BioC 3.5: CHECK report for scsR on toluca2

Package: scsR

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scsR_1.11.0.tar.gz

StartedAt: 2017-04-23 09:39:06 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 09:42:18 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 191.8 seconds

RetCode: 0

Status:  OK

CheckDir: scsR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scsR_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/scsR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.11.0’
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 20.723  1.115  34.538
benchmark_shared_hits    2.754  0.182   5.066
* 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-3.5-bioc/meat/scsR.Rcheck/00check.log’
for details.

* installing *source* package ‘scsR’ ...
** R
** data
** inst
** preparing 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	0.947	0.064	1.680
add_seed	0.246	0.013	0.300
benchmark_shared_hits	2.754	0.182	5.066
bydf	0.459	0.024	0.792
check_consistency	2.246	0.059	3.227
compare_sorted_geneSets	20.723	1.115	34.538
create_sd_matrix	0.403	0.021	0.714
delColDf	0.246	0.010	0.298
delete_undefined_rows	0.688	0.027	0.819
enrichment_geneSet	0.467	0.020	0.498
enrichment_heatmap	0.437	0.013	0.452
get_sd_quant	1.344	0.064	1.439
get_seed_oligos_df	0.936	0.040	1.012
intersectAll	0.002	0.000	0.002
launch_RSA	0.464	0.019	0.491
median_replicates	1.013	0.047	1.093
plot_screen_hits	3.105	0.162	3.333
plot_seeds_methods	2.450	0.139	2.701
randomSortOnVal	0.236	0.008	0.245
randomizeInner	0.228	0.007	0.235
removeSharedOffTargets	0.862	0.024	0.886
renameColDf	0.229	0.010	0.239
replace_non_null_elements	0.250	0.008	0.260
seed_correction	0.583	0.019	0.612
seed_correction_pooled	0.572	0.025	0.611
seed_removal	0.515	0.021	0.550
seeds_analysis	1.684	0.076	2.061
sortInner	0.335	0.015	0.483
split_df	0.324	0.013	0.418
transcribe_seqs	0.480	0.022	0.766