BioC 3.3: CHECK report for scsR on linux2.bioconductor.org

Package: scsR

Version: 1.7.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings scsR_1.7.0.tar.gz

StartedAt: 2015-10-27 07:54:22 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:56:35 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 132.8 seconds

RetCode: 0

Status:  OK

CheckDir: scsR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings scsR_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/scsR.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.7.0’
* 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’
Undefined global functions or variables:
  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 ... [46s/45s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 19.678  0.442  19.996
* 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-3.3-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	0.321	0.004	0.322
add_seed	0.383	0.003	0.385
benchmark_shared_hits	2.977	0.035	2.999
bydf	0.467	0.007	0.474
check_consistency	1.404	0.032	1.435
compare_sorted_geneSets	19.678	0.442	19.996
create_sd_matrix	0.253	0.008	0.259
delColDf	0.217	0.004	0.221
delete_undefined_rows	0.478	0.000	0.477
enrichment_geneSet	0.370	0.003	0.373
enrichment_heatmap	0.326	0.004	0.330
get_sd_quant	1.052	0.020	1.072
get_seed_oligos_df	1.023	0.022	1.036
intersectAll	0.002	0.000	0.002
launch_RSA	0.529	0.016	0.542
median_replicates	0.993	0.037	1.030
plot_screen_hits	2.087	0.049	2.106
plot_seeds_methods	2.750	0.041	2.715
randomSortOnVal	0.176	0.008	0.184
randomizeInner	0.228	0.012	0.239
removeSharedOffTargets	0.624	0.000	0.619
renameColDf	0.214	0.000	0.214
replace_non_null_elements	0.280	0.000	0.279
seed_correction	0.598	0.012	0.604
seed_correction_pooled	0.593	0.012	0.605
seed_removal	0.334	0.004	0.335
seeds_analysis	1.247	0.031	1.259
sortInner	0.262	0.014	0.272
split_df	0.213	0.000	0.213
transcribe_seqs	0.300	0.004	0.303