BioC 3.0: CHECK report for scsR on perceval

Package: scsR

Version: 1.3.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch scsR_1.3.2.tar.gz

StartedAt: 2015-04-10 06:12:33 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 06:17:54 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 321.2 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_1.3.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/scsR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.3.2’
* 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 ... [26s/28s] 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 ... [75s/75s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 30.556  1.578  32.325
benchmark_shared_hits    5.077  0.244   5.315
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.833	0.055	0.888
add_seed	0.236	0.010	0.246
benchmark_shared_hits	5.077	0.244	5.315
bydf	0.524	0.025	0.551
check_consistency	2.820	0.089	2.929
compare_sorted_geneSets	30.556	1.578	32.325
create_sd_matrix	0.386	0.025	0.412
delColDf	0.244	0.011	0.255
delete_undefined_rows	0.560	0.037	0.601
enrichment_geneSet	0.509	0.042	0.554
enrichment_heatmap	0.457	0.021	0.479
get_sd_quant	1.478	0.111	1.604
get_seed_oligos_df	1.163	0.079	1.241
intersectAll	0.004	0.000	0.004
launch_RSA	0.627	0.041	0.667
median_replicates	1.137	0.111	1.462
plot_screen_hits	2.504	0.186	2.688
plot_seeds_methods	3.252	0.415	3.620
randomSortOnVal	0.249	0.017	0.265
randomizeInner	0.232	0.010	0.242
removeSharedOffTargets	1.037	0.044	1.074
renameColDf	0.247	0.032	0.279
replace_non_null_elements	0.244	0.024	0.268
seed_correction	0.653	0.055	0.698
seed_correction_pooled	0.713	0.060	0.762
seed_removal	0.573	0.044	0.612
seeds_analysis	2.274	0.182	2.442
sortInner	0.416	0.049	0.528
split_df	0.315	0.027	0.371
transcribe_seqs	0.440	0.035	0.546