BioC 3.1: CHECK report for scsR on morelia

Package: scsR

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scsR_1.4.0.tar.gz

StartedAt: 2015-10-09 06:07:50 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 06:10:54 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 184.1 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/scsR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.4.0’
* 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/13s] 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 ... [50s/50s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 19.303  1.854  21.279
* 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-3.1-bioc/meat/scsR.Rcheck/00check.log’
for details.

* installing *source* package ‘scsR’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (scsR)

name	user	system	elapsed
add_rank_col	0.371	0.017	0.386
add_seed	0.267	0.010	0.281
benchmark_shared_hits	2.711	0.181	2.878
bydf	0.406	0.014	0.418
check_consistency	1.436	0.062	1.497
compare_sorted_geneSets	19.303	1.854	21.279
create_sd_matrix	0.319	0.028	0.345
delColDf	0.253	0.008	0.264
delete_undefined_rows	0.415	0.035	0.451
enrichment_geneSet	0.526	0.072	0.599
enrichment_heatmap	0.431	0.013	0.449
get_sd_quant	1.237	0.104	1.342
get_seed_oligos_df	1.132	0.086	1.215
intersectAll	0.002	0.000	0.002
launch_RSA	0.434	0.063	0.496
median_replicates	0.752	0.061	0.816
plot_screen_hits	1.891	0.185	2.086
plot_seeds_methods	2.460	0.390	2.857
randomSortOnVal	0.189	0.009	0.199
randomizeInner	0.268	0.034	0.304
removeSharedOffTargets	0.799	0.045	0.844
renameColDf	0.227	0.047	0.282
replace_non_null_elements	0.222	0.007	0.231
seed_correction	0.565	0.040	0.629
seed_correction_pooled	0.539	0.034	0.578
seed_removal	0.486	0.043	0.536
seeds_analysis	1.782	0.177	1.983
sortInner	0.263	0.018	0.280
split_df	0.300	0.024	0.328
transcribe_seqs	0.315	0.021	0.334