BioC 3.1: CHECK report for scsR on moscato2

Package: scsR

Version: 1.4.0

Command: rm -rf scsR.buildbin-libdir scsR.Rcheck && mkdir scsR.buildbin-libdir scsR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.4.0.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.4.0.tar.gz

StartedAt: 2015-10-09 06:02:57 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 06:07:22 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 265.5 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-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.4.0.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.4.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/scsR.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.4.0'
* 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' ... [48s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 17.82   0.14   17.95
** running examples for arch 'x64' ... [52s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 21.44   0.11   21.63
* 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

Status: 2 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/scsR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'scsR' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'scsR' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'scsR' as scsR_1.4.0.zip
* DONE (scsR)

name	user	system	elapsed
add_rank_col	0.38	0.00	0.37
add_seed	0.34	0.00	0.35
benchmark_shared_hits	2.87	0.01	2.88
bydf	0.44	0.01	0.45
check_consistency	2.09	0.05	2.14
compare_sorted_geneSets	17.82	0.14	17.95
create_sd_matrix	0.33	0.00	0.33
delColDf	0.34	0.00	0.34
delete_undefined_rows	0.56	0.03	0.59
enrichment_geneSet	0.5	0.0	0.5
enrichment_heatmap	0.47	0.02	0.49
get_sd_quant	1.09	0.00	1.09
get_seed_oligos_df	1.26	0.03	1.30
intersectAll	0	0	0
launch_RSA	0.69	0.01	0.70
median_replicates	1.62	0.07	1.69
plot_screen_hits	2.54	0.01	2.55
plot_seeds_methods	2.19	0.03	2.22
randomSortOnVal	0.42	0.00	0.42
randomizeInner	0.43	0.00	0.42
removeSharedOffTargets	1.02	0.00	1.03
renameColDf	0.27	0.00	0.26
replace_non_null_elements	0.27	0.00	0.27
seed_correction	0.56	0.00	0.56
seed_correction_pooled	0.64	0.02	0.65
seed_removal	0.45	0.00	0.46
seeds_analysis	1.53	0.00	1.53
sortInner	0.33	0.00	0.32
split_df	0.29	0.00	0.30
transcribe_seqs	0.31	0.03	0.34

name	user	system	elapsed
add_rank_col	0.36	0.00	0.38
add_seed	0.46	0.00	0.47
benchmark_shared_hits	3.12	0.00	3.12
bydf	0.41	0.00	0.40
check_consistency	1.84	0.06	1.91
compare_sorted_geneSets	21.44	0.11	21.63
create_sd_matrix	0.48	0.00	0.49
delColDf	0.39	0.00	0.39
delete_undefined_rows	0.92	0.00	0.93
enrichment_geneSet	0.51	0.00	0.55
enrichment_heatmap	0.57	0.00	0.56
get_sd_quant	1.34	0.00	1.55
get_seed_oligos_df	1.10	0.02	1.12
intersectAll	0	0	0
launch_RSA	0.57	0.00	0.59
median_replicates	1.10	0.00	1.11
plot_screen_hits	1.84	0.03	1.87
plot_seeds_methods	2.31	0.01	2.33
randomSortOnVal	0.33	0.00	0.32
randomizeInner	0.34	0.02	0.36
removeSharedOffTargets	0.97	0.00	0.97
renameColDf	0.27	0.00	0.26
replace_non_null_elements	0.25	0.00	0.25
seed_correction	0.56	0.02	0.58
seed_correction_pooled	0.5	0.0	0.5
seed_removal	0.43	0.00	0.44
seeds_analysis	1.69	0.00	1.69
sortInner	0.28	0.00	0.28
split_df	0.33	0.01	0.34
transcribe_seqs	0.34	0.00	0.35