BioC 2.14: CHECK report for scsR on zin2

Package: scsR

Version: 1.0.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings scsR_1.0.0.tar.gz

StartedAt: 2014-10-08 02:42:02 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 02:44:30 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 147.9 seconds

RetCode: 0

Status:  OK

CheckDir: scsR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings scsR_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/scsR.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.0.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘Biostrings’ ‘IRanges’ ‘plyr’ ‘STRINGdb’ ‘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 ... [10s/11s] 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 ... OK
* 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 ... [41s/42s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 15.165   0.26  15.455
* 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.14-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	0.396	0.012	0.412
add_seed	0.328	0.004	0.334
benchmark_shared_hits	3.652	0.048	3.707
bydf	0.428	0.012	0.441
check_consistency	1.740	0.016	1.760
compare_sorted_geneSets	15.165	0.260	15.455
create_sd_matrix	0.272	0.004	0.277
delColDf	0.312	0.012	0.325
delete_undefined_rows	0.424	0.000	0.426
enrichment_geneSet	0.344	0.000	0.343
enrichment_heatmap	0.280	0.000	0.279
get_sd_quant	1.248	0.016	1.264
get_seed_oligos_df	0.972	0.032	1.007
intersectAll	0	0	0
launch_RSA	0.488	0.016	0.502
median_replicates	0.780	0.024	0.804
plot_screen_hits	1.813	0.064	1.878
plot_seeds_methods	1.512	0.040	1.555
randomSortOnVal	0.168	0.000	0.167
randomizeInner	0.168	0.004	0.169
removeSharedOffTargets	1.140	0.028	1.170
renameColDf	0.164	0.000	0.166
replace_non_null_elements	0.168	0.000	0.169
seed_correction	0.552	0.008	0.565
seed_removal	0.464	0.004	0.469
seeds_analysis	2.080	0.036	2.118
sortInner	0.256	0.016	0.273
split_df	0.240	0.004	0.246
transcribe_seqs	0.304	0.012	0.318