BioC 2.14: CHECK report for scsR on morelia

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 01:29:52 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:33:13 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 200.3 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-darwin13.1.0 (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 ... [14s/16s] 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 ... [54s/55s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 19.609  1.025  20.723
* 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	0.507	0.028	0.609
add_seed	0.362	0.010	0.372
benchmark_shared_hits	4.183	0.216	4.416
bydf	0.536	0.028	0.562
check_consistency	2.261	0.058	2.322
compare_sorted_geneSets	19.609	1.025	20.723
create_sd_matrix	0.341	0.022	0.362
delColDf	0.377	0.016	0.392
delete_undefined_rows	0.500	0.021	0.522
enrichment_geneSet	0.418	0.027	0.446
enrichment_heatmap	0.335	0.016	0.353
get_sd_quant	1.518	0.097	1.601
get_seed_oligos_df	1.255	0.081	1.325
intersectAll	0.001	0.000	0.001
launch_RSA	0.564	0.034	0.594
median_replicates	1.090	0.070	1.162
plot_screen_hits	2.489	0.163	2.681
plot_seeds_methods	1.848	0.154	1.996
randomSortOnVal	0.205	0.015	0.220
randomizeInner	0.198	0.012	0.210
removeSharedOffTargets	1.485	0.086	1.562
renameColDf	0.190	0.009	0.199
replace_non_null_elements	0.204	0.008	0.213
seed_correction	0.689	0.041	0.725
seed_removal	0.558	0.029	0.584
seeds_analysis	2.654	0.157	2.791
sortInner	0.344	0.023	0.364
split_df	0.303	0.013	0.316
transcribe_seqs	0.430	0.022	0.451