CRAN Package Check Results for Package coxmeg

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

Check Details

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