BioC 3.2: CHECK report for scsR on perceval

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: 2015-11-10 09:20:30 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 09:23:58 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 207.7 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 scsR_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/scsR.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.6.0’
* 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 ... [14s/15s] 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 ... [57s/58s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 22.546  1.242   24.61
* 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	0.462	0.027	0.492
add_seed	0.279	0.010	0.291
benchmark_shared_hits	3.105	0.198	3.438
bydf	0.489	0.019	0.518
check_consistency	2.301	0.060	2.373
compare_sorted_geneSets	22.546	1.242	24.610
create_sd_matrix	0.362	0.019	0.389
delColDf	0.279	0.009	0.288
delete_undefined_rows	0.516	0.019	0.536
enrichment_geneSet	0.527	0.020	0.546
enrichment_heatmap	0.474	0.018	0.492
get_sd_quant	1.464	0.107	1.622
get_seed_oligos_df	1.010	0.082	1.126
intersectAll	0.002	0.001	0.002
launch_RSA	0.490	0.027	0.533
median_replicates	1.060	0.084	1.145
plot_screen_hits	2.021	0.147	2.240
plot_seeds_methods	2.518	0.360	2.915
randomSortOnVal	0.263	0.009	0.272
randomizeInner	0.265	0.010	0.277
removeSharedOffTargets	1.012	0.035	1.064
renameColDf	0.261	0.007	0.269
replace_non_null_elements	0.264	0.008	0.273
seed_correction	0.603	0.037	0.668
seed_correction_pooled	0.579	0.033	0.632
seed_removal	0.517	0.024	0.554
seeds_analysis	1.850	0.112	2.055
sortInner	0.338	0.023	0.357
split_df	0.304	0.011	0.319
transcribe_seqs	0.383	0.016	0.408