BioC 3.2: CHECK report for scsR on linux1.bioconductor.org

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: 2015-10-27 07:56:55 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:59:16 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 140.3 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 3.2.2 (2015-08-14)
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [45s/44s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 18.846  0.386  19.073
* 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	0.351	0.012	0.356
add_seed	0.439	0.003	0.441
benchmark_shared_hits	2.651	0.077	2.738
bydf	0.476	0.008	0.484
check_consistency	1.503	0.014	1.518
compare_sorted_geneSets	18.846	0.386	19.073
create_sd_matrix	0.359	0.000	0.357
delColDf	0.222	0.004	0.226
delete_undefined_rows	0.525	0.000	0.527
enrichment_geneSet	0.564	0.006	0.575
enrichment_heatmap	0.515	0.004	0.519
get_sd_quant	1.005	0.022	1.016
get_seed_oligos_df	0.754	0.006	0.747
intersectAll	0.001	0.000	0.001
launch_RSA	0.539	0.000	0.534
median_replicates	1.036	0.010	1.046
plot_screen_hits	1.839	0.025	1.832
plot_seeds_methods	2.375	0.034	2.338
randomSortOnVal	0.173	0.004	0.176
randomizeInner	0.169	0.008	0.177
removeSharedOffTargets	0.743	0.004	0.743
renameColDf	0.203	0.004	0.207
replace_non_null_elements	0.275	0.004	0.279
seed_correction	0.433	0.000	0.427
seed_correction_pooled	0.377	0.001	0.373
seed_removal	0.328	0.005	0.329
seeds_analysis	1.441	0.028	1.451
sortInner	0.221	0.013	0.230
split_df	0.196	0.004	0.200
transcribe_seqs	0.264	0.000	0.261