BioC 3.4: CHECK report for scsR on moscato1

Package: scsR

Version: 1.9.0

Command: rm -rf scsR.buildbin-libdir scsR.Rcheck && mkdir scsR.buildbin-libdir scsR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.9.0.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.9.0.tar.gz

StartedAt: 2016-09-20 16:14:44 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 16:18:28 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 223.7 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 && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.9.0.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.9.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/scsR.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.9.0'
* 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 18.29    0.1   18.38
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 18.89   0.07   18.98
* 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
  'D:/biocbld/bbs-3.4-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_1.9.0.zip
* DONE (scsR)

name	user	system	elapsed
add_rank_col	0.41	0.00	0.41
add_seed	0.26	0.00	0.27
benchmark_shared_hits	2.64	0.05	2.68
bydf	0.45	0.01	0.47
check_consistency	1.87	0.03	1.90
compare_sorted_geneSets	18.29	0.10	18.38
create_sd_matrix	0.34	0.00	0.34
delColDf	0.23	0.01	0.25
delete_undefined_rows	0.50	0.02	0.52
enrichment_geneSet	0.72	0.03	0.75
enrichment_heatmap	0.72	0.01	0.73
get_sd_quant	1.51	0.02	1.53
get_seed_oligos_df	1.20	0.05	1.25
intersectAll	0	0	0
launch_RSA	0.56	0.01	0.58
median_replicates	0.93	0.05	0.98
plot_screen_hits	1.60	0.06	1.66
plot_seeds_methods	1.95	0.02	1.96
randomSortOnVal	0.23	0.00	0.24
randomizeInner	0.23	0.00	0.23
removeSharedOffTargets	0.86	0.01	0.87
renameColDf	0.25	0.00	0.25
replace_non_null_elements	0.26	0.00	0.26
seed_correction	0.52	0.00	0.52
seed_correction_pooled	0.5	0.0	0.5
seed_removal	0.42	0.03	0.45
seeds_analysis	1.46	0.02	1.48
sortInner	0.32	0.00	0.31
split_df	0.28	0.00	0.29
transcribe_seqs	0.33	0.00	0.33

name	user	system	elapsed
add_rank_col	0.38	0.02	0.39
add_seed	0.44	0.00	0.43
benchmark_shared_hits	2.51	0.08	2.64
bydf	0.39	0.00	0.39
check_consistency	1.89	0.00	1.89
compare_sorted_geneSets	18.89	0.07	18.98
create_sd_matrix	0.39	0.00	0.39
delColDf	0.21	0.02	0.23
delete_undefined_rows	0.52	0.01	0.53
enrichment_geneSet	0.51	0.00	0.52
enrichment_heatmap	0.42	0.00	0.42
get_sd_quant	1.33	0.04	1.35
get_seed_oligos_df	0.85	0.00	0.86
intersectAll	0.02	0.00	0.01
launch_RSA	0.45	0.00	0.46
median_replicates	0.88	0.04	0.92
plot_screen_hits	1.72	0.00	1.72
plot_seeds_methods	2.07	0.02	2.09
randomSortOnVal	0.22	0.00	0.22
randomizeInner	0.23	0.01	0.25
removeSharedOffTargets	0.83	0.04	0.86
renameColDf	0.20	0.03	0.23
replace_non_null_elements	0.23	0.00	0.24
seed_correction	0.60	0.00	0.59
seed_correction_pooled	0.57	0.00	0.58
seed_removal	0.58	0.00	0.58
seeds_analysis	1.59	0.00	1.59
sortInner	0.30	0.01	0.31
split_df	0.28	0.00	0.28
transcribe_seqs	0.34	0.00	0.34