BioC 3.6: CHECK report for scsR on tokay1

Package: scsR

Version: 1.13.0

Command: rm -rf scsR.buildbin-libdir scsR.Rcheck && mkdir scsR.buildbin-libdir scsR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.13.0.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.13.0.tar.gz

StartedAt: 2017-08-16 02:21:33 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:25:05 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 211.5 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-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.13.0.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.13.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-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 '1.13.0'
* 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 12.77   0.03    12.8
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 19.08   0.19   19.34
* 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-3.6-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_1.13.0.zip
* DONE (scsR)

name	user	system	elapsed
add_rank_col	0.68	0.02	0.69
add_seed	0.23	0.00	0.24
benchmark_shared_hits	2.00	0.06	2.06
bydf	0.34	0.00	0.34
check_consistency	1.27	0.03	1.30
compare_sorted_geneSets	12.77	0.03	12.80
create_sd_matrix	0.29	0.02	0.31
delColDf	0.24	0.01	0.25
delete_undefined_rows	0.51	0.02	0.53
enrichment_geneSet	0.47	0.01	0.48
enrichment_heatmap	0.47	0.02	0.49
get_sd_quant	0.84	0.01	0.86
get_seed_oligos_df	0.66	0.04	0.69
intersectAll	0	0	0
launch_RSA	0.41	0.00	0.40
median_replicates	0.67	0.03	0.71
plot_screen_hits	2.2	0.0	2.2
plot_seeds_methods	1.35	0.04	1.39
randomSortOnVal	0.25	0.00	0.25
randomizeInner	0.21	0.02	0.23
removeSharedOffTargets	0.66	0.02	0.68
renameColDf	0.22	0.00	0.21
replace_non_null_elements	0.23	0.01	0.25
seed_correction	0.43	0.00	0.43
seed_correction_pooled	0.39	0.00	0.39
seed_removal	0.36	0.00	0.36
seeds_analysis	0.97	0.05	1.02
sortInner	0.28	0.01	0.29
split_df	0.27	0.00	0.27
transcribe_seqs	0.34	0.00	0.34

name	user	system	elapsed
add_rank_col	1.15	0.05	1.23
add_seed	0.32	0.01	0.33
benchmark_shared_hits	2.76	0.02	2.78
bydf	0.43	0.00	0.42
check_consistency	1.87	0.03	1.91
compare_sorted_geneSets	19.08	0.19	19.34
create_sd_matrix	0.55	0.06	0.61
delColDf	0.18	0.00	0.19
delete_undefined_rows	0.42	0.03	0.45
enrichment_geneSet	0.43	0.00	0.43
enrichment_heatmap	0.37	0.03	0.40
get_sd_quant	1.00	0.05	1.05
get_seed_oligos_df	0.86	0.00	0.86
intersectAll	0	0	0
launch_RSA	0.55	0.01	0.58
median_replicates	0.76	0.00	0.78
plot_screen_hits	3.24	0.05	3.28
plot_seeds_methods	2.17	0.06	2.25
randomSortOnVal	0.28	0.03	0.31
randomizeInner	0.31	0.02	0.33
removeSharedOffTargets	0.91	0.02	0.92
renameColDf	0.28	0.00	0.28
replace_non_null_elements	0.25	0.00	0.25
seed_correction	0.56	0.03	0.59
seed_correction_pooled	0.45	0.00	0.46
seed_removal	0.47	0.01	0.48
seeds_analysis	1.28	0.02	1.29
sortInner	0.29	0.00	0.30
split_df	0.21	0.05	0.25
transcribe_seqs	0.50	0.01	0.51