Last updated on 2020-01-20 01:50:18 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.9 | 103.86 | 408.74 | 512.60 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.9 | 76.64 | 317.80 | 394.44 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.9 | 672.84 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.9 | 655.49 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 1.0.9 | 256.00 | 567.00 | 823.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 1.0.9 | 217.00 | 590.00 | 807.00 | OK | |
| r-patched-linux-x86_64 | 1.0.9 | 88.06 | 406.43 | 494.49 | OK | |
| r-patched-solaris-x86 | 1.0.9 | 4.40 | ERROR | |||
| r-release-linux-x86_64 | 1.0.9 | 88.66 | 381.58 | 470.24 | OK | |
| r-release-windows-ix86+x86_64 | 1.0.9 | 255.00 | 431.00 | 686.00 | OK | |
| r-release-osx-x86_64 | 1.0.9 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0.9 | 159.00 | 433.00 | 592.00 | OK | |
| r-oldrel-osx-x86_64 | 1.0.9 | ERROR |
Version: 1.0.9
Check: installed package size
Result: NOTE
installed size is 17.2Mb
sub-directories of 1Mb or more:
libs 16.7Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 1.0.9
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘coxme’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 1.0.9
Check: package dependencies
Result: ERROR
Package required but not available: ‘SNPRelate’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-patched-solaris-x86
Version: 1.0.9
Check: examples
Result: ERROR
Running examples in ‘coxmeg-Ex.R’ failed
The error most likely occurred in:
> ### Name: coxmeg_plink
> ### Title: Perform GWAS using a Cox mixed-effects model with plink files as
> ### input
> ### Aliases: coxmeg_plink
> ### Keywords: Cox mixed-effects model
>
> ### ** Examples
>
> library(Matrix)
> library(MASS)
> library(coxmeg)
>
> ## build a block-diagonal relatedness matrix
> n_f <- 600
> mat_list <- list()
> size <- rep(5,n_f)
> offd <- 0.5
> for(i in 1:n_f)
+ {
+ mat_list[[i]] <- matrix(offd,size[i],size[i])
+ diag(mat_list[[i]]) <- 1
+ }
> sigma <- as.matrix(bdiag(mat_list))
>
> ## Estimate variance component under a null model
> pheno = system.file("extdata", "ex_pheno.txt", package = "coxmeg")
> cov = system.file("extdata", "ex_cov.txt", package = "coxmeg")
> bed = system.file("extdata", "example_null.bed", package = "coxmeg")
> bed = substr(bed,1,nchar(bed)-4)
> re = coxmeg_plink(pheno,sigma,type='bd',bed=bed,tmp_dir=tempdir(),cov_file=cov,
+ detap='diagonal',order=1)
Remove 0 subjects censored before the first failure.
There is/are 1 covariates. The sample size included is 3000.
The relatedness matrix is treated as sparse.
The relatedness matrix is inverted.
The method for computing the determinant is 'diagonal'.
Solver: Cholesky decomposition (RcppEigen=TRUE).
The variance component is estimated. Start analyzing SNPs...
Start snpgdsBED2GDS ...
BED file: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/coxmeg.Rcheck/coxmeg/extdata/example_null.bed" in the SNP-major mode (Sample X SNP)
FAM file: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/coxmeg.Rcheck/coxmeg/extdata/example_null.fam", DONE.
BIM file: "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/coxmeg.Rcheck/coxmeg/extdata/example_null.bim", DONE.
Sun Jan 19 04:22:02 2020 store sample id, snp id, position, and chromosome.
start writing: 3000 samples, 20 SNPs ...
Sun Jan 19 04:22:02 2020 0%
Sun Jan 19 04:22:02 2020 100%
Sun Jan 19 04:22:02 2020 Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file '/tmp/RtmpSrKleG/tmp_26550866.gds' (18.7K)
# of fragments: 38
save to '/tmp/RtmpSrKleG/tmp_26550866.gds.tmp'
rename '/tmp/RtmpSrKleG/tmp_26550866.gds.tmp' (18.4K, reduced: 240B)
# of fragments: 18
Excluding 0 SNP on non-autosomes
Excluding 0 SNP (monomorphic: TRUE, MAF: 0.05, missing rate: 0)
The order is set to be 1.
Error in af_inc[, "afreq"] : incorrect number of dimensions
Calls: coxmeg_plink -> cbind
Execution halted
Flavor: r-oldrel-osx-x86_64
Version: 1.0.9
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 112-132 (COXMEG_example.Rmd)
Error: processing vignette 'COXMEG_example.Rmd' failed with diagnostics:
incorrect number of dimensions
Execution halted
Flavor: r-oldrel-osx-x86_64