BioC 3.5: CHECK report for scsR on oaxaca

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: 2017-03-04 08:50:36 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 08:53:18 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 161.8 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 --no-vignettes --timings scsR_1.11.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/scsR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 19.997  1.147  21.401
* 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	0.907	0.055	0.973
add_seed	0.250	0.009	0.259
benchmark_shared_hits	2.743	0.169	2.899
bydf	0.402	0.017	0.418
check_consistency	2.244	0.053	2.296
compare_sorted_geneSets	19.997	1.147	21.401
create_sd_matrix	0.433	0.023	0.640
delColDf	0.252	0.008	0.278
delete_undefined_rows	0.703	0.021	0.761
enrichment_geneSet	0.485	0.021	0.513
enrichment_heatmap	0.394	0.015	0.414
get_sd_quant	1.322	0.077	1.590
get_seed_oligos_df	0.903	0.048	1.010
intersectAll	0.002	0.000	0.002
launch_RSA	0.524	0.026	0.574
median_replicates	1.029	0.051	1.123
plot_screen_hits	3.356	0.209	3.990
plot_seeds_methods	2.530	0.166	2.710
randomSortOnVal	0.214	0.014	0.238
randomizeInner	0.269	0.014	0.322
removeSharedOffTargets	0.863	0.036	0.902
renameColDf	0.173	0.008	0.182
replace_non_null_elements	0.229	0.012	0.241
seed_correction	0.570	0.030	0.597
seed_correction_pooled	0.641	0.038	0.676
seed_removal	0.450	0.024	0.474
seeds_analysis	1.702	0.098	1.939
sortInner	0.343	0.019	0.361
split_df	0.282	0.014	0.296
transcribe_seqs	0.458	0.025	0.519