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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:motifbreakR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings motifbreakR_2.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/motifbreakR.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '2.6.1'
* 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:
  Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'motifbreakR'
  Warning: replacing previous import 'S4Vectors::as.data.frame' by 'motifStack::as.data.frame' when loading 'motifbreakR'
See 'C:/Users/biocbuild/bbs-3.13-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
Namespaces in Imports field not imported from:
  'compiler' 'grImport'
  All declared Imports should be used.
Package in Depends field not imported from: 'MotifDb'
  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
formatVcfOut: no visible binding for global variable 'search.genome'
plotMotifLogoStack.2: no visible global function definition for 'par'
preparePWM: no visible binding for global variable 'threshold'
snps.from.file: no visible binding for global variable 'DNA_ALPHABET'
wScore: no visible global function definition for 'scoreMotif'
Undefined global functions or variables:
  DNA_ALPHABET par scoreMotif search.genome threshold
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 ... WARNING
Undocumented code objects:
  'rs1006140' 'variants.from.file'
Undocumented data sets:
  'rs1006140'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'motifbreakR'
  'legacy.score'

Undocumented arguments in documentation object 'scoreAllWindows'
  'snp.seq' 'snp.seq.rc' 'pwm' 'from' 'to' 'pwm.range' 'calcp'

Undocumented arguments in documentation object 'snps.from.file'
  'indels'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
snps.from.rsid 60.27   1.39   61.69
motifbreakR    13.20   1.24   14.44
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
snps.from.rsid 41.25   1.36   42.61
motifbreakR    13.69   0.25   13.95
* 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: 3 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/motifbreakR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/motifbreakR_2.6.1.tar.gz && rm -rf motifbreakR.buildbin-libdir && mkdir motifbreakR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=motifbreakR.buildbin-libdir motifbreakR_2.6.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL motifbreakR_2.6.1.zip && rm motifbreakR_2.6.1.tar.gz motifbreakR_2.6.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 33 1791k   33  603k    0     0  1335k      0  0:00:01 --:--:--  0:00:01 1335k
100 1791k  100 1791k    0     0  1834k      0 --:--:-- --:--:-- --:--:-- 1833k

install for i386

* installing *source* package 'motifbreakR' ...
** using staged installation
** 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'
Warning: replacing previous import 'S4Vectors::as.data.frame' by 'motifStack::as.data.frame' 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  
    factorbook                              html  
    hocomoco                                html  
    homer                                   html  
    motifbreakR                             html  
    motifbreakR_motif                       html  
    plotMB                                  html  
    scoreAllWindows                         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'
Warning: replacing previous import 'S4Vectors::as.data.frame' by 'motifStack::as.data.frame' 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'
Warning: replacing previous import 'S4Vectors::as.data.frame' by 'motifStack::as.data.frame' 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'
Warning: replacing previous import 'S4Vectors::as.data.frame' by 'motifStack::as.data.frame' when loading 'motifbreakR'
* MD5 sums
packaged installation of 'motifbreakR' as motifbreakR_2.6.1.zip
* DONE (motifbreakR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'motifbreakR' successfully unpacked and MD5 sums checked