Package: scsR

Version: 1.19.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scsR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scsR_1.19.0.tar.gz

StartedAt: 2019-04-09 03:38:02 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:40:53 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 171.1 seconds

RetCode: 0

Status:  OK

CheckDir: scsR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scsR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scsR_1.19.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/scsR.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scsR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scsR’ version ‘1.19.0’
* 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 for sufficient/correct file permissions ... 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
* 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
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 22.476  1.471  23.939
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/scsR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL scsR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘scsR’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (scsR)

name	user	system	elapsed
add_rank_col	0.636	0.045	0.682
add_seed	0.219	0.009	0.232
benchmark_shared_hits	2.232	0.153	2.413
bydf	0.498	0.031	0.527
check_consistency	2.063	0.070	2.159
compare_sorted_geneSets	22.476	1.471	23.939
create_sd_matrix	0.395	0.023	0.422
delColDf	0.201	0.009	0.211
delete_undefined_rows	0.425	0.022	0.451
enrichment_geneSet	0.424	0.028	0.457
enrichment_heatmap	0.354	0.008	0.364
get_sd_quant	1.283	0.084	1.361
get_seed_oligos_df	1.078	0.063	1.139
intersectAll	0.001	0.000	0.002
launch_RSA	0.512	0.028	0.541
median_replicates	0.838	0.042	0.890
plot_screen_hits	2.415	0.152	2.560
plot_seeds_methods	3.174	0.227	3.393
randomSortOnVal	0.264	0.010	0.282
randomizeInner	0.250	0.012	0.262
removeSharedOffTargets	0.864	0.036	0.904
renameColDf	0.208	0.008	0.219
replace_non_null_elements	0.234	0.009	0.244
seed_correction	0.698	0.037	0.736
seed_correction_pooled	0.683	0.038	0.718
seed_removal	0.525	0.022	0.551
seeds_analysis	1.884	0.115	1.992
sortInner	0.343	0.015	0.361
split_df	0.314	0.012	0.330
transcribe_seqs	0.414	0.018	0.431