BioC 3.0: CHECK report for scsR on moscato1

Package: scsR

Version: 1.3.2

Command: rm -rf scsR.buildbin-libdir scsR.Rcheck && mkdir scsR.buildbin-libdir scsR.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.3.2.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.3.2.tar.gz

StartedAt: 2015-04-10 05:27:49 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 05:33:40 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 351.3 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-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.3.2.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.3.2.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/scsR.Rcheck'
* using R version 3.1.3 (2015-03-09)
* 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 '1.3.2'
* 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' ... [56s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 23.26   0.03   23.42
** running examples for arch 'x64' ... [63s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 27.52   0.11   27.63
* 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-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_1.3.2.zip
* DONE (scsR)

name	user	system	elapsed
add_rank_col	0.67	0.00	0.67
add_seed	0.25	0.02	0.27
benchmark_shared_hits	3.13	0.03	3.17
bydf	0.44	0.00	0.43
check_consistency	2.32	0.06	2.55
compare_sorted_geneSets	23.26	0.03	23.42
create_sd_matrix	0.36	0.00	0.36
delColDf	0.25	0.00	0.25
delete_undefined_rows	0.48	0.01	0.50
enrichment_geneSet	0.52	0.02	0.53
enrichment_heatmap	0.45	0.03	0.48
get_sd_quant	1.09	0.02	1.11
get_seed_oligos_df	1.01	0.00	1.01
intersectAll	0	0	0
launch_RSA	0.66	0.00	0.66
median_replicates	1.01	0.01	1.03
plot_screen_hits	2.11	0.00	2.10
plot_seeds_methods	2.20	0.00	3.07
randomSortOnVal	0.42	0.00	0.42
randomizeInner	0.38	0.02	0.39
removeSharedOffTargets	1.17	0.01	1.19
renameColDf	0.26	0.00	0.26
replace_non_null_elements	0.47	0.00	0.47
seed_correction	0.84	0.00	0.84
seed_correction_pooled	0.72	0.00	0.72
seed_removal	0.51	0.00	0.52
seeds_analysis	1.95	0.00	1.95
sortInner	0.33	0.00	0.32
split_df	0.33	0.00	0.33
transcribe_seqs	0.36	0.02	0.38

name	user	system	elapsed
add_rank_col	0.83	0.01	1.01
add_seed	0.34	0.02	0.36
benchmark_shared_hits	4.71	0.00	4.72
bydf	0.6	0.0	0.6
check_consistency	3.21	0.00	3.21
compare_sorted_geneSets	27.52	0.11	27.63
create_sd_matrix	0.37	0.00	0.37
delColDf	0.25	0.00	0.25
delete_undefined_rows	0.53	0.02	0.54
enrichment_geneSet	0.41	0.01	0.43
enrichment_heatmap	0.40	0.02	0.42
get_sd_quant	1.17	0.00	1.17
get_seed_oligos_df	1.00	0.02	1.01
intersectAll	0	0	0
launch_RSA	0.7	0.0	0.7
median_replicates	0.80	0.06	0.86
plot_screen_hits	2.13	0.01	2.15
plot_seeds_methods	2.39	0.00	2.39
randomSortOnVal	0.30	0.00	0.29
randomizeInner	0.32	0.02	0.35
removeSharedOffTargets	1.37	0.00	1.37
renameColDf	0.27	0.01	0.29
replace_non_null_elements	0.23	0.00	0.23
seed_correction	0.55	0.00	0.55
seed_correction_pooled	0.59	0.00	0.59
seed_removal	0.55	0.02	0.56
seeds_analysis	1.9	0.0	1.9
sortInner	0.30	0.02	0.31
split_df	0.28	0.00	0.29
transcribe_seqs	0.37	0.01	0.39