BioC 3.5: CHECK report for scsR on tokay2

Package: scsR

Version: 1.12.0

Command: rm -rf scsR.buildbin-libdir scsR.Rcheck && mkdir scsR.buildbin-libdir scsR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.12.0.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.12.0.tar.gz

StartedAt: 2017-10-18 02:53:29 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:57:20 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 230.9 seconds

RetCode: 0

Status:  OK

CheckDir: scsR.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf scsR.buildbin-libdir scsR.Rcheck && mkdir scsR.buildbin-libdir scsR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.12.0.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/scsR.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 16.97   0.21   17.19
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 19.92   0.16   20.09
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/scsR.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'scsR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scsR' as scsR_1.12.0.zip
* DONE (scsR)

name	user	system	elapsed
add_rank_col	1.06	0.04	1.11
add_seed	0.38	0.02	0.39
benchmark_shared_hits	2.39	0.08	2.47
bydf	0.35	0.01	0.36
check_consistency	1.42	0.03	1.45
compare_sorted_geneSets	16.97	0.21	17.19
create_sd_matrix	0.33	0.01	0.35
delColDf	0.23	0.00	0.23
delete_undefined_rows	0.45	0.03	0.48
enrichment_geneSet	0.57	0.05	0.61
enrichment_heatmap	0.53	0.02	0.55
get_sd_quant	1.39	0.00	1.41
get_seed_oligos_df	0.61	0.03	0.64
intersectAll	0	0	0
launch_RSA	0.39	0.00	0.39
median_replicates	1.2	0.0	1.2
plot_screen_hits	2.67	0.03	2.70
plot_seeds_methods	1.52	0.05	1.57
randomSortOnVal	0.28	0.00	0.28
randomizeInner	0.36	0.00	0.36
removeSharedOffTargets	0.69	0.03	0.72
renameColDf	0.23	0.02	0.25
replace_non_null_elements	0.24	0.00	0.24
seed_correction	0.57	0.00	0.57
seed_correction_pooled	0.61	0.01	0.63
seed_removal	0.59	0.02	0.60
seeds_analysis	1.52	0.00	1.52
sortInner	0.47	0.02	0.48
split_df	0.39	0.01	0.41
transcribe_seqs	0.59	0.02	0.61

name	user	system	elapsed
add_rank_col	0.94	0.05	1.02
add_seed	0.22	0.01	0.23
benchmark_shared_hits	2.75	0.03	2.78
bydf	0.42	0.03	0.45
check_consistency	1.80	0.11	1.91
compare_sorted_geneSets	19.92	0.16	20.09
create_sd_matrix	0.53	0.01	0.55
delColDf	0.36	0.02	0.38
delete_undefined_rows	0.63	0.00	0.62
enrichment_geneSet	0.75	0.02	0.77
enrichment_heatmap	0.39	0.00	0.39
get_sd_quant	1.23	0.03	1.28
get_seed_oligos_df	0.72	0.01	0.73
intersectAll	0	0	0
launch_RSA	0.44	0.02	0.46
median_replicates	0.73	0.00	0.73
plot_screen_hits	3.00	0.03	3.03
plot_seeds_methods	1.58	0.03	1.61
randomSortOnVal	0.18	0.00	0.18
randomizeInner	0.2	0.0	0.2
removeSharedOffTargets	0.77	0.00	0.77
renameColDf	0.28	0.05	0.33
replace_non_null_elements	0.27	0.01	0.28
seed_correction	0.5	0.0	0.5
seed_correction_pooled	0.43	0.02	0.45
seed_removal	0.86	0.00	0.86
seeds_analysis	1.14	0.00	1.14
sortInner	0.43	0.01	0.44
split_df	0.29	0.02	0.31
transcribe_seqs	0.41	0.02	0.42