BioC 3.2: CHECK report for scsR on zin1

Package: scsR

Version: 1.6.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings scsR_1.6.0.tar.gz

StartedAt: 2016-04-23 05:14:38 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 05:16:47 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 129.0 seconds

RetCode: 0

Status:  OK

CheckDir: scsR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings scsR_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/scsR.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-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 ‘1.6.0’
* 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 ... [9s/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’
* 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 ... [40s/40s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 16.338  0.314  16.843
* 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
  ‘/home/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	0.374	0.012	0.399
add_seed	0.392	0.000	0.405
benchmark_shared_hits	2.229	0.024	2.344
bydf	0.360	0.011	0.385
check_consistency	1.628	0.012	1.719
compare_sorted_geneSets	16.338	0.314	16.843
create_sd_matrix	0.323	0.008	0.416
delColDf	0.221	0.004	0.225
delete_undefined_rows	0.433	0.000	0.432
enrichment_geneSet	0.458	0.004	0.463
enrichment_heatmap	0.404	0.008	0.447
get_sd_quant	1.128	0.016	1.202
get_seed_oligos_df	0.741	0.028	0.773
intersectAll	0.000	0.000	0.002
launch_RSA	0.401	0.008	0.410
median_replicates	0.751	0.020	0.770
plot_screen_hits	1.392	0.020	1.403
plot_seeds_methods	1.838	0.125	1.942
randomSortOnVal	0.228	0.000	0.228
randomizeInner	0.232	0.000	0.232
removeSharedOffTargets	0.791	0.020	0.810
renameColDf	0.221	0.008	0.228
replace_non_null_elements	0.241	0.004	0.244
seed_correction	0.470	0.008	0.476
seed_correction_pooled	0.466	0.004	0.468
seed_removal	0.359	0.004	0.362
seeds_analysis	1.292	0.013	1.296
sortInner	0.271	0.004	0.273
split_df	0.284	0.000	0.283
transcribe_seqs	0.323	0.004	0.325