BioC 3.2: CHECK report for scsR on moscato1

Package: scsR

Version: 1.5.0

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_1.5.0.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_1.5.0.tar.gz

StartedAt: 2015-08-20 10:09:38 -0700 (Thu, 20 Aug 2015)

EndedAt: 2015-08-20 10:14:53 -0700 (Thu, 20 Aug 2015)

EllapsedTime: 314.6 seconds

RetCode: 0

Status:  OK

CheckDir: scsR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_1.5.0.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_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-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 '1.5.0'
* 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' ... [54s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 21.14   0.11   21.24
** running examples for arch 'x64' ... [61s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
compare_sorted_geneSets 23.6   0.05   23.87
* 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_1.5.0.zip
* DONE (scsR)

name	user	system	elapsed
add_rank_col	0.41	0.02	0.42
add_seed	0.47	0.00	0.47
benchmark_shared_hits	3.16	0.05	3.21
bydf	0.41	0.01	0.42
check_consistency	2.18	0.03	2.22
compare_sorted_geneSets	21.14	0.11	21.24
create_sd_matrix	0.55	0.00	0.55
delColDf	0.31	0.00	0.31
delete_undefined_rows	0.58	0.03	0.61
enrichment_geneSet	0.64	0.02	0.65
enrichment_heatmap	0.54	0.00	0.55
get_sd_quant	1.34	0.05	1.39
get_seed_oligos_df	1.24	0.00	1.23
intersectAll	0.01	0.00	0.02
launch_RSA	0.53	0.01	0.54
median_replicates	1.20	0.03	1.67
plot_screen_hits	2.44	0.02	2.45
plot_seeds_methods	2.15	0.01	2.17
randomSortOnVal	0.30	0.02	0.31
randomizeInner	0.45	0.00	0.45
removeSharedOffTargets	1.57	0.02	1.60
renameColDf	0.28	0.00	0.28
replace_non_null_elements	0.37	0.01	0.39
seed_correction	0.66	0.00	0.66
seed_correction_pooled	0.55	0.00	0.54
seed_removal	0.71	0.00	0.72
seeds_analysis	2.31	0.02	2.32
sortInner	0.5	0.0	0.5
split_df	0.53	0.00	0.53
transcribe_seqs	0.53	0.00	0.53

name	user	system	elapsed
add_rank_col	0.62	0.00	0.66
add_seed	0.56	0.00	0.56
benchmark_shared_hits	3.57	0.06	3.66
bydf	0.45	0.00	0.46
check_consistency	2.16	0.03	2.18
compare_sorted_geneSets	23.60	0.05	23.87
create_sd_matrix	0.39	0.00	0.39
delColDf	0.25	0.00	0.25
delete_undefined_rows	0.61	0.00	0.61
enrichment_geneSet	0.77	0.01	0.78
enrichment_heatmap	0.65	0.02	0.67
get_sd_quant	1.49	0.01	1.50
get_seed_oligos_df	1.15	0.00	1.17
intersectAll	0	0	0
launch_RSA	0.72	0.02	0.73
median_replicates	1.53	0.09	1.63
plot_screen_hits	2.10	0.00	3.58
plot_seeds_methods	3.08	0.02	3.11
randomSortOnVal	0.31	0.01	0.33
randomizeInner	0.28	0.00	0.28
removeSharedOffTargets	1.18	0.00	1.18
renameColDf	0.25	0.00	0.25
replace_non_null_elements	0.3	0.0	0.3
seed_correction	0.73	0.02	0.75
seed_correction_pooled	0.61	0.00	0.61
seed_removal	0.53	0.00	0.53
seeds_analysis	1.92	0.03	1.95
sortInner	0.30	0.02	0.31
split_df	0.28	0.00	0.27
transcribe_seqs	0.54	0.00	0.54