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: 2017-08-16 02:46:55 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:50:47 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 231.8 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 3.4.1 (2017-06-30)
* 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 16.03   0.14   16.17
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 16.92   0.13   17.06
* 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	0.75	0.03	0.78
add_seed	0.25	0.02	0.26
benchmark_shared_hits	2.42	0.09	2.52
bydf	0.41	0.02	0.42
check_consistency	1.33	0.03	1.36
compare_sorted_geneSets	16.03	0.14	16.17
create_sd_matrix	0.47	0.01	0.49
delColDf	0.28	0.02	0.30
delete_undefined_rows	0.55	0.01	0.56
enrichment_geneSet	0.50	0.03	0.53
enrichment_heatmap	0.48	0.03	0.52
get_sd_quant	0.84	0.02	0.86
get_seed_oligos_df	0.82	0.03	0.84
intersectAll	0	0	0
launch_RSA	0.47	0.02	0.49
median_replicates	0.88	0.01	0.89
plot_screen_hits	2.25	0.02	2.28
plot_seeds_methods	1.95	0.04	2.00
randomSortOnVal	0.28	0.00	0.28
randomizeInner	0.27	0.00	0.27
removeSharedOffTargets	0.89	0.04	0.92
renameColDf	0.41	0.01	0.42
replace_non_null_elements	0.34	0.00	0.34
seed_correction	0.49	0.02	0.50
seed_correction_pooled	0.56	0.03	0.60
seed_removal	0.56	0.01	0.58
seeds_analysis	1.39	0.02	1.40
sortInner	0.38	0.02	0.39
split_df	0.40	0.01	0.42
transcribe_seqs	0.55	0.00	0.55

name	user	system	elapsed
add_rank_col	1.11	0.00	1.12
add_seed	0.35	0.00	0.34
benchmark_shared_hits	2.77	0.01	2.78
bydf	0.50	0.03	0.53
check_consistency	1.70	0.05	1.75
compare_sorted_geneSets	16.92	0.13	17.06
create_sd_matrix	0.54	0.00	0.54
delColDf	0.31	0.01	0.32
delete_undefined_rows	0.56	0.00	0.57
enrichment_geneSet	0.38	0.03	0.40
enrichment_heatmap	0.39	0.02	0.41
get_sd_quant	0.98	0.01	1.00
get_seed_oligos_df	0.77	0.00	0.76
intersectAll	0	0	0
launch_RSA	0.52	0.02	0.53
median_replicates	0.61	0.03	0.64
plot_screen_hits	2.57	0.05	2.63
plot_seeds_methods	1.86	0.01	1.87
randomSortOnVal	0.19	0.00	0.19
randomizeInner	0.19	0.00	0.19
removeSharedOffTargets	0.66	0.00	0.65
renameColDf	0.28	0.02	0.30
replace_non_null_elements	0.37	0.00	0.38
seed_correction	0.66	0.00	0.67
seed_correction_pooled	0.44	0.00	0.44
seed_removal	0.4	0.0	0.4
seeds_analysis	1.35	0.01	1.36
sortInner	0.34	0.02	0.36
split_df	0.25	0.00	0.25
transcribe_seqs	0.38	0.00	0.38