BioC 3.3: CHECK report for scsR on moscato2

Package: scsR

Version: 1.8.0

Command: rm -rf scsR.buildbin-libdir scsR.Rcheck && mkdir scsR.buildbin-libdir scsR.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.8.0.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.8.0.tar.gz

StartedAt: 2016-10-13 08:43:43 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 08:48:24 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 281.0 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 && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.8.0.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.8.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-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 '1.8.0'
* 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 17.67   0.12    17.8
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 23.68   0.06   23.74
* 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
  'E:/biocbld/bbs-3.3-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_1.8.0.zip
* DONE (scsR)

name	user	system	elapsed
add_rank_col	0.59	0.05	0.67
add_seed	0.30	0.00	0.29
benchmark_shared_hits	2.67	0.03	2.70
bydf	0.61	0.02	0.63
check_consistency	2.34	0.03	2.37
compare_sorted_geneSets	17.67	0.12	17.80
create_sd_matrix	0.35	0.00	0.34
delColDf	0.34	0.02	0.36
delete_undefined_rows	0.62	0.00	0.62
enrichment_geneSet	0.53	0.02	0.55
enrichment_heatmap	0.48	0.01	0.50
get_sd_quant	1.45	0.02	1.78
get_seed_oligos_df	1.00	0.00	1.25
intersectAll	0	0	0
launch_RSA	0.48	0.00	0.48
median_replicates	1.08	0.03	1.11
plot_screen_hits	1.56	0.03	1.59
plot_seeds_methods	2.34	0.01	2.36
randomSortOnVal	0.25	0.00	0.25
randomizeInner	0.27	0.02	0.28
removeSharedOffTargets	1.04	0.04	1.10
renameColDf	0.25	0.02	0.26
replace_non_null_elements	0.28	0.00	0.28
seed_correction	0.52	0.00	0.52
seed_correction_pooled	0.67	0.04	0.71
seed_removal	0.68	0.04	0.72
seeds_analysis	1.86	0.03	1.89
sortInner	0.37	0.01	0.39
split_df	0.44	0.00	0.44
transcribe_seqs	0.46	0.02	0.49

name	user	system	elapsed
add_rank_col	0.47	0.05	0.51
add_seed	0.62	0.02	0.64
benchmark_shared_hits	3.18	0.03	3.21
bydf	0.58	0.00	0.58
check_consistency	2.08	0.06	2.14
compare_sorted_geneSets	23.68	0.06	23.74
create_sd_matrix	0.66	0.00	0.66
delColDf	0.25	0.00	0.25
delete_undefined_rows	0.57	0.02	0.59
enrichment_geneSet	0.72	0.01	0.73
enrichment_heatmap	0.62	0.03	0.66
get_sd_quant	1.69	0.02	1.70
get_seed_oligos_df	1.01	0.02	1.54
intersectAll	0	0	0
launch_RSA	0.53	0.01	0.55
median_replicates	1.26	0.05	1.31
plot_screen_hits	2.20	0.01	2.21
plot_seeds_methods	2.87	0.03	2.90
randomSortOnVal	0.29	0.00	0.29
randomizeInner	0.26	0.02	0.28
removeSharedOffTargets	0.84	0.00	0.84
renameColDf	0.24	0.00	0.23
replace_non_null_elements	0.29	0.02	0.31
seed_correction	0.67	0.00	0.67
seed_correction_pooled	0.7	0.0	0.7
seed_removal	0.64	0.00	0.64
seeds_analysis	2.03	0.00	2.03
sortInner	0.44	0.00	0.44
split_df	0.32	0.03	0.36
transcribe_seqs	0.57	0.00	0.56