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: 2015-10-27 12:08:31 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 12:12:02 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 210.8 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 ... [15s/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 ... 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 22.109  1.262  24.222
* 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	0.479	0.035	0.524
add_seed	0.264	0.011	0.276
benchmark_shared_hits	3.091	0.188	3.323
bydf	0.499	0.022	0.534
check_consistency	2.043	0.071	2.116
compare_sorted_geneSets	22.109	1.262	24.222
create_sd_matrix	0.366	0.020	0.390
delColDf	0.283	0.020	0.302
delete_undefined_rows	0.510	0.024	0.534
enrichment_geneSet	0.530	0.029	0.559
enrichment_heatmap	0.478	0.015	0.493
get_sd_quant	1.458	0.090	1.593
get_seed_oligos_df	0.994	0.068	1.086
intersectAll	0.002	0.000	0.002
launch_RSA	0.498	0.028	0.536
median_replicates	1.048	0.088	1.138
plot_screen_hits	2.011	0.140	2.205
plot_seeds_methods	2.486	0.319	2.828
randomSortOnVal	0.245	0.008	0.254
randomizeInner	0.250	0.008	0.259
removeSharedOffTargets	1.032	0.034	1.077
renameColDf	0.258	0.006	0.264
replace_non_null_elements	0.262	0.007	0.270
seed_correction	0.608	0.033	0.658
seed_correction_pooled	0.581	0.035	0.640
seed_removal	0.522	0.024	0.562
seeds_analysis	2.105	0.122	2.303
sortInner	0.326	0.024	0.346
split_df	0.311	0.011	0.327
transcribe_seqs	0.386	0.017	0.414