Package: scsR

Version: 1.14.0

Command: rm -rf scsR.buildbin-libdir scsR.Rcheck && mkdir scsR.buildbin-libdir scsR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.14.0.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.14.0.tar.gz

StartedAt: 2018-04-12 03:02:00 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:05:30 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 210.4 seconds

RetCode: 0

Status:  OK

CheckDir: scsR.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf scsR.buildbin-libdir scsR.Rcheck && mkdir scsR.buildbin-libdir scsR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.14.0.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/scsR.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'scsR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scsR' version '1.14.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'STRINGdb' 'BiocGenerics' 'Biostrings' 'IRanges' 'plyr' 'tcltk'
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 'scsR' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
OPIrsaScore : <anonymous>: no visible global function definition for
  'phyper'
enrichment_geneSet: no visible global function definition for 'phyper'
enrichment_heatmap: no visible global function definition for
  'heatmap.2'
get_seed_oligos_df: no visible global function definition for
  'txtProgressBar'
get_seed_oligos_df: no visible global function definition for
  'setTxtProgressBar'
get_seed_oligos_df: no visible global function definition for 'phyper'
get_seed_oligos_df: no visible global function definition for 'ks.test'
plot_seed_score_sd: no visible global function definition for 'lm'
plot_seed_score_sd: no visible global function definition for
  'cor.test'
seed_correction: no visible global function definition for
  'txtProgressBar'
seed_correction: no visible global function definition for
  'setTxtProgressBar'
seed_correction_pooled: no visible global function definition for
  'txtProgressBar'
seed_correction_pooled: no visible global function definition for
  'setTxtProgressBar'
seed_removal: no visible global function definition for
  'txtProgressBar'
seed_removal: no visible global function definition for
  'setTxtProgressBar'
seeds_analysis : <anonymous>: no visible global function definition for
  'ks.test'
seeds_analysis: no visible global function definition for 'phyper'
transcribe_seqs: no visible global function definition for
  'txtProgressBar'
transcribe_seqs: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  cor.test heatmap.2 ks.test lm phyper setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "cor.test", "ks.test", "lm", "phyper")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 14.11   0.19    14.3
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 17.09   0.14   17.25
* 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-3.6-bioc/meat/scsR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'scsR' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'scsR'
    finding HTML links ... done
    OPIrsa                                  html  
    OPIrsaScore                             html  
    add_rank_col                            html  
    add_seed                                html  
    benchmark_shared_hits                   html  
    bydf                                    html  
    check_consistency                       html  
    compare_sorted_geneSets                 html  
    create_sd_matrix                        html  
    delColDf                                html  
    delete_undefined_rows                   html  
    enrichment_geneSet                      html  
    enrichment_heatmap                      html  
    get_sd_quant                            html  
    get_seed_oligos_df                      html  
    intersectAll                            html  
    launch_RSA                              html  
    median_replicates                       html  
    miRBase_20                              html  
    plot_screen_hits                        html  
    plot_seeds_methods                      html  
    randomSortOnVal                         html  
    randomizeInner                          html  
    removeSharedOffTargets                  html  
    renameColDf                             html  
    replace_non_null_elements               html  
    seed_correction                         html  
    seed_correction_pooled                  html  
    seed_removal                            html  
    seeds_analysis                          html  
    sortInner                               html  
    split_df                                html  
    transcribe_seqs                         html  
    uuk_screen                              html  
    uuk_screen_dh                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'scsR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scsR' as scsR_1.14.0.zip
* DONE (scsR)
In R CMD INSTALL
In R CMD INSTALL