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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PrInCE.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings PrInCE_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/PrInCE.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 'PrInCE/DESCRIPTION' ... OK
* this is package 'PrInCE' version '1.8.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .lintr
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'PrInCE' 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
calculate_features: no visible global function definition for
  'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
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 ... WARNING
Undocumented arguments in documentation object 'calculate_autocorrelation'
  'min_replicates'

Undocumented arguments in documentation object 'calculate_features'
  'n_pairs'

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 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
predict_ensemble    5.36   0.26    5.63
calculate_precision 4.98   0.23    5.22
PrInCE              5.00   0.18    5.19
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
PrInCE              5.39   0.11    8.39
calculate_precision 5.13   0.14    5.27
predict_ensemble    5.03   0.14    5.17
* 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 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/PrInCE.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/PrInCE_1.8.0.tar.gz && rm -rf PrInCE.buildbin-libdir && mkdir PrInCE.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PrInCE.buildbin-libdir PrInCE_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL PrInCE_1.8.0.zip && rm PrInCE_1.8.0.tar.gz PrInCE_1.8.0.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
 12 1811k   12  221k    0     0   738k      0  0:00:02 --:--:--  0:00:02  737k
100 1811k  100 1811k    0     0  2188k      0 --:--:-- --:--:-- --:--:-- 2187k

install for i386

* installing *source* package 'PrInCE' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
Loading required namespace: PrInCE
Registered S3 method overwritten by 'quantmod':
  method            from
  as.zoo.data.frame zoo 
*** installing help indices
  converting help for package 'PrInCE'
    finding HTML links ... done
    PrInCE                                  html  
    finding level-2 HTML links ... done

    adjacency_matrix_from_data_frame        html  
    adjacency_matrix_from_list              html  
    aic                                     html  
    build_gaussians                         html  
    calculate_autocorrelation               html  
    calculate_features                      html  
    calculate_precision                     html  
    check_gaussians                         html  
    choose_gaussians                        html  
    clean_profile                           html  
    clean_profiles                          html  
    co_apex                                 html  
    concatenate_features                    html  
    detect_complexes                        html  
    filter_profiles                         html  
    fit_curve                               html  
    fit_gaussians                           html  
    gold_standard                           html  
    impute_neighbors                        html  
    is_unweighted                           html  
    is_weighted                             html  
    kristensen                              html  
    kristensen_gaussians                    html  
    make_feature_from_data_frame            html  
    make_feature_from_expression            html  
    make_initial_conditions                 html  
    make_labels                             html  
    match_matrix_dimensions                 html  
    predict_ensemble                        html  
    predict_interactions                    html  
    replace_missing_data                    html  
    scott                                   html  
    scott_gaussians                         html  
    threshold_precision                     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 'PrInCE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PrInCE' as PrInCE_1.8.0.zip
* DONE (PrInCE)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'PrInCE' successfully unpacked and MD5 sums checked