Multiple platform build/check report for BioC 3.9 - CHECK report for motifbreakR on tokay2

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:motifbreakR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings motifbreakR_1.13.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/motifbreakR.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'motifbreakR/DESCRIPTION' ... OK
* this is package 'motifbreakR' version '1.13.0'
* 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 'motifbreakR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpW4ieRv/R.INSTALL1c5015de15e0/motifbreakR/man/example.results.Rd:7: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpW4ieRv/R.INSTALL1c5015de15e0/motifbreakR/man/example.results.Rd:12: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'motifbreakR'
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/motifbreakR.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Packages in Depends field not imported from:
  'MotifDb' 'grid'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotMotifLogoStack.2: no visible global function definition for 'par'
snps.from.file: no visible global function definition for 'info'
snps.from.file: no visible global function definition for 'rowRanges'
snps.from.rsid: no visible global function definition for 'snpsById'
Undefined global functions or variables:
  info par rowRanges snpsById
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE file.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'motifbreakR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: motifbreakR
> ### Title: Predict The Disruptiveness Of Single Nucleotide Polymorphisms On
> ###   Transcription Factor Binding Sites.
> ### Aliases: motifbreakR
> 
> ### ** Examples
> 
> library(BSgenome.Hsapiens.UCSC.hg19)
Loading required package: BSgenome
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: rtracklayer
>  # prepare variants
>  load(system.file("extdata",
+                   "pca.enhancer.snps.rda",
+                   package = "motifbreakR")) # loads snps.mb
>  pca.enhancer.snps <- sample(snps.mb, 20)
>  # Get motifs to interrogate
>  data(hocomoco)
>  motifs <- sample(hocomoco, 50)
>  # run motifbreakR
>  results <- motifbreakR(pca.enhancer.snps,
+                         motifs, threshold = 0.85,
+                         method = "ic",
+                         BPPARAM=BiocParallel::SerialParam())
Error in 1:cores : NA/NaN argument
Calls: motifbreakR -> sapply
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'motifbreakR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: motifbreakR
> ### Title: Predict The Disruptiveness Of Single Nucleotide Polymorphisms On
> ###   Transcription Factor Binding Sites.
> ### Aliases: motifbreakR
> 
> ### ** Examples
> 
> library(BSgenome.Hsapiens.UCSC.hg19)
Loading required package: BSgenome
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: rtracklayer
>  # prepare variants
>  load(system.file("extdata",
+                   "pca.enhancer.snps.rda",
+                   package = "motifbreakR")) # loads snps.mb
>  pca.enhancer.snps <- sample(snps.mb, 20)
>  # Get motifs to interrogate
>  data(hocomoco)
>  motifs <- sample(hocomoco, 50)
>  # run motifbreakR
>  results <- motifbreakR(pca.enhancer.snps,
+                         motifs, threshold = 0.85,
+                         method = "ic",
+                         BPPARAM=BiocParallel::SerialParam())
Error in 1:cores : NA/NaN argument
Calls: motifbreakR -> sapply
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 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/motifbreakR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/motifbreakR_1.13.0.tar.gz && rm -rf motifbreakR.buildbin-libdir && mkdir motifbreakR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=motifbreakR.buildbin-libdir motifbreakR_1.13.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL motifbreakR_1.13.0.zip && rm motifbreakR_1.13.0.tar.gz motifbreakR_1.13.0.zip
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100 1356k  100 1356k    0     0  17.5M      0 --:--:-- --:--:-- --:--:-- 19.1M

install for i386

* installing *source* package 'motifbreakR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
See system.file("LICENSE", package="MotifDb") for use restrictions.
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'motifbreakR'
** help
*** installing help indices
  converting help for package 'motifbreakR'
    finding HTML links ... done
    calculatePvalue                         html  
    finding level-2 HTML links ... done

    encodemotif                             html  
    example.results                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpW4ieRv/R.INSTALL1c5015de15e0/motifbreakR/man/example.results.Rd:7: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpW4ieRv/R.INSTALL1c5015de15e0/motifbreakR/man/example.results.Rd:12: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    factorbook                              html  
    hocomoco                                html  
    homer                                   html  
    motifbreakR                             html  
    motifbreakR_motif                       html  
    plotMB                                  html  
    snps.from.file                          html  
    snps.from.rsid                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
See system.file("LICENSE", package="MotifDb") for use restrictions.
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'motifbreakR'
** testing if installed package can be loaded from final location
See system.file("LICENSE", package="MotifDb") for use restrictions.
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'motifbreakR'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'motifbreakR' ...
** testing if installed package can be loaded
See system.file("LICENSE", package="MotifDb") for use restrictions.
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'motifbreakR'
* MD5 sums
packaged installation of 'motifbreakR' as motifbreakR_1.13.0.zip
* DONE (motifbreakR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'motifbreakR' successfully unpacked and MD5 sums checked

CHECK report for motifbreakR on tokay2

Summary

Command output

Installation output

Tests output

Example timings