CRAN Package Check Results for Package kinship2

Last updated on 2019-03-22 16:01:02 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.6.4 8.88 97.12 106.00 OK
r-devel-linux-x86_64-debian-gcc 1.6.4 9.29 77.15 86.44 OK
r-devel-linux-x86_64-fedora-clang 1.6.4 128.33 OK
r-devel-linux-x86_64-fedora-gcc 1.6.4 123.18 OK
r-devel-windows-ix86+x86_64 1.6.4 22.00 104.00 126.00 OK
r-patched-linux-x86_64 1.6.4 9.11 93.68 102.79 OK
r-patched-solaris-x86 1.6.4 187.00 OK
r-release-linux-x86_64 1.6.4 7.48 93.71 101.19 OK
r-release-windows-ix86+x86_64 1.6.4 12.00 113.00 125.00 OK
r-release-osx-x86_64 1.6.4 OK
r-oldrel-windows-ix86+x86_64 1.6.4 11.00 132.00 143.00 ERROR
r-oldrel-osx-x86_64 1.6.4 OK

Check Details

Version: 1.6.4
Check: tests
Result: ERROR
     Running 'failure.R' [6s]
     Comparing 'failure.Rout' to 'failure.Rout.save' ... OK
     Running 'kin1.R' [4s]
     Comparing 'kin1.Rout' to 'kin1.Rout.save' ... OK
     Running 'makefam.R' [2s]
     Comparing 'makefam.Rout' to 'makefam.Rout.save' ... OK
     Running 'monozygote.R' [3s]
     Comparing 'monozygote.Rout' to 'monozygote.Rout.save' ... OK
     Running 'subscript.R' [3s]
     Comparing 'subscript.Rout' to 'subscript.Rout.save' ... OK
     Running 'test.kinX.R' [4s]
    Running the tests in 'tests/test.kinX.R' failed.
    Complete output:
     >
     > ## test pedigree from bioinformatics manuscript
     > ## try x-chrom kinship
     > ## also has inbreeding and twins, for quick check
     > require(kinship2)
     Loading required package: kinship2
     Loading required package: Matrix
     Loading required package: quadprog
     > ped2mat <- matrix(c(1,1,0,0,1,
     + 1,2,0,0,2,
     + 1,3,1,2,1,
     + 1,4,1,2,2,
     + 1,5,0,0,2,
     + 1,6,0,0,1,
     + 1,7,3,5,2,
     + 1,8,6,4,1,
     + 1,9,6,4,1,
     + 1,10,8,7,2),ncol=5,byrow=TRUE)
     >
     > ped2df <- as.data.frame(ped2mat)
     > names(ped2df) <- c("fam", "id", "dad", "mom", "sex")
     > ## 1 2 3 4 5 6 7 8 9 10,11,12,13,14,15,16
     > ped2df$disease= c(NA,NA,1,0,0,0,0,1,1,1)
     > ped2df$smoker= c(0,NA,0,0,1,1,1,0,0,0)
     > ped2df$availstatus=c(0,0, 1,1,0,1,1,1,1,1)
     > ped2df$vitalstatus=c(1,1, 1,0,1,0,0,0,0,0)
     >
     > ped2 <- with(ped2df, pedigree(id, dad, mom, sex, status=vitalstatus,
     + affected=cbind(disease,smoker, availstatus), relation=matrix(c(8,9,1),ncol=3)))
     >
     > ## regular kinship matrix
     > kinship(ped2)
     1 2 3 4 5 6 7 8 9 10
     1 0.500 0.000 0.2500 0.2500 0.000 0.000 0.12500 0.12500 0.12500 0.12500
     2 0.000 0.500 0.2500 0.2500 0.000 0.000 0.12500 0.12500 0.12500 0.12500
     3 0.250 0.250 0.5000 0.2500 0.000 0.000 0.25000 0.12500 0.12500 0.18750
     4 0.250 0.250 0.2500 0.5000 0.000 0.000 0.12500 0.25000 0.25000 0.18750
     5 0.000 0.000 0.0000 0.0000 0.500 0.000 0.25000 0.00000 0.00000 0.12500
     6 0.000 0.000 0.0000 0.0000 0.000 0.500 0.00000 0.25000 0.25000 0.12500
     7 0.125 0.125 0.2500 0.1250 0.250 0.000 0.50000 0.06250 0.06250 0.28125
     8 0.125 0.125 0.1250 0.2500 0.000 0.250 0.06250 0.50000 0.50000 0.28125
     9 0.125 0.125 0.1250 0.2500 0.000 0.250 0.06250 0.50000 0.50000 0.28125
     10 0.125 0.125 0.1875 0.1875 0.125 0.125 0.28125 0.28125 0.28125 0.53125
     >
     > kinship(ped2, chr="X")
     1 2 3 4 5 6 7 8 9 10
     1 1.00 0.00 0.000 0.5000 0.000 0 0.0000 0.5000 0.5000 0.2500
     2 0.00 0.50 0.500 0.2500 0.000 0 0.2500 0.2500 0.2500 0.2500
     3 0.00 0.50 1.000 0.2500 0.000 0 0.5000 0.2500 0.2500 0.3750
     4 0.50 0.25 0.250 0.5000 0.000 0 0.1250 0.5000 0.5000 0.3125
     5 0.00 0.00 0.000 0.0000 0.500 0 0.2500 0.0000 0.0000 0.1250
     6 0.00 0.00 0.000 0.0000 0.000 1 0.0000 0.0000 0.0000 0.0000
     7 0.00 0.25 0.500 0.1250 0.250 0 0.5000 0.1250 0.1250 0.3125
     8 0.50 0.25 0.250 0.5000 0.000 0 0.1250 1.0000 1.0000 0.5625
     9 0.50 0.25 0.250 0.5000 0.000 0 0.1250 1.0000 1.0000 0.5625
     10 0.25 0.25 0.375 0.3125 0.125 0 0.3125 0.5625 0.5625 0.5625
     >
     > ped2$sex[9] <- "unknown"
     >
     > ## regular again, should be same as above
     > kinship(ped2)
     1 2 3 4 5 6 7 8 9 10
     1 0.500 0.000 0.2500 0.2500 0.000 0.000 0.12500 0.12500 0.12500 0.12500
     2 0.000 0.500 0.2500 0.2500 0.000 0.000 0.12500 0.12500 0.12500 0.12500
     3 0.250 0.250 0.5000 0.2500 0.000 0.000 0.25000 0.12500 0.12500 0.18750
     4 0.250 0.250 0.2500 0.5000 0.000 0.000 0.12500 0.25000 0.25000 0.18750
     5 0.000 0.000 0.0000 0.0000 0.500 0.000 0.25000 0.00000 0.00000 0.12500
     6 0.000 0.000 0.0000 0.0000 0.000 0.500 0.00000 0.25000 0.25000 0.12500
     7 0.125 0.125 0.2500 0.1250 0.250 0.000 0.50000 0.06250 0.06250 0.28125
     8 0.125 0.125 0.1250 0.2500 0.000 0.250 0.06250 0.50000 0.50000 0.28125
     9 0.125 0.125 0.1250 0.2500 0.000 0.250 0.06250 0.50000 0.50000 0.28125
     10 0.125 0.125 0.1875 0.1875 0.125 0.125 0.28125 0.28125 0.28125 0.53125
     >
     > ## now with unknown sex, gets NAs
     > kinship(ped2, chrtype="X")
     1 2 3 4 5 6 7 8 9 10
     1 1.00 0.00 0.000 0.5000 0.000 0 0.0000 0.5000 NA 0.2500
     2 0.00 0.50 0.500 0.2500 0.000 0 0.2500 0.2500 NA 0.2500
     3 0.00 0.50 1.000 0.2500 0.000 0 0.5000 0.2500 NA 0.3750
     4 0.50 0.25 0.250 0.5000 0.000 0 0.1250 0.5000 NA 0.3125
     5 0.00 0.00 0.000 0.0000 0.500 0 0.2500 0.0000 NA 0.1250
     6 0.00 0.00 0.000 0.0000 0.000 1 0.0000 0.0000 NA 0.0000
     7 0.00 0.25 0.500 0.1250 0.250 0 0.5000 0.1250 NA 0.3125
     8 0.50 0.25 0.250 0.5000 0.000 0 0.1250 1.0000 1 0.5625
     9 NA NA NA NA NA NA NA NA NA NA
     10 0.25 0.25 0.375 0.3125 0.125 0 0.3125 0.5625 NA 0.5625
     >
     > ped2$sex[9]="unknown"
     > kinship(ped2, chrtype="x")
     1 2 3 4 5 6 7 8 9 10
     1 1.00 0.00 0.000 0.5000 0.000 0 0.0000 0.5000 NA 0.2500
     2 0.00 0.50 0.500 0.2500 0.000 0 0.2500 0.2500 NA 0.2500
     3 0.00 0.50 1.000 0.2500 0.000 0 0.5000 0.2500 NA 0.3750
     4 0.50 0.25 0.250 0.5000 0.000 0 0.1250 0.5000 NA 0.3125
     5 0.00 0.00 0.000 0.0000 0.500 0 0.2500 0.0000 NA 0.1250
     6 0.00 0.00 0.000 0.0000 0.000 1 0.0000 0.0000 NA 0.0000
     7 0.00 0.25 0.500 0.1250 0.250 0 0.5000 0.1250 NA 0.3125
     8 0.50 0.25 0.250 0.5000 0.000 0 0.1250 1.0000 1 0.5625
     9 NA NA NA NA NA NA NA NA NA NA
     10 0.25 0.25 0.375 0.3125 0.125 0 0.3125 0.5625 NA 0.5625
     >
     >
     > # all descendants of sex=unknown to be NAs as well
     > ped2$sex[8]="unknown"
     > kinship(ped2, chr="X")
     1 2 3 4 5 6 7 8 9 10
     1 1.0 0.00 0.00 0.500 0.00 0 0.000 NA NA NA
     2 0.0 0.50 0.50 0.250 0.00 0 0.250 NA NA NA
     3 0.0 0.50 1.00 0.250 0.00 0 0.500 NA NA NA
     4 0.5 0.25 0.25 0.500 0.00 0 0.125 NA NA NA
     5 0.0 0.00 0.00 0.000 0.50 0 0.250 NA NA NA
     6 0.0 0.00 0.00 0.000 0.00 1 0.000 NA NA NA
     7 0.0 0.25 0.50 0.125 0.25 0 0.500 NA NA NA
     8 NA NA NA NA NA NA NA NA NA NA
     9 NA NA NA NA NA NA NA NA NA NA
     10 NA NA NA NA NA NA NA NA NA NA
     >
     >
     > ## testing kinship2 on pedigreeList when only one subject in a family
     > peddf <- rbind(ped2df, c(2,1,0,0,1,1,0,1,0))
     >
     > peds <- with(peddf, pedigree(id, dad, mom, sex, status=vitalstatus,fam=fam,
     + affected=cbind(disease,smoker, availstatus)))
     >
     > kinfam <- kinship(peds)
     >
     > kinfam
     11 x 11 sparse Matrix of class "dsCMatrix"
     Error in isFALSE(suppRows) : could not find function "isFALSE"
     Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 1.6.4
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Loading required package: kinship2
    Loading required package: Matrix
    Loading required package: quadprog
    Error: processing vignette 'pedigree.snw' failed with diagnostics:
    could not find function "isFALSE"
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64