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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SCATE.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SCATE_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/SCATE.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 'SCATE/DESCRIPTION' ... OK
* this is package 'SCATE' version '1.4.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'parallel', 'preprocessCore', 'splines', 'splines2', 'xgboost',
  'SCATEData', 'Rtsne', 'mclust'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'SCATE' 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 ... NOTE
Package in Depends field not imported from: 'SCATEData'
  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
SCATE : SCATEsingle: no visible global function definition for
  'IRanges'
cellcluster : <anonymous>: no visible global function definition for
  'IRanges'
extractfeature: no visible global function definition for 'IRanges'
makedatabase: no visible global function definition for 'IRanges'
makedatabase: no visible global function definition for 'seqlevels'
peakcall: no visible global function definition for 'IRanges'
Undefined global functions or variables:
  IRanges seqlevels
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
peakcall    117.46   7.19  104.61
SCATE       109.24  10.54  101.80
cellcluster  29.36   0.64   31.07
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
SCATEpipeline 123.06   1.69  106.01
SCATE         114.27   2.03   99.06
peakcall      103.85   0.99   87.18
cellcluster    23.96   0.39   24.40
* 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 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/SCATE.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/SCATE_1.4.0.tar.gz && rm -rf SCATE.buildbin-libdir && mkdir SCATE.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SCATE.buildbin-libdir SCATE_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL SCATE_1.4.0.zip && rm SCATE_1.4.0.tar.gz SCATE_1.4.0.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
 63  258k   63  164k    0     0   718k      0 --:--:-- --:--:-- --:--:--  718k
100  258k  100  258k    0     0   505k      0 --:--:-- --:--:-- --:--:--  505k

install for i386

* installing *source* package 'SCATE' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
snapshotDate(): 2021-10-19
** help
*** installing help indices
  converting help for package 'SCATE'
    finding HTML links ... done
    SCATE                                   html  
    SCATEpipeline                           html  
    cellcluster                             html  
    extractfeature                          html  
    makedatabase                            html  
    peakcall                                html  
    satacprocess                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
snapshotDate(): 2021-10-19
** testing if installed package can be loaded from final location
snapshotDate(): 2021-10-19
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'SCATE' ...
** testing if installed package can be loaded
snapshotDate(): 2021-10-19
* MD5 sums
packaged installation of 'SCATE' as SCATE_1.4.0.zip
* DONE (SCATE)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'SCATE' successfully unpacked and MD5 sums checked