BioC 3.2: CHECK report for scsR on windows1.bioconductor.org

Package: scsR

Version: 1.6.0

Command: rm -rf scsR.buildbin-libdir scsR.Rcheck && mkdir scsR.buildbin-libdir scsR.Rcheck && C:\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 && C:\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: 2015-10-27 05:28:12 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:31:33 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 200.8 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 && C:\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  && C:\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 'C:/biocbld/bbs-3.2-bioc/meat/scsR.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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' ... [35s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
compare_sorted_geneSets 13.2   0.19   13.39
** running examples for arch 'x64' ... [41s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 17.28   0.17   17.49
* 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
  'C:/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	0.3	0.0	0.3
add_seed	0.23	0.00	0.24
benchmark_shared_hits	2.33	0.03	2.35
bydf	0.33	0.00	0.33
check_consistency	1.63	0.06	1.69
compare_sorted_geneSets	13.20	0.19	13.39
create_sd_matrix	0.44	0.00	0.44
delColDf	0.18	0.00	0.19
delete_undefined_rows	0.42	0.00	0.42
enrichment_geneSet	0.41	0.00	0.41
enrichment_heatmap	0.37	0.02	0.39
get_sd_quant	0.83	0.01	0.84
get_seed_oligos_df	0.64	0.00	0.64
intersectAll	0	0	0
launch_RSA	0.36	0.00	0.36
median_replicates	0.77	0.02	0.79
plot_screen_hits	1.32	0.01	1.34
plot_seeds_methods	1.44	0.00	1.44
randomSortOnVal	0.16	0.07	0.22
randomizeInner	0.22	0.00	0.21
removeSharedOffTargets	0.70	0.00	0.71
renameColDf	0.22	0.00	0.22
replace_non_null_elements	0.22	0.00	0.21
seed_correction	0.48	0.01	0.50
seed_correction_pooled	0.39	0.00	0.40
seed_removal	0.35	0.00	0.34
seeds_analysis	1.31	0.00	1.31
sortInner	0.26	0.00	0.27
split_df	0.25	0.00	0.25
transcribe_seqs	0.29	0.02	0.29

name	user	system	elapsed
add_rank_col	0.31	0.00	0.31
add_seed	0.5	0.0	0.5
benchmark_shared_hits	2.61	0.01	2.62
bydf	0.38	0.03	0.41
check_consistency	1.7	0.0	1.7
compare_sorted_geneSets	17.28	0.17	17.49
create_sd_matrix	0.35	0.02	0.36
delColDf	0.2	0.0	0.2
delete_undefined_rows	0.39	0.02	0.41
enrichment_geneSet	0.38	0.03	0.40
enrichment_heatmap	0.40	0.01	0.42
get_sd_quant	0.99	0.02	1.00
get_seed_oligos_df	0.70	0.01	0.72
intersectAll	0	0	0
launch_RSA	0.37	0.00	0.38
median_replicates	0.71	0.02	0.72
plot_screen_hits	1.42	0.00	1.42
plot_seeds_methods	1.73	0.02	1.76
randomSortOnVal	0.21	0.01	0.22
randomizeInner	0.18	0.00	0.19
removeSharedOffTargets	1	0	1
renameColDf	0.19	0.02	0.20
replace_non_null_elements	0.19	0.00	0.19
seed_correction	0.45	0.00	0.45
seed_correction_pooled	0.52	0.01	0.54
seed_removal	0.36	0.00	0.36
seeds_analysis	1.56	0.02	1.57
sortInner	0.23	0.00	0.24
split_df	0.21	0.01	0.22
transcribe_seqs	0.25	0.00	0.25