* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/tempoR.Rcheck’
* using R Under development (unstable) (2023-03-24 r84037)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2)
    GNU Fortran (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2)
* running under: Fedora 34 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘tempoR/DESCRIPTION’ ... OK
* this is package ‘tempoR’ version ‘1.0.4.4’
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘tempoR’ can be installed ... 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 ... OK
* 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 loading without being on the library search path ... 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 line widths ... 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking examples with --run-donttest ... ERROR
Running examples in ‘tempoR-Ex.R’ failed
The error most likely occurred in:

> ### Name: tempo.permutationTest
> ### Title: Permutation testing for TEMPO
> ### Aliases: tempo.permutationTest
> 
> ### ** Examples
> 
> data("dflatExample")
> data("gse32472Example")
> data("gse32472ExampleTempoResults")
> 
> ## No test: 
> # Cross-validation can be run seperately once the initial model-building and scoring is complete.
> # Note that running this example may take several minutes.
> results = tempo.runInstance(ctrl=gse32472Example$ctrl,
+     test=gse32472Example$test,
+     genesets=dflatExample,
+     X=gse32472Example$data,
+     Y=gse32472Example$age)
[1] "1: positive regulation of immunoglobulin production"
[1] "2: cochlea development"
[1] "3: regulation of immunoglobulin production"
[1] "4: response to cAMP"
[1] "5: cerebral cortex radial glia guided migration"
[1] "6: neural crest cell differentiation"
[1] "7: prostanoid biosynthetic process"
[1] "8: neural precursor cell proliferation"
[1] "9: hormone metabolic process"
[1] "10: regulation of endoplasmic reticulum unfolded protein response"
[1] "11: detection of bacterium"
[1] "12: cholesterol biosynthetic process"
[1] "13: histone H3-K9 methylation"
[1] "14: protein targeting to plasma membrane"
[1] "15: pattern recognition receptor signaling pathway"
[1] "16: positive regulation of branching involved in ureteric bud morphogenesis"
[1] "17: positive regulation of execution phase of apoptosis"
[1] "18: negative regulation of multi-organism process"
[1] "19: regulation of bone remodeling"
[1] "20: negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage"
> results = tempo.permutationTest(mainResult=results,
+     ctrl=gse32472Example$ctrl,
+     test=gse32472Example$test,
+     genesets=dflatExample,
+     X=gse32472Example$data,
+     Y=gse32472Example$age,
+     nCores=-1)
[1] "Beginning permutation testing for 500 permutations on 32 cores."
Error in .check_ncores(length(names)) : 32 simultaneous processes spawned
Calls: tempo.permutationTest -> <Anonymous> -> makePSOCKcluster -> .check_ncores
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [9s/10s] OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/tempoR.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 0:33.77, 24.78 + 5.54