BioC 3.3: CHECK report for scsR on morelia

Package: scsR

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scsR_1.7.0.tar.gz

StartedAt: 2015-10-22 11:05:12 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 11:07:31 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 138.1 seconds

RetCode: 0

Status:  OK

CheckDir: scsR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scsR_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/scsR.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.7.0’
* 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 ... [8s/9s] 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’
Undefined global functions or variables:
  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 ... [37s/38s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 14.881  0.786  16.327
* 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-3.3-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	0.317	0.023	0.339
add_seed	0.277	0.011	0.289
benchmark_shared_hits	2.285	0.099	2.383
bydf	0.394	0.024	0.417
check_consistency	1.447	0.044	1.493
compare_sorted_geneSets	14.881	0.786	16.327
create_sd_matrix	0.279	0.014	0.293
delColDf	0.202	0.009	0.211
delete_undefined_rows	0.350	0.013	0.363
enrichment_geneSet	0.396	0.014	0.409
enrichment_heatmap	0.340	0.014	0.355
get_sd_quant	0.965	0.061	1.025
get_seed_oligos_df	0.657	0.041	0.696
intersectAll	0.001	0.000	0.001
launch_RSA	0.337	0.017	0.354
median_replicates	0.706	0.052	0.758
plot_screen_hits	1.210	0.077	1.285
plot_seeds_methods	1.725	0.226	2.456
randomSortOnVal	0.179	0.007	0.187
randomizeInner	0.174	0.006	0.180
removeSharedOffTargets	0.632	0.026	0.658
renameColDf	0.173	0.006	0.178
replace_non_null_elements	0.180	0.005	0.185
seed_correction	0.439	0.019	0.457
seed_correction_pooled	0.427	0.020	0.447
seed_removal	0.326	0.011	0.336
seeds_analysis	1.105	0.055	1.159
sortInner	0.224	0.014	0.237
split_df	0.217	0.007	0.225
transcribe_seqs	0.249	0.010	0.260