##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pwrEWAS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pwrEWAS_1.9.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/pwrEWAS.Rcheck’
* using R Under development (unstable) (2022-03-02 r81842)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pwrEWAS/DESCRIPTION’ ... OK
* this is package ‘pwrEWAS’ version ‘1.9.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘pwrEWAS’ can be installed ... OK
* 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 ... 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘pwrEWAS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pwrEWAS
> ### Title: pwrEWAS - A computationally efficient tool for comprehensive
> ###   power estimation in EWAS
> ### Aliases: pwrEWAS
> ### Keywords: DNAm microarray power
> 
> ### ** Examples
> 
> outDelta <- pwrEWAS(minTotSampleSize = 10,
+     maxTotSampleSize = 20,
+     SampleSizeSteps = 10,
+     NcntPer = 0.5,
+     targetDelta = c(0.2, 0.5),
+     J = 1000,
+     targetDmCpGs = 10,
+     tissueType = "Adult (PBMC)",
+     detectionLimit = 0.01,
+     DMmethod = "limma",
+     FDRcritVal = 0.05,
+     core = 2,
+     sims = 30)
snapshotDate(): 2022-03-01
see ?pwrEWAS.data and browseVignettes('pwrEWAS.data') for documentation
loading from cache
[2022-03-12 05:14:18] Finding tau...done [2022-03-12 05:14:20]
[1] "The following taus were chosen: 0.05859375, 0.15234375"
[2022-03-12 05:14:20] Running simulation

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  |==================                                                    |  25%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |====================================================                  |  75%
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  |======================================================================| 100%
[2022-03-12 05:14:20] Running simulation ... done [2022-03-12 05:14:46]
>     
> outSD <- pwrEWAS(minTotSampleSize = 10,
+     maxTotSampleSize = 20,
+     SampleSizeSteps = 10,
+     NcntPer = 0.5,
+     deltaSD = c(0.02, 0.03),
+     J = 1000,
+     targetDmCpGs = 10,
+     tissueType = "Adult (PBMC)",
+     detectionLimit = 0.01,
+     DMmethod = "limma",
+     FDRcritVal = 0.05,
+     core = 2,
+     sims = 30)
snapshotDate(): 2022-03-01
see ?pwrEWAS.data and browseVignettes('pwrEWAS.data') for documentation
downloading 1 resources
retrieving 1 resource
Warning: download failed
  web resource path: ‘https://experimenthub.bioconductor.org/fetch/3094’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/filea12137ad2e3a’
  reason: Internal Server Error (HTTP 500).
Warning: bfcdownload() failed
  rid: BFC197
  file: ‘https://experimenthub.bioconductor.org/fetch/3094’
  reason: download failed
Warning: download failed
  hub path: ‘https://experimenthub.bioconductor.org/fetch/3094’
  cache resource: ‘EH3078 : 3094’
  reason: download failed; see warnings()
Error: failed to load resource
  name: EH3078
  title: Adult (PBMC)
  reason: 1 resources failed to download
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  pwrEWAS RUnit Tests - 1 test function, 1 error, 0 failures
  ERROR in test_pwrEWAS: Error : failed to load resource
    name: EH3078
    title: Adult (PBMC)
    reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
  
  Test files with failing tests
  
     test_pwrEWAS.R 
       test_pwrEWAS 
  
  
  Error in BiocGenerics:::testPackage("pwrEWAS") : 
    unit tests failed for package pwrEWAS
  Execution halted
* 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: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/pwrEWAS.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pwrEWAS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘pwrEWAS’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pwrEWAS)

R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("pwrEWAS")
snapshotDate(): 2022-03-01
see ?pwrEWAS.data and browseVignettes('pwrEWAS.data') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
Timing stopped at: 31.42 33.77 153.9
Error : failed to load resource
  name: EH3078
  title: Adult (PBMC)
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning message:
file '9cd63be202e5_3094' has magic number '<89>HDF'
  Use of save versions prior to 2 is deprecated 


RUNIT TEST PROTOCOL -- Sat Mar 12 05:17:35 2022 
*********************************************** 
Number of test functions: 1 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
pwrEWAS RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in test_pwrEWAS: Error : failed to load resource
  name: EH3078
  title: Adult (PBMC)
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded

Test files with failing tests

   test_pwrEWAS.R 
     test_pwrEWAS 


Error in BiocGenerics:::testPackage("pwrEWAS") : 
  unit tests failed for package pwrEWAS
Execution halted