Package: polyester

Version: 1.22.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:polyester.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings polyester_1.22.0.tar.gz

StartedAt: 2020-04-15 05:35:31 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:38:31 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 180.5 seconds

RetCode: 0

Status:  OK

CheckDir: polyester.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:polyester.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings polyester_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/polyester.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'polyester/DESCRIPTION' ... OK
* this is package 'polyester' version '1.22.0'
* 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 'polyester' 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
Namespace in Imports field not imported from: 'zlibbioc'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
add_platform_error: no visible binding for global variable 'model1'
add_platform_error: no visible binding for global variable 'model2'
add_platform_error: no visible binding for global variable 'model4'
add_platform_error: no visible binding for global variable 'model5'
add_platform_error: no visible binding for global variable 'model3'
add_platform_error: no visible binding for global variable 'model6'
add_platform_error: no visible binding for global variable 'model7'
generate_fragments: no visible binding for global variable
  'empirical_density'
generate_fragments: no visible binding for global variable 'rnaf'
generate_fragments: no visible binding for global variable 'cdnaf'
Undefined global functions or variables:
  cdnaf empirical_density model1 model2 model3 model4 model5 model6
  model7 rnaf
* 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 or elapsed time > 5s
                     user system elapsed
add_gc_bias         13.38   0.08   14.14
create_read_numbers  8.53   0.86    9.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
add_gc_bias         13.60   0.14   13.73
create_read_numbers 10.73   0.25   10.99
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/polyester.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/polyester_1.22.0.tar.gz && rm -rf polyester.buildbin-libdir && mkdir polyester.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=polyester.buildbin-libdir polyester_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL polyester_1.22.0.zip && rm polyester_1.22.0.tar.gz polyester_1.22.0.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
100 1870k  100 1870k    0     0  33.4M      0 --:--:-- --:--:-- --:--:-- 35.8M

install for i386

* installing *source* package 'polyester' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'polyester'
    finding HTML links ... done
    NB                                      html  
    add_error                               html  
    add_gc_bias                             html  
    add_platform_error                      html  
    cdnaf                                   html  
    count_transcripts                       html  
    create_read_numbers                     html  
    empirical_density                       html  
    finding level-2 HTML links ... done

    fpkm_to_counts                          html  
    generate_fragments                      html  
    getAttributeField                       html  
    get_params                              html  
    get_reads                               html  
    gtf_dataframe                           html  
    loessfit1                               html  
    loessfit2                               html  
    loessfit3                               html  
    loessfit4                               html  
    loessfit5                               html  
    loessfit6                               html  
    loessfit7                               html  
    model1                                  html  
    model2                                  html  
    model3                                  html  
    model4                                  html  
    model5                                  html  
    model6                                  html  
    model7                                  html  
    polyester                               html  
    reverse_complement                      html  
    rnaf                                    html  
    seq_gtf                                 html  
    simulate_experiment                     html  
    simulate_experiment_countmat            html  
    simulate_experiment_empirical           html  
    write_reads                             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 'polyester' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'polyester' as polyester_1.22.0.zip
* DONE (polyester)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'polyester' successfully unpacked and MD5 sums checked