3)
    > save <- Ginv(x)
    Error in svd(x, LINPACK = FALSE) :
     the LINPACK argument has been defunct since R 3.1.0
    Calls: Ginv -> svd
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.7.9
Check: tests
Result: ERROR
     Running ‘test.haplo.cc.R’ [26s/30s]
     Running ‘test.haplo.em.R’ [26s/31s]
     Comparing ‘test.haplo.em.Rout’ to ‘test.haplo.em.Rout.save’ ... OK
     Running ‘test.haplo.power.R’
     Comparing ‘test.haplo.power.Rout’ to ‘test.haplo.power.Rout.save’ ... OK
    Running the tests in ‘tests/test.haplo.cc.R’ failed.
    Complete output:
     > #$Author: sinnwell $
     > #$Date: 2011/12/05 20:53:27 $
     > #$Header: /projects/genetics/cvs/cvsroot/haplo.stats/test/test.haplo.cc.R,v 1.1 2011/12/05 20:53:27 sinnwell Exp $
     > #$Locker: $
     > #$Log: test.haplo.cc.R,v $
     > #Revision 1.1 2011/12/05 20:53:27 sinnwell
     > #changed from .q to .R, to work with R check
     > #
     > #
     > #library(genetics) or library(haplo.stats) for R
     >
     > ## package: haplo.stats
     > ## test script: haplo.cc
     >
     > ## settings
     > verbose=TRUE
     > options(width=140)
     > require(haplo.stats)
     Loading required package: haplo.stats
     > tmp <- Sys.setlocale("LC_ALL", "C")
     > tmp <- Sys.getlocale()
     >
     >
     > # Jason Sinnwell, created 3/2004, updated 9/2014
     > # Mayo Clinic, Biostatistics
     >
     > if(verbose) cat("setting up data...\n")
     setting up data...
     >
     > label <- c("DQB","DRB","B")
     >
     > if(exists("is.R") && is.function(is.R) && is.R()) data(hla.demo)
     > y.bin <- 1*(hla.demo$resp.cat=="low")
     >
     > geno <- as.matrix(hla.demo[,c(17,18,21:24)])
     >
     > # commented code was to check data that goes into haplo.cc
     > # and gets pasted together in the huge data.frame.
     >
     > # sink(file="results.haplo.cc.txt")
     >
     > seed <- c(17, 53, 1, 40, 37, 0, 62, 56, 5, 52, 12, 1)
     > set.seed(seed)
     >
     > # group.hla <- haplo.group(y.bin, geno, miss.val=0, locus.label=label,
     > # control=haplo.em.control(n.try=1))
     > # set.seed(seed)
     > if(verbose) cat("hla data \n")
     hla data
     > cc.hla <- haplo.cc(y.bin, geno, miss.val=0,locus.label=label,
     + control=haplo.glm.control(haplo.min.count=8,
     + em.c=haplo.em.control()))
     Error in svd(x, LINPACK = FALSE) :
     the LINPACK argument has been defunct since R 3.1.0
     Calls: haplo.cc -> haplo.score -> Ginv -> svd
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.7.9
Check: tests
Result: ERROR
     Running ‘test.haplo.cc.R’ [27s/30s]
     Running ‘test.haplo.em.R’ [28s/33s]
     Comparing ‘test.haplo.em.Rout’ to ‘test.haplo.em.Rout.save’ ... OK
     Running ‘test.haplo.power.R’
     Comparing ‘test.haplo.power.Rout’ to ‘test.haplo.power.Rout.save’ ... OK
    Running the tests in ‘tests/test.haplo.cc.R’ failed.
    Complete output:
     > #$Author: sinnwell $
     > #$Date: 2011/12/05 20:53:27 $
     > #$Header: /projects/genetics/cvs/cvsroot/haplo.stats/test/test.haplo.cc.R,v 1.1 2011/12/05 20:53:27 sinnwell Exp $
     > #$Locker: $
     > #$Log: test.haplo.cc.R,v $
     > #Revision 1.1 2011/12/05 20:53:27 sinnwell
     > #changed from .q to .R, to work with R check
     > #
     > #
     > #library(genetics) or library(haplo.stats) for R
     >
     > ## package: haplo.stats
     > ## test script: haplo.cc
     >
     > ## settings
     > verbose=TRUE
     > options(width=140)
     > require(haplo.stats)
     Loading required package: haplo.stats
     > tmp <- Sys.setlocale("LC_ALL", "C")
     > tmp <- Sys.getlocale()
     >
     >
     > # Jason Sinnwell, created 3/2004, updated 9/2014
     > # Mayo Clinic, Biostatistics
     >
     > if(verbose) cat("setting up data...\n")
     setting up data...
     >
     > label <- c("DQB","DRB","B")
     >
     > if(exists("is.R") && is.function(is.R) && is.R()) data(hla.demo)
     > y.bin <- 1*(hla.demo$resp.cat=="low")
     >
     > geno <- as.matrix(hla.demo[,c(17,18,21:24)])
     >
     > # commented code was to check data that goes into haplo.cc
     > # and gets pasted together in the huge data.frame.
     >
     > # sink(file="results.haplo.cc.txt")
     >
     > seed <- c(17, 53, 1, 40, 37, 0, 62, 56, 5, 52, 12, 1)
     > set.seed(seed)
     >
     > # group.hla <- haplo.group(y.bin, geno, miss.val=0, locus.label=label,
     > # control=haplo.em.control(n.try=1))
     > # set.seed(seed)
     > if(verbose) cat("hla data \n")
     hla data
     > cc.hla <- haplo.cc(y.bin, geno, miss.val=0,locus.label=label,
     + control=haplo.glm.control(haplo.min.count=8,
     + em.c=haplo.em.control()))
     Error in svd(x, LINPACK = FALSE) :
     the LINPACK argument has been defunct since R 3.1.0
     Calls: haplo.cc -> haplo.score -> Ginv -> svd
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.7.9
Check: running examples for arch ‘i386’
Result: ERROR
    Running examples in 'haplo.stats-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: Ginv
    > ### Title: Compute Generalized Inverse of Input Matrix
    > ### Aliases: Ginv
    > ### Keywords: matrix
    >
    > ### ** Examples
    >
    > # for matrix x, extract the generalized inverse and
    > # rank of x as follows
    > x <- matrix(c(1,2,1,2,3,2),ncol=3)
    > save <- Ginv(x)
    Error in svd(x, LINPACK = FALSE) :
     the LINPACK argument has been defunct since R 3.1.0
    Calls: Ginv -> svd
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 1.7.9
Check: running examples for arch ‘x64’
Result: ERROR
    Running examples in 'haplo.stats-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: Ginv
    > ### Title: Compute Generalized Inverse of Input Matrix
    > ### Aliases: Ginv
    > ### Keywords: matrix
    >
    > ### ** Examples
    >
    > # for matrix x, extract the generalized inverse and
    > # rank of x as follows
    > x <- matrix(c(1,2,1,2,3,2),ncol=3)
    > save <- Ginv(x)
    Error in svd(x, LINPACK = FALSE) :
     the LINPACK argument has been defunct since R 3.1.0
    Calls: Ginv -> svd
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 1.7.9
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'test.haplo.cc.R' [18s]
     Running 'test.haplo.em.R' [20s]
     Comparing 'test.haplo.em.Rout' to 'test.haplo.em.Rout.save' ... OK
     Running 'test.haplo.power.R' [5s]
     Comparing 'test.haplo.power.Rout' to 'test.haplo.power.Rout.save' ... OK
    Running the tests in 'tests/test.haplo.cc.R' failed.
    Complete output:
     > #$Author: sinnwell $
     > #$Date: 2011/12/05 20:53:27 $
     > #$Header: /projects/genetics/cvs/cvsroot/haplo.stats/test/test.haplo.cc.R,v 1.1 2011/12/05 20:53:27 sinnwell Exp $
     > #$Locker: $
     > #$Log: test.haplo.cc.R,v $
     > #Revision 1.1 2011/12/05 20:53:27 sinnwell
     > #changed from .q to .R, to work with R check
     > #
     > #
     > #library(genetics) or library(haplo.stats) for R
     >
     > ## package: haplo.stats
     > ## test script: haplo.cc
     >
     > ## settings
     > verbose=TRUE
     > options(width=140)
     > require(haplo.stats)
     Loading required package: haplo.stats
     > tmp <- Sys.setlocale("LC_ALL", "C")
     > tmp <- Sys.getlocale()
     >
     >
     > # Jason Sinnwell, created 3/2004, updated 9/2014
     > # Mayo Clinic, Biostatistics
     >
     > if(verbose) cat("setting up data...\n")
     setting up data...
     >
     > label <- c("DQB","DRB","B")
     >
     > if(exists("is.R") && is.function(is.R) && is.R()) data(hla.demo)
     > y.bin <- 1*(hla.demo$resp.cat=="low")
     >
     > geno <- as.matrix(hla.demo[,c(17,18,21:24)])
     >
     > # commented code was to check data that goes into haplo.cc
     > # and gets pasted together in the huge data.frame.
     >
     > # sink(file="results.haplo.cc.txt")
     >
     > seed <- c(17, 53, 1, 40, 37, 0, 62, 56, 5, 52, 12, 1)
     > set.seed(seed)
     >
     > # group.hla <- haplo.group(y.bin, geno, miss.val=0, locus.label=label,
     > # control=haplo.em.control(n.try=1))
     > # set.seed(seed)
     > if(verbose) cat("hla data \n")
     hla data
     > cc.hla <- haplo.cc(y.bin, geno, miss.val=0,locus.label=label,
     + control=haplo.glm.control(haplo.min.count=8,
     + em.c=haplo.em.control()))
     Error in svd(x, LINPACK = FALSE) :
     the LINPACK argument has been defunct since R 3.1.0
     Calls: haplo.cc -> haplo.score -> Ginv -> svd
     Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 1.7.9
Check: running tests for arch ‘x64’
Result: ERROR
     Running 'test.haplo.cc.R' [21s]
     Running 'test.haplo.em.R' [23s]
     Comparing 'test.haplo.em.Rout' to 'test.haplo.em.Rout.save' ... OK
     Running 'test.haplo.power.R' [4s]
     Comparing 'test.haplo.power.Rout' to 'test.haplo.power.Rout.save' ... OK
    Running the tests in 'tests/test.haplo.cc.R' failed.
    Complete output:
     > #$Author: sinnwell $
     > #$Date: 2011/12/05 20:53:27 $
     > #$Header: /projects/genetics/cvs/cvsroot/haplo.stats/test/test.haplo.cc.R,v 1.1 2011/12/05 20:53:27 sinnwell Exp $
     > #$Locker: $
     > #$Log: test.haplo.cc.R,v $
     > #Revision 1.1 2011/12/05 20:53:27 sinnwell
     > #changed from .q to .R, to work with R check
     > #
     > #
     > #library(genetics) or library(haplo.stats) for R
     >
     > ## package: haplo.stats
     > ## test script: haplo.cc
     >
     > ## settings
     > verbose=TRUE
     > options(width=140)
     > require(haplo.stats)
     Loading required package: haplo.stats
     > tmp <- Sys.setlocale("LC_ALL", "C")
     > tmp <- Sys.getlocale()
     >
     >
     > # Jason Sinnwell, created 3/2004, updated 9/2014
     > # Mayo Clinic, Biostatistics
     >
     > if(verbose) cat("setting up data...\n")
     setting up data...
     >
     > label <- c("DQB","DRB","B")
     >
     > if(exists("is.R") && is.function(is.R) && is.R()) data(hla.demo)
     > y.bin <- 1*(hla.demo$resp.cat=="low")
     >
     > geno <- as.matrix(hla.demo[,c(17,18,21:24)])
     >
     > # commented code was to check data that goes into haplo.cc
     > # and gets pasted together in the huge data.frame.
     >
     > # sink(file="results.haplo.cc.txt")
     >
     > seed <- c(17, 53, 1, 40, 37, 0, 62, 56, 5, 52, 12, 1)
     > set.seed(seed)
     >
     > # group.hla <- haplo.group(y.bin, geno, miss.val=0, locus.label=label,
     > # control=haplo.em.control(n.try=1))
     > # set.seed(seed)
     > if(verbose) cat("hla data \n")
     hla data
     > cc.hla <- haplo.cc(y.bin, geno, miss.val=0,locus.label=label,
     + control=haplo.glm.control(haplo.min.count=8,
     + em.c=haplo.em.control()))
     Error in svd(x, LINPACK = FALSE) :
     the LINPACK argument has been defunct since R 3.1.0
     Calls: haplo.cc -> haplo.score -> Ginv -> svd
     Execution halted
Flavor: r-devel-windows-ix86+x86_64