BioC 3.2: CHECK report for scsR on oaxaca

Package: scsR

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scsR_1.6.0.tar.gz

StartedAt: 2016-04-23 04:14:30 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 04:17:39 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 189.0 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/scsR.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.6.0’
* 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 ... [13s/14s] 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
enrichment_heatmap: no visible global function definition for
  ‘heatmap.2’
* 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 ... [51s/55s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 20.25  1.022  22.183
* 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-3.2-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	0.477	0.027	0.520
add_seed	0.451	0.011	0.471
benchmark_shared_hits	2.699	0.173	3.022
bydf	0.493	0.020	0.553
check_consistency	2.002	0.052	2.108
compare_sorted_geneSets	20.250	1.022	22.183
create_sd_matrix	0.377	0.019	0.395
delColDf	0.241	0.016	0.257
delete_undefined_rows	0.485	0.022	0.507
enrichment_geneSet	0.546	0.020	0.567
enrichment_heatmap	0.463	0.018	0.482
get_sd_quant	1.326	0.081	1.402
get_seed_oligos_df	0.935	0.059	0.988
intersectAll	0.002	0.000	0.001
launch_RSA	0.470	0.023	0.491
median_replicates	1.037	0.065	1.110
plot_screen_hits	2.012	0.118	2.168
plot_seeds_methods	2.460	0.309	2.783
randomSortOnVal	0.246	0.010	0.256
randomizeInner	0.245	0.011	0.256
removeSharedOffTargets	0.766	0.031	1.191
renameColDf	0.262	0.011	0.275
replace_non_null_elements	0.238	0.009	0.307
seed_correction	0.574	0.030	0.601
seed_correction_pooled	0.568	0.030	0.595
seed_removal	0.508	0.022	0.528
seeds_analysis	1.645	0.098	1.738
sortInner	0.311	0.021	0.329
split_df	0.298	0.011	0.308
transcribe_seqs	0.401	0.019	0.419