BioC 3.1: CHECK report for scsR on petty

Package: scsR

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scsR_1.4.0.tar.gz

StartedAt: 2015-10-09 01:54:04 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:58:53 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 288.8 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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/scsR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.4.0’
* 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 ... [20s/20s] 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 ... [82s/82s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 32.853  1.706  34.521
* 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-3.1-bioc/meat/scsR.Rcheck/00check.log’
for details.

* installing *source* package ‘scsR’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (scsR)

name	user	system	elapsed
add_rank_col	0.633	0.038	0.672
add_seed	0.354	0.013	0.367
benchmark_shared_hits	4.349	0.273	4.625
bydf	0.734	0.029	0.794
check_consistency	3.091	0.102	3.224
compare_sorted_geneSets	32.853	1.706	34.521
create_sd_matrix	0.443	0.023	0.462
delColDf	0.398	0.013	0.414
delete_undefined_rows	0.775	0.028	0.804
enrichment_geneSet	0.798	0.041	0.839
enrichment_heatmap	0.691	0.030	0.722
get_sd_quant	2.146	0.122	2.252
get_seed_oligos_df	1.765	0.098	1.849
intersectAll	0.002	0.000	0.002
launch_RSA	0.764	0.047	0.807
median_replicates	1.599	0.113	1.718
plot_screen_hits	2.933	0.194	3.093
plot_seeds_methods	3.765	0.483	4.148
randomSortOnVal	0.346	0.020	0.367
randomizeInner	0.362	0.020	0.382
removeSharedOffTargets	1.409	0.067	1.471
renameColDf	0.281	0.011	0.292
replace_non_null_elements	0.305	0.011	0.316
seed_correction	0.886	0.044	0.923
seed_correction_pooled	0.878	0.045	0.918
seed_removal	0.762	0.033	0.792
seeds_analysis	2.736	0.148	2.861
sortInner	0.471	0.035	0.500
split_df	0.486	0.015	0.500
transcribe_seqs	0.531	0.022	0.550