Last updated on 2020-08-07 01:49:47 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.7.9 | 19.09 | 173.58 | 192.67 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.7.9 | 16.95 | 134.63 | 151.58 | 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 | 68.00 | 268.00 | 336.00 | ERROR | |
| r-patched-linux-x86_64 | 1.7.9 | 18.68 | 218.74 | 237.42 | OK | |
| r-patched-solaris-x86 | 1.7.9 | 551.00 | OK | |||
| r-release-linux-x86_64 | 1.7.9 | 18.89 | 217.65 | 236.54 | OK | |
| r-release-macos-x86_64 | 1.7.9 | OK | ||||
| r-release-windows-ix86+x86_64 | 1.7.9 | 46.00 | 435.00 | 481.00 | OK | |
| r-oldrel-macos-x86_64 | 1.7.9 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.7.9 | 37.00 | 371.00 | 408.00 | OK |
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' [19s/21s]
Running 'test.haplo.em.R' [21s/24s]
Comparing 'test.haplo.em.Rout' to 'test.haplo.em.Rout.save' ... OK
Running 'test.haplo.power.R' [5s/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$resp.cat=="low")
>
> geno <- as.matrix(hla.demo[,c(17,18,21:24)])
>
> # commented code was to check data that goes into haplo.cc
> # and gets pasted together in the huge data.frame.
>
> # sink(file="results.haplo.cc.txt")
>
> seed <- c(17, 53, 1, 40, 37, 0, 62, 56, 5, 52, 12, 1)
> set.seed(seed)
>
> # group.hla <- haplo.group(y.bin, geno, miss.val=0, locus.label=label,
> # control=haplo.em.control(n.try=1))
> # set.seed(seed)
> if(verbose) cat("hla data \n")
hla data
> cc.hla <- haplo.cc(y.bin, geno, miss.val=0,locus.label=label,
+ control=haplo.glm.control(haplo.min.count=8,
+ em.c=haplo.em.control()))
Error in svd(x, LINPACK = FALSE) :
the LINPACK argument has been defunct since R 3.1.0
Calls: haplo.cc -> haplo.score -> Ginv -> svd
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.7.9
Check: tests
Result: ERROR
Running ‘test.haplo.cc.R’ [18s/26s]
Running ‘test.haplo.em.R’ [18s/25s]
Comparing ‘test.haplo.em.Rout’ to ‘test.haplo.em.Rout.save’ ... OK
Running ‘test.haplo.power.R’ [3s/5s]
Comparing ‘test.haplo.power.Rout’ to ‘test.haplo.power.Rout.save’ ... OK
Running the tests in ‘tests/test.haplo.cc.R’ failed.
Complete output:
> #$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' [19s]
Running 'test.haplo.em.R' [21s]
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$resp.cat=="low")
>
> geno <- as.matrix(hla.demo[,c(17,18,21:24)])
>
> # commented code was to check data that goes into haplo.cc
> # and gets pasted together in the huge data.frame.
>
> # sink(file="results.haplo.cc.txt")
>
> seed <- c(17, 53, 1, 40, 37, 0, 62, 56, 5, 52, 12, 1)
> set.seed(seed)
>
> # group.hla <- haplo.group(y.bin, geno, miss.val=0, locus.label=label,
> # control=haplo.em.control(n.try=1))
> # set.seed(seed)
> if(verbose) cat("hla data \n")
hla data
> cc.hla <- haplo.cc(y.bin, geno, miss.val=0,locus.label=label,
+ control=haplo.glm.control(haplo.min.count=8,
+ em.c=haplo.em.control()))
Error in svd(x, LINPACK = FALSE) :
the LINPACK argument has been defunct since R 3.1.0
Calls: haplo.cc -> haplo.score -> Ginv -> svd
Execution halted
Flavor: r-devel-windows-ix86+x86_64
Version: 1.7.9
Check: running tests for arch ‘x64’
Result: ERROR
Running 'test.haplo.cc.R' [23s]
Running 'test.haplo.em.R' [26s]
Comparing 'test.haplo.em.Rout' to 'test.haplo.em.Rout.save' ... OK
Running 'test.haplo.power.R' [5s]
Comparing 'test.haplo.power.Rout' to 'test.haplo.power.Rout.save' ... OK
Running the tests in 'tests/test.haplo.cc.R' failed.
Complete output:
> #$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