BioC 3.0: CHECK report for scsR on zin1

Package: scsR

Version: 1.3.2

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings scsR_1.3.2.tar.gz

StartedAt: 2015-04-10 04:12:27 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 04:15:30 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 182.9 seconds

RetCode: 0

Status:  OK

CheckDir: scsR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings scsR_1.3.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/scsR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.3.2’
* 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/14s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [48s/48s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 20.053  0.292  20.426
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-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	0.532	0.008	0.549
add_seed	0.208	0.000	0.207
benchmark_shared_hits	2.756	0.024	2.786
bydf	0.376	0.012	0.390
check_consistency	1.664	0.028	1.694
compare_sorted_geneSets	20.053	0.292	20.426
create_sd_matrix	0.292	0.008	0.301
delColDf	0.209	0.004	0.213
delete_undefined_rows	0.440	0.008	0.445
enrichment_geneSet	0.444	0.004	0.447
enrichment_heatmap	0.384	0.008	0.394
get_sd_quant	1.080	0.012	1.096
get_seed_oligos_df	0.892	0.008	0.898
intersectAll	0.004	0.000	0.001
launch_RSA	0.444	0.004	0.451
median_replicates	0.844	0.012	0.860
plot_screen_hits	1.896	0.024	1.925
plot_seeds_methods	2.148	0.068	2.221
randomSortOnVal	0.216	0.008	0.226
randomizeInner	0.248	0.000	0.246
removeSharedOffTargets	0.836	0.004	0.844
renameColDf	0.208	0.008	0.219
replace_non_null_elements	0.216	0.004	0.221
seed_correction	0.528	0.008	0.538
seed_correction_pooled	0.508	0.008	0.520
seed_removal	0.460	0.004	0.463
seeds_analysis	1.688	0.032	1.721
sortInner	0.276	0.012	0.289
split_df	0.276	0.004	0.283
transcribe_seqs	0.324	0.000	0.325