BioC 3.5: CHECK report for scsR on malbec2

Package: scsR

Version: 1.12.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings scsR_1.12.0.tar.gz

StartedAt: 2017-08-16 02:10:37 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:12:45 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 128.2 seconds

RetCode: 0

Status:  OK

CheckDir: scsR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings scsR_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/scsR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.12.0’
* 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 ... 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
OPIrsaScore : <anonymous>: no visible global function definition for
  ‘phyper’
enrichment_geneSet: no visible global function definition for ‘phyper’
enrichment_heatmap: no visible global function definition for
  ‘heatmap.2’
get_seed_oligos_df: no visible global function definition for
  ‘txtProgressBar’
get_seed_oligos_df: no visible global function definition for
  ‘setTxtProgressBar’
get_seed_oligos_df: no visible global function definition for ‘phyper’
get_seed_oligos_df: no visible global function definition for ‘ks.test’
plot_seed_score_sd: no visible global function definition for ‘lm’
plot_seed_score_sd: no visible global function definition for
  ‘cor.test’
seed_correction: no visible global function definition for
  ‘txtProgressBar’
seed_correction: no visible global function definition for
  ‘setTxtProgressBar’
seed_correction_pooled: no visible global function definition for
  ‘txtProgressBar’
seed_correction_pooled: no visible global function definition for
  ‘setTxtProgressBar’
seed_removal: no visible global function definition for
  ‘txtProgressBar’
seed_removal: no visible global function definition for
  ‘setTxtProgressBar’
seeds_analysis : <anonymous>: no visible global function definition for
  ‘ks.test’
seeds_analysis: no visible global function definition for ‘phyper’
transcribe_seqs: no visible global function definition for
  ‘txtProgressBar’
transcribe_seqs: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  cor.test heatmap.2 ks.test lm phyper setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "cor.test", "ks.test", "lm", "phyper")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 16.276  0.384  16.774
* 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-3.5-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	0.904	0.028	0.933
add_seed	0.196	0.000	0.195
benchmark_shared_hits	2.208	0.036	2.250
bydf	0.328	0.000	0.326
check_consistency	1.816	0.024	1.844
compare_sorted_geneSets	16.276	0.384	16.774
create_sd_matrix	0.632	0.016	0.645
delColDf	0.188	0.004	0.192
delete_undefined_rows	0.320	0.000	0.319
enrichment_geneSet	0.564	0.004	0.569
enrichment_heatmap	0.604	0.000	0.601
get_sd_quant	1.132	0.008	1.156
get_seed_oligos_df	0.724	0.016	0.739
intersectAll	0.000	0.000	0.002
launch_RSA	0.468	0.016	0.487
median_replicates	0.800	0.008	0.809
plot_screen_hits	2.892	0.080	2.966
plot_seeds_methods	2.180	0.068	2.250
randomSortOnVal	0.204	0.000	0.204
randomizeInner	0.208	0.000	0.208
removeSharedOffTargets	0.904	0.012	0.918
renameColDf	0.300	0.000	0.302
replace_non_null_elements	0.192	0.004	0.199
seed_correction	0.592	0.024	0.615
seed_correction_pooled	0.532	0.008	0.547
seed_removal	0.444	0.016	0.461
seeds_analysis	1.144	0.024	1.164
sortInner	0.248	0.008	0.254
split_df	0.244	0.000	0.245
transcribe_seqs	0.356	0.012	0.367