BioC 3.2: CHECK report for scsR on moscato1

Package: scsR

Version: 1.6.0

Command: rm -rf scsR.buildbin-libdir scsR.Rcheck && mkdir scsR.buildbin-libdir scsR.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.6.0.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.6.0.tar.gz

StartedAt: 2016-04-23 07:19:23 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 07:25:07 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 344.0 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 && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.6.0.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.6.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/scsR.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.6.0'
* 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
enrichment_heatmap: no visible global function definition for
  'heatmap.2'
* 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' ... [57s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 21.62   0.12   21.78
** running examples for arch 'x64' ... [63s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 25.79   0.17   25.97
* 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-3.2-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_1.6.0.zip
* DONE (scsR)

name	user	system	elapsed
add_rank_col	0.56	0.00	0.56
add_seed	0.26	0.00	0.27
benchmark_shared_hits	2.84	0.02	3.06
bydf	0.64	0.01	0.65
check_consistency	2.16	0.10	2.92
compare_sorted_geneSets	21.62	0.12	21.78
create_sd_matrix	0.39	0.00	0.39
delColDf	0.35	0.02	0.36
delete_undefined_rows	0.65	0.01	0.67
enrichment_geneSet	0.80	0.04	0.83
enrichment_heatmap	0.59	0.01	0.61
get_sd_quant	1.42	0.02	1.59
get_seed_oligos_df	1.23	0.00	1.23
intersectAll	0.02	0.00	0.02
launch_RSA	0.58	0.00	0.57
median_replicates	1.70	0.04	1.75
plot_screen_hits	1.99	0.02	2.01
plot_seeds_methods	2.55	0.00	2.55
randomSortOnVal	0.40	0.01	0.42
randomizeInner	0.45	0.02	0.47
removeSharedOffTargets	1.16	0.02	1.17
renameColDf	0.4	0.0	0.4
replace_non_null_elements	0.33	0.01	0.35
seed_correction	1.03	0.02	1.04
seed_correction_pooled	0.66	0.01	0.67
seed_removal	0.85	0.02	0.87
seeds_analysis	2.13	0.01	2.14
sortInner	0.39	0.02	0.41
split_df	0.43	0.01	0.45
transcribe_seqs	0.5	0.0	0.5

name	user	system	elapsed
add_rank_col	0.54	0.01	0.67
add_seed	0.67	0.03	0.70
benchmark_shared_hits	3.31	0.05	3.36
bydf	0.59	0.01	0.62
check_consistency	2.59	0.08	3.17
compare_sorted_geneSets	25.79	0.17	25.97
create_sd_matrix	0.56	0.00	0.56
delColDf	0.35	0.04	0.37
delete_undefined_rows	0.81	0.03	0.84
enrichment_geneSet	0.69	0.01	0.70
enrichment_heatmap	0.55	0.03	0.58
get_sd_quant	1.63	0.05	1.68
get_seed_oligos_df	1.30	0.03	1.33
intersectAll	0	0	0
launch_RSA	0.7	0.0	0.7
median_replicates	1.19	0.06	1.25
plot_screen_hits	1.87	0.00	1.87
plot_seeds_methods	2.85	0.07	2.92
randomSortOnVal	0.31	0.03	0.34
randomizeInner	0.3	0.0	0.3
removeSharedOffTargets	1.44	0.01	1.45
renameColDf	0.31	0.03	0.35
replace_non_null_elements	0.37	0.02	0.39
seed_correction	0.91	0.00	0.90
seed_correction_pooled	0.88	0.02	0.89
seed_removal	0.83	0.00	0.83
seeds_analysis	2.25	0.01	2.26
sortInner	0.43	0.02	0.45
split_df	0.31	0.01	0.33
transcribe_seqs	0.53	0.02	0.55