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### Running command:
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### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:epistasisGA.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings epistasisGA_1.1.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/epistasisGA.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'epistasisGA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'epistasisGA' version '1.1.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'epistasisGA' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in 'NEWS.md':
No news entries found.
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/epistasisGA/libs/x64/epistasisGA.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'epistasisGA-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: global.test
> ### Title: A function to run a global test of the null hypothesis that
> ### there are no SNP-disease associations across a range of chromosome
> ### sizes
> ### Aliases: global.test
>
> ### ** Examples
>
>
> data(case)
> data(dad)
> data(mom)
> data(snp.annotations)
> library(Matrix)
> set.seed(1400)
> block.ld.mat <- as.matrix(bdiag(list(
+ matrix(rep(TRUE, 25^2), nrow = 25),
+ matrix(rep(TRUE, 25^2), nrow = 25),
+ matrix(rep(TRUE, 25^2), nrow = 25),
+ matrix(rep(TRUE, 25^2), nrow = 25)
+ )))
>
> pp.list <- preprocess.genetic.data(case[, 1:10],
+ father.genetic.data = dad[, 1:10],
+ mother.genetic.data = mom[, 1:10],
+ block.ld.mat = block.ld.mat[1:10, 1:10]
+ )
> ## run GA for observed data
>
> # observed data chromosome size 2
> run.gadgets(pp.list,
+ n.chromosomes = 5, chromosome.size = 2, results.dir = "tmp_2",
+ cluster.type = "interactive", registryargs = list(
+ file.dir = "tmp_reg",
+ seed = 1500
+ ),
+ generations = 2, n.islands = 2, island.cluster.size = 1,
+ n.migrations = 0
+ )
No readable configuration file found
Created registry in 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/epistasisGA.Rcheck/tmp_reg' using cluster functions 'Interactive'
Adding 2 jobs ...
Submitting 2 jobs in 1 chunks using cluster functions 'Interactive' ...
> combined.res2 <- combine.islands(
+ "tmp_2", snp.annotations[1:10, ], pp.list,
+ 2
+ )
> unlink("tmp_reg", recursive = TRUE)
>
> # observed data chromosome size 3
> run.gadgets(pp.list,
+ n.chromosomes = 5, chromosome.size = 3, results.dir = "tmp_3",
+ cluster.type = "interactive", registryargs = list(
+ file.dir = "tmp_reg",
+ seed = 1500
+ ),
+ generations = 2, n.islands = 2, island.cluster.size = 1,
+ n.migrations = 0
+ )
No readable configuration file found
Created registry in 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/epistasisGA.Rcheck/tmp_reg' using cluster functions 'Interactive'
Adding 2 jobs ...
Submitting 2 jobs in 1 chunks using cluster functions 'Interactive' ...
> combined.res3 <- combine.islands(
+ "tmp_3", snp.annotations[1:10, ], pp.list,
+ 2
+ )
> unlink("tmp_reg", recursive = TRUE)
>
> # create three permuted datasets
> set.seed(1400)
> perm.data.list <- permute.dataset(case[, 1:10],
+ father.genetic.data = dad[, 1:10],
+ mother.genetic.data = mom[, 1:10],
+ n.permutations = 3
+ )
>
> # pre-process permuted data
> p1.list <- preprocess.genetic.data(perm.data.list[["permutation1"]]$case,
+ complement.genetic.data = perm.data.list[["permutation1"]]$comp,
+ block.ld.mat = block.ld.mat[1:10, 1:10]
+ )
>
> p2.list <- preprocess.genetic.data(perm.data.list[["permutation2"]]$case,
+ complement.genetic.data = perm.data.list[["permutation2"]]$comp,
+ block.ld.mat = block.ld.mat[1:10, 1:10]
+ )
>
> p3.list <- preprocess.genetic.data(perm.data.list[["permutation3"]]$case,
+ complement.genetic.data = perm.data.list[["permutation3"]]$comp,
+ block.ld.mat = block.ld.mat[1:10, 1:10]
+ )
>
> ## run GA for permuted data
>
> # permutation 1, chromosome size 2
> run.gadgets(p1.list,
+ n.chromosomes = 5, chromosome.size = 2, results.dir = "p1_tmp_2",
+ cluster.type = "interactive", registryargs = list(
+ file.dir = "tmp_reg",
+ seed = 1500
+ ),
+ generations = 2, n.islands = 2, island.cluster.size = 1,
+ n.migrations = 0
+ )
No readable configuration file found
Created registry in 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/epistasisGA.Rcheck/tmp_reg' using cluster functions 'Interactive'
Adding 2 jobs ...
Submitting 2 jobs in 1 chunks using cluster functions 'Interactive' ...
> p1.combined.res2 <- combine.islands(
+ "p1_tmp_2", snp.annotations[1:10, ],
+ p1.list, 2
+ )
> unlink("tmp_reg", recursive = TRUE)
>
> # permutation 1, chromosome size 3
> run.gadgets(p1.list,
+ n.chromosomes = 5, chromosome.size = 3, results.dir = "p1_tmp_3",
+ cluster.type = "interactive", registryargs = list(
+ file.dir = "tmp_reg",
+ seed = 1500
+ ),
+ generations = 2, n.islands = 2, island.cluster.size = 1,
+ n.migrations = 0
+ )
No readable configuration file found
Created registry in 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/epistasisGA.Rcheck/tmp_reg' using cluster functions 'Interactive'
Adding 2 jobs ...
Submitting 2 jobs in 1 chunks using cluster functions 'Interactive' ...
Error: [EPERM] Failed to move 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/epistasisGA.Rcheck/tmp_reg/registry.new.rds'to 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/epistasisGA.Rcheck/tmp_reg/registry.rds': operation not permitted
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/epistasisGA.Rcheck/00check.log'
for details.