BioC 2.14: CHECK report for scsR on moscato2

Package: scsR

Version: 1.0.0

Command: rm -rf scsR.buildbin-libdir && mkdir scsR.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.0.0.tar.gz >scsR-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.0.0.tar.gz

StartedAt: 2014-10-08 05:00:30 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 05:04:55 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 265.0 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 && mkdir scsR.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.0.0.tar.gz >scsR-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.0.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/scsR.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-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 '1.0.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics' 'Biostrings' 'IRanges' 'plyr' 'STRINGdb' '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 ... OK
* 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' ... [46s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 16.71   0.11   16.82
** running examples for arch 'x64' ... [53s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 18.23   0.08   18.31
benchmark_shared_hits    7.62   0.03    7.67
* 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

NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.14-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_1.0.0.zip
* DONE (scsR)

name	user	system	elapsed
add_rank_col	0.54	0.00	0.54
add_seed	0.28	0.03	0.32
benchmark_shared_hits	3.84	0.02	3.85
bydf	0.69	0.01	0.70
check_consistency	2.29	0.03	2.39
compare_sorted_geneSets	16.71	0.11	16.82
create_sd_matrix	0.29	0.02	0.31
delColDf	0.21	0.00	0.22
delete_undefined_rows	0.62	0.00	0.62
enrichment_geneSet	0.53	0.00	0.55
enrichment_heatmap	0.35	0.03	0.37
get_sd_quant	1.56	0.00	1.56
get_seed_oligos_df	1.21	0.02	1.23
intersectAll	0.02	0.00	0.02
launch_RSA	0.48	0.00	0.48
median_replicates	0.92	0.04	0.97
plot_screen_hits	2.18	0.00	2.18
plot_seeds_methods	1.65	0.02	1.67
randomSortOnVal	0.30	0.00	0.31
randomizeInner	0.28	0.00	0.28
removeSharedOffTargets	1.16	0.05	1.20
renameColDf	0.2	0.0	0.2
replace_non_null_elements	0.22	0.01	0.23
seed_correction	0.66	0.00	0.66
seed_removal	0.48	0.02	0.50
seeds_analysis	2.26	0.01	2.28
sortInner	0.32	0.00	0.31
split_df	0.28	0.00	0.28
transcribe_seqs	0.34	0.00	0.34

name	user	system	elapsed
add_rank_col	0.53	0.03	0.57
add_seed	0.48	0.01	0.50
benchmark_shared_hits	7.62	0.03	7.67
bydf	0.48	0.00	0.49
check_consistency	2.22	0.05	2.26
compare_sorted_geneSets	18.23	0.08	18.31
create_sd_matrix	0.30	0.01	0.32
delColDf	0.17	0.00	0.17
delete_undefined_rows	0.66	0.00	0.65
enrichment_geneSet	0.34	0.00	0.35
enrichment_heatmap	0.31	0.00	0.31
get_sd_quant	1.50	0.02	1.51
get_seed_oligos_df	1.25	0.00	1.25
intersectAll	0.01	0.00	0.01
launch_RSA	0.50	0.02	0.52
median_replicates	0.94	0.03	0.97
plot_screen_hits	2.21	0.00	2.23
plot_seeds_methods	1.63	0.00	1.62
randomSortOnVal	0.18	0.00	0.19
randomizeInner	0.19	0.01	0.20
removeSharedOffTargets	1.25	0.02	1.26
renameColDf	0.17	0.00	0.17
replace_non_null_elements	0.19	0.00	0.18
seed_correction	0.62	0.00	0.63
seed_removal	0.53	0.00	0.53
seeds_analysis	2.60	0.00	2.61
sortInner	0.31	0.00	0.31
split_df	0.29	0.00	0.28
transcribe_seqs	0.32	0.01	0.36