BioC 3.1: CHECK report for scsR on zin2

Package: scsR

Version: 1.4.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings scsR_1.4.0.tar.gz

StartedAt: 2015-10-09 05:21:15 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:23:17 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 121.5 seconds

RetCode: 0

Status:  OK

CheckDir: scsR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings scsR_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-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 ‘1.4.0’
* 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/8s] 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 ... [37s/36s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 14.925  0.319   15.16
* 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-3.1-bioc/meat/scsR.Rcheck/00check.log’
for details.

* installing *source* package ‘scsR’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (scsR)

name	user	system	elapsed
add_rank_col	0.290	0.012	0.315
add_seed	0.190	0.004	0.193
benchmark_shared_hits	2.307	0.041	2.345
bydf	0.354	0.004	0.357
check_consistency	1.528	0.012	1.538
compare_sorted_geneSets	14.925	0.319	15.160
create_sd_matrix	0.276	0.004	0.279
delColDf	0.202	0.000	0.201
delete_undefined_rows	0.451	0.000	0.451
enrichment_geneSet	0.405	0.000	0.405
enrichment_heatmap	0.357	0.000	0.357
get_sd_quant	1.009	0.015	1.019
get_seed_oligos_df	0.671	0.017	0.682
intersectAll	0.001	0.000	0.002
launch_RSA	0.353	0.008	0.359
median_replicates	0.666	0.016	0.687
plot_screen_hits	1.347	0.036	1.372
plot_seeds_methods	1.637	0.089	1.701
randomSortOnVal	0.193	0.000	0.200
randomizeInner	0.192	0.004	0.196
removeSharedOffTargets	0.681	0.012	0.691
renameColDf	0.193	0.000	0.193
replace_non_null_elements	0.196	0.000	0.196
seed_correction	0.410	0.008	0.416
seed_correction_pooled	0.413	0.004	0.414
seed_removal	0.359	0.008	0.365
seeds_analysis	1.328	0.017	1.335
sortInner	0.240	0.008	0.247
split_df	0.247	0.000	0.247
transcribe_seqs	0.269	0.000	0.268