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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SynExtend.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SynExtend_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/SynExtend.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SynExtend/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SynExtend' version '1.6.0'
* 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 'SynExtend' 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SequenceSimilarity: no visible binding for global variable 'PFASUM'
Undefined global functions or variables:
  PFASUM
* 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' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
ExtractBy         304.21   0.94  305.18
DisjointSet       285.47   0.59  286.22
PairSummaries     113.26   0.53  113.82
NucleotideOverlap  85.50   0.42   85.92
gffToDataFrame     23.27   0.03   23.30
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
ExtractBy         332.20   0.35  332.57
DisjointSet       324.13   0.48  324.66
PairSummaries     139.24   0.13  143.28
NucleotideOverlap 102.29   0.26  102.58
gffToDataFrame     34.96   0.00   38.41
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/SynExtend.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/SynExtend_1.6.0.tar.gz && rm -rf SynExtend.buildbin-libdir && mkdir SynExtend.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SynExtend.buildbin-libdir SynExtend_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL SynExtend_1.6.0.zip && rm SynExtend_1.6.0.tar.gz SynExtend_1.6.0.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
 27 1629k   27  441k    0     0   787k      0  0:00:02 --:--:--  0:00:02  786k
100 1629k  100 1629k    0     0  1218k      0  0:00:01  0:00:01 --:--:-- 1219k

install for i386

* installing *source* package 'SynExtend' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SynExtend'
    finding HTML links ... done
    DisjointSet                             html  
    finding level-2 HTML links ... done

    EstimateRearrangementScenarios          html  
    ExtractBy                               html  
    FindSets                                html  
    Generic                                 html  
    LinkedPairs-class                       html  
    NucleotideOverlap                       html  
    PairSummaries                           html  
    SequenceSimilarity                      html  
    SubSetPairs                             html  
    gffToDataFrame                          html  
** 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

install for x64

* installing *source* package 'SynExtend' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SynExtend' as SynExtend_1.6.0.zip
* DONE (SynExtend)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'SynExtend' successfully unpacked and MD5 sums checked