Last updated on 2020-08-07 01:50:33 CEST.
| Package | ERROR | WARN | NOTE | OK |
|---|---|---|---|---|
| fam.recrisk | 12 | |||
| haplo.stats | 5 | 7 | ||
| ibdreg | 1 | 5 | 6 | |
| kinship2 | 12 | |||
| pedgene | 12 | |||
| pleio | 12 | |||
| regmed | 12 | |||
| vcpen | 4 | 8 |
Current CRAN status: OK: 12
Current CRAN status: ERROR: 5, OK: 7
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
Current CRAN status: ERROR: 1, NOTE: 5, OK: 6
Version: 0.2.5
Check: top-level files
Result: NOTE
Non-standard file/directory found at top level:
'perl'
Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64
Version: 0.2.5
Check: R code for possible problems
Result: NOTE
create.ibd.dat: no visible global function definition for 'read.table'
create.pairs.frame: no visible global function definition for 'terms'
ibd.moments: no visible global function definition for 'var'
ibdreg: no visible global function definition for 'terms'
ibdreg: no visible global function definition for 'as.formula'
linkage.tests: no visible global function definition for 'pchisq'
pchibar: no visible global function definition for 'pchisq'
plot.linkage.all: no visible global function definition for 'title'
plotpval: no visible global function definition for 'lines'
sim.ibd.var: no visible global function definition for 'read.table'
sim.mark.prop: no visible global function definition for 'runif'
Undefined global functions or variables:
as.formula lines pchisq read.table runif terms title var
Consider adding
importFrom("graphics", "lines", "title")
importFrom("stats", "as.formula", "pchisq", "runif", "terms", "var")
importFrom("utils", "read.table")
to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64, r-release-macos-x86_64
Version: 0.2.5
Check: examples
Result: ERROR
Running examples in 'ibdreg-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
>
> ### ** 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-linux-x86_64-debian-clang
Version: 0.3.1
Check: compiled code
Result: NOTE
File ‘ibdreg/libs/ibdreg.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.2.5
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
‘ped7.pre’
Flavor: r-patched-linux-x86_64
Version: 0.2.5
Check: R code for possible problems
Result: NOTE
create.ibd.dat: no visible global function definition for 'read.table'
create.pairs.frame: no visible global function definition for 'terms'
ibd.moments: no visible global function definition for 'var'
ibdreg: no visible global function definition for 'terms'
ibdreg: no visible global function definition for 'as.formula'
linkage.tests: no visible global function definition for 'pchisq'
pchibar: no visible global function definition for 'pchisq'
plot.linkage.all: no visible global function definition for 'plot'
plot.linkage.all: no visible global function definition for 'title'
plotpval: no visible global function definition for 'plot'
plotpval: no visible global function definition for 'lines'
sim.ibd.var: no visible global function definition for 'read.table'
sim.mark.prop: no visible global function definition for 'runif'
Undefined global functions or variables:
as.formula lines pchisq plot read.table runif terms title var
Consider adding
importFrom("graphics", "lines", "plot", "title")
importFrom("stats", "as.formula", "pchisq", "runif", "terms", "var")
importFrom("utils", "read.table")
to your NAMESPACE file.
Flavor: r-oldrel-windows-ix86+x86_64
Current CRAN status: OK: 12
Current CRAN status: OK: 12
Current CRAN status: OK: 12
Current CRAN status: OK: 12
Current CRAN status: WARN: 4, OK: 8
Version: 1.7
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
vcpen.cpp:906:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
vcpen.cpp:907:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
vcpen.cpp:959:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-fedora-clang, r-release-macos-x86_64, r-oldrel-macos-x86_64