Package: StarBioTrek

Version: 1.6.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:StarBioTrek.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings StarBioTrek_1.6.0.tar.gz

StartedAt: 2018-10-17 05:03:05 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 05:10:56 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 470.6 seconds

RetCode: 0

Status:  OK

CheckDir: StarBioTrek.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:StarBioTrek.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings StarBioTrek_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/StarBioTrek.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'StarBioTrek/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'StarBioTrek' version '1.6.0'
* 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 'StarBioTrek' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
* 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
getKEGGdata: no visible binding for global variable 'Carbohydrate'
getKEGGdata: no visible binding for global variable 'Energy'
getKEGGdata: no visible binding for global variable 'Lipid'
getKEGGdata: no visible binding for global variable 'Aminoacid'
getKEGGdata: no visible binding for global variable 'Glybio_met'
getKEGGdata: no visible binding for global variable 'Cofa_vita_met'
getKEGGdata: no visible binding for global variable 'Transcription'
getKEGGdata: no visible binding for global variable 'Translation'
getKEGGdata: no visible binding for global variable
  'Folding_sorting_and_degradation'
getKEGGdata: no visible binding for global variable
  'Replication_and_repair'
getKEGGdata: no visible binding for global variable
  'Signal_transduction'
getKEGGdata: no visible binding for global variable
  'Signaling_molecules_and_interaction'
getKEGGdata: no visible binding for global variable
  'Transport_and_catabolism'
getKEGGdata: no visible binding for global variable
  'Cell_growth_and_death'
getKEGGdata: no visible binding for global variable
  'Cellular_community'
getKEGGdata: no visible binding for global variable 'Immune_system'
getKEGGdata: no visible binding for global variable 'Endocrine_system'
getKEGGdata: no visible binding for global variable
  'Circulatory_system'
getKEGGdata: no visible binding for global variable 'Digestive_system'
getKEGGdata: no visible binding for global variable 'Excretory_system'
getKEGGdata: no visible binding for global variable 'Nervous_system'
getKEGGdata: no visible binding for global variable 'Sensory_system'
svm_classification: no visible binding for global variable 'Target'
Undefined global functions or variables:
  Aminoacid Carbohydrate Cell_growth_and_death Cellular_community
  Circulatory_system Cofa_vita_met Digestive_system Endocrine_system
  Energy Excretory_system Folding_sorting_and_degradation Glybio_met
  Immune_system Lipid Nervous_system Replication_and_repair
  Sensory_system Signal_transduction
  Signaling_molecules_and_interaction Target Transcription Translation
  Transport_and_catabolism
* 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
IPPI        18.47   1.59   20.09
getNETdata  14.28   3.68   18.39
getKEGGdata  4.06   0.28    6.72
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
IPPI        14.82   0.38   15.20
getNETdata   9.62   3.47   13.54
getKEGGdata  3.89   0.10    6.54
* 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-3.7-bioc/meat/StarBioTrek.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/StarBioTrek_1.6.0.tar.gz && rm -rf StarBioTrek.buildbin-libdir && mkdir StarBioTrek.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=StarBioTrek.buildbin-libdir StarBioTrek_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL StarBioTrek_1.6.0.zip && rm StarBioTrek_1.6.0.tar.gz StarBioTrek_1.6.0.zip
###
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                                 Dload  Upload   Total   Spent    Left  Speed

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100 6760k  100 6760k    0     0  55.0M      0 --:--:-- --:--:-- --:--:-- 58.9M

install for i386

* installing *source* package 'StarBioTrek' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'StarBioTrek'
    finding HTML links ... done
    Data_CANCER_normUQ_filt                 html  
    GE_matrix                               html  
    IPPI                                    html  
    SelectedSample                          html  
    StarBioTrek                             html  
    average                                 html  
    ds_score_crtlk                          html  
    euc_dist_crtlk                          html  
    getKEGGdata                             html  
    getNETdata                              html  
    list_path_net                           html  
    list_path_plot                          html  
    matrix_plot                             html  
    netw                                    html  
    norm                                    html  
    path                                    html  
    path_net                                html  
    plotting_cross_talk                     html  
    proc_path                               html  
    process_matrix                          html  
    score_euc_dist                          html  
    select_class                            html  
    st_dv                                   html  
    svm_classification                      html  
    tumo                                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'StarBioTrek' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'StarBioTrek' as StarBioTrek_1.6.0.zip
* DONE (StarBioTrek)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'StarBioTrek' successfully unpacked and MD5 sums checked
In R CMD INSTALL