BioC 2.14: CHECK report for scsR on petty

Package: scsR

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch scsR_1.0.0.tar.gz

StartedAt: 2014-10-08 00:04:59 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:11:28 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 388.6 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 --no-multiarch scsR_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/scsR.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.0.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘Biostrings’ ‘IRanges’ ‘plyr’ ‘STRINGdb’ ‘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 ... [23s/31s] 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 ... OK
* 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 ... [95s/103s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 32.716  1.761  36.563
benchmark_shared_hits    8.838  0.376   9.840
seeds_analysis           4.568  0.271   5.118
plot_screen_hits         4.151  0.280   5.340
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.866	0.057	1.116
add_seed	0.626	0.018	0.657
benchmark_shared_hits	8.838	0.376	9.840
bydf	0.812	0.045	0.862
check_consistency	3.970	0.117	4.258
compare_sorted_geneSets	32.716	1.761	36.563
create_sd_matrix	0.835	0.047	0.899
delColDf	0.281	0.018	0.306
delete_undefined_rows	0.811	0.038	0.876
enrichment_geneSet	0.902	0.040	0.974
enrichment_heatmap	0.498	0.028	0.538
get_sd_quant	2.717	0.173	3.114
get_seed_oligos_df	2.168	0.137	2.462
intersectAll	0.002	0.000	0.003
launch_RSA	0.971	0.059	1.106
median_replicates	1.825	0.156	2.231
plot_screen_hits	4.151	0.280	5.340
plot_seeds_methods	3.215	0.295	3.911
randomSortOnVal	0.312	0.017	0.343
randomizeInner	0.317	0.019	0.346
removeSharedOffTargets	2.564	0.151	2.893
renameColDf	0.299	0.016	0.329
replace_non_null_elements	0.307	0.014	0.324
seed_correction	1.148	0.076	1.335
seed_removal	0.987	0.053	1.094
seeds_analysis	4.568	0.271	5.118
sortInner	0.556	0.047	0.628
split_df	0.505	0.027	0.565
transcribe_seqs	0.656	0.043	0.737