BioC 3.2: CHECK report for scsR on oaxaca

Package: scsR

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scsR_1.5.0.tar.gz

StartedAt: 2015-08-24 03:43:58 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 03:47:25 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 207.2 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 scsR_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/scsR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.5.0’
* 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 ... [13s/18s] 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 ... [54s/56s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 21.032  1.017  22.639
* 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	0.445	0.026	0.664
add_seed	0.441	0.008	0.466
benchmark_shared_hits	2.983	0.177	3.570
bydf	0.477	0.017	0.496
check_consistency	2.148	0.053	2.261
compare_sorted_geneSets	21.032	1.017	22.639
create_sd_matrix	0.369	0.016	0.386
delColDf	0.270	0.006	0.277
delete_undefined_rows	0.493	0.016	0.510
enrichment_geneSet	0.516	0.019	0.535
enrichment_heatmap	0.515	0.017	0.532
get_sd_quant	1.225	0.065	1.295
get_seed_oligos_df	1.065	0.055	1.179
intersectAll	0.002	0.000	0.002
launch_RSA	0.520	0.021	0.542
median_replicates	1.136	0.067	1.209
plot_screen_hits	2.251	0.120	2.378
plot_seeds_methods	2.705	0.252	2.964
randomSortOnVal	0.276	0.010	0.286
randomizeInner	0.278	0.007	0.286
removeSharedOffTargets	1.021	0.032	1.054
renameColDf	0.271	0.015	0.287
replace_non_null_elements	0.267	0.012	0.280
seed_correction	0.613	0.031	0.649
seed_correction_pooled	0.594	0.031	0.625
seed_removal	0.544	0.026	0.570
seeds_analysis	1.830	0.095	1.935
sortInner	0.349	0.025	0.375
split_df	0.322	0.015	0.337
transcribe_seqs	0.422	0.019	0.443