Package: scsR

Version: 1.19.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:scsR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings scsR_1.19.0.tar.gz

StartedAt: 2019-04-09 03:31:32 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:34:05 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 152.5 seconds

RetCode: 0

Status:  OK

CheckDir: scsR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:scsR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings scsR_1.19.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/scsR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.19.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compare_sorted_geneSets 19.465  0.749   20.17
* 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-3.9-bioc/meat/scsR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL scsR
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘scsR’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scsR)

name	user	system	elapsed
add_rank_col	0.637	0.048	0.673
add_seed	0.284	0.008	0.291
benchmark_shared_hits	2.476	0.072	2.544
bydf	0.444	0.076	0.512
check_consistency	1.584	0.036	1.619
compare_sorted_geneSets	19.465	0.749	20.170
create_sd_matrix	0.409	0.024	0.432
delColDf	0.310	0.004	0.315
delete_undefined_rows	0.473	0.008	0.481
enrichment_geneSet	0.574	0.012	0.586
enrichment_heatmap	0.515	0.004	0.519
get_sd_quant	0.910	0.161	1.036
get_seed_oligos_df	0.844	0.113	0.934
intersectAll	0.001	0.000	0.001
launch_RSA	0.443	0.008	0.449
median_replicates	0.725	0.004	0.728
plot_screen_hits	1.387	0.138	1.492
plot_seeds_methods	2.234	0.402	2.605
randomSortOnVal	0.264	0.004	0.268
randomizeInner	0.198	0.000	0.198
removeSharedOffTargets	0.658	0.016	0.673
renameColDf	0.230	0.000	0.231
replace_non_null_elements	0.246	0.000	0.246
seed_correction	0.540	0.081	0.611
seed_correction_pooled	0.587	0.053	0.626
seed_removal	0.329	0.037	0.363
seeds_analysis	1.357	0.153	1.507
sortInner	0.362	0.012	0.373
split_df	0.308	0.008	0.316
transcribe_seqs	0.414	0.016	0.430