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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:enrichTF.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings enrichTF_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/enrichTF.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'enrichTF/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'enrichTF' 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 'enrichTF' 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 ... NOTE
Warning in options(stringsAsFactors = TRUE) :
  'options(stringsAsFactors = TRUE)' is deprecated and will be disabled

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
** 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 ... NOTE
Warning in options(stringsAsFactors = TRUE) :
  'options(stringsAsFactors = TRUE)' is deprecated and will be disabled

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
** 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
processing,TissueOpennessConserve: no visible binding for global
  variable 'X2'
Undefined global functions or variables:
  X2
* 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
GeneOntology              21.97   2.14   24.22
TissueOpennessSpecificity 23.49   0.00   23.61
GenBackground              5.08   1.70   13.29
Pipelines                  1.58   0.03   23.77
MotifsInRegions            1.02   0.03   19.99
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
TissueOpennessSpecificity 27.09   0.04   27.19
GeneOntology              18.41   1.42   19.97
GenBackground              5.32   1.11   12.99
MotifsInRegions            1.58   0.08   20.32
Pipelines                  1.44   0.08   20.48
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* 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-3.12-bioc/meat/enrichTF.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/enrichTF_1.6.0.tar.gz && rm -rf enrichTF.buildbin-libdir && mkdir enrichTF.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=enrichTF.buildbin-libdir enrichTF_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL enrichTF_1.6.0.zip && rm enrichTF_1.6.0.tar.gz enrichTF_1.6.0.zip
###
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                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1003k  100 1003k    0     0  33.9M      0 --:--:-- --:--:-- --:--:-- 35.0M

install for i386

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

    GeneOntology                            html  
    MotifsInRegions                         html  
    Pipelines                               html  
    RegionConnectTargetGene                 html  
    SingleSampleReport                      html  
    TFsEnrichInRegions                      html  
    TissueOpennessConserve                  html  
    TissueOpennessSpecificity               html  
    UnzipAndMergeBed                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in options(stringsAsFactors = TRUE) :
  'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
** testing if installed package can be loaded from final location
Warning in options(stringsAsFactors = TRUE) :
  'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'enrichTF' ...
** testing if installed package can be loaded
Warning in options(stringsAsFactors = TRUE) :
  'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
* MD5 sums
packaged installation of 'enrichTF' as enrichTF_1.6.0.zip
* DONE (enrichTF)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'enrichTF' successfully unpacked and MD5 sums checked