BioC 3.3: CHECK report for scsR on windows2.bioconductor.org

Package: scsR

Version: 1.7.0

Command: rm -rf scsR.buildbin-libdir scsR.Rcheck && mkdir scsR.buildbin-libdir scsR.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.7.0.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.7.0.tar.gz

StartedAt: 2015-10-27 05:55:55 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:59:09 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 193.5 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 && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scsR.buildbin-libdir scsR_1.7.0.tar.gz >scsR.Rcheck\00install.out 2>&1 && cp scsR.Rcheck\00install.out scsR-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=scsR.buildbin-libdir --install="check:scsR-install.out" --force-multiarch --no-vignettes --timings scsR_1.7.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/scsR.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* 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 '1.7.0'
* 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'
Undefined global functions or variables:
  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' ... [37s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 14.83   0.13   14.97
** running examples for arch 'x64' ... [41s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
compare_sorted_geneSets 18.19   0.15   18.36
* 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-3.3-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_1.7.0.zip
* DONE (scsR)

name	user	system	elapsed
add_rank_col	0.33	0.01	0.34
add_seed	0.21	0.00	0.21
benchmark_shared_hits	2.14	0.05	2.19
bydf	0.33	0.00	0.33
check_consistency	1.58	0.03	1.61
compare_sorted_geneSets	14.83	0.13	14.97
create_sd_matrix	0.29	0.01	0.31
delColDf	0.21	0.00	0.20
delete_undefined_rows	0.40	0.02	0.42
enrichment_geneSet	0.42	0.03	0.46
enrichment_heatmap	0.40	0.00	0.39
get_sd_quant	0.78	0.01	0.80
get_seed_oligos_df	1.09	0.00	1.09
intersectAll	0	0	0
launch_RSA	0.36	0.00	0.36
median_replicates	0.75	0.04	0.79
plot_screen_hits	1.31	0.00	1.31
plot_seeds_methods	1.54	0.01	1.56
randomSortOnVal	0.22	0.00	0.22
randomizeInner	0.25	0.00	0.25
removeSharedOffTargets	0.85	0.03	0.87
renameColDf	0.33	0.00	0.33
replace_non_null_elements	0.32	0.02	0.35
seed_correction	0.60	0.00	0.59
seed_correction_pooled	0.37	0.00	0.37
seed_removal	0.44	0.01	0.46
seeds_analysis	1.56	0.02	1.58
sortInner	0.40	0.00	0.41
split_df	0.36	0.01	0.37
transcribe_seqs	0.41	0.00	0.41

name	user	system	elapsed
add_rank_col	0.26	0.03	0.30
add_seed	0.49	0.00	0.49
benchmark_shared_hits	2.40	0.04	2.43
bydf	0.38	0.01	0.39
check_consistency	1.92	0.05	1.97
compare_sorted_geneSets	18.19	0.15	18.36
create_sd_matrix	0.26	0.00	0.27
delColDf	0.45	0.02	0.47
delete_undefined_rows	0.41	0.02	0.42
enrichment_geneSet	0.42	0.00	0.43
enrichment_heatmap	0.31	0.01	0.32
get_sd_quant	0.93	0.02	0.95
get_seed_oligos_df	0.74	0.00	0.74
intersectAll	0	0	0
launch_RSA	0.37	0.00	0.37
median_replicates	0.69	0.01	0.70
plot_screen_hits	1.41	0.00	1.41
plot_seeds_methods	1.97	0.05	2.02
randomSortOnVal	0.17	0.03	0.20
randomizeInner	0.2	0.0	0.2
removeSharedOffTargets	0.72	0.02	0.74
renameColDf	0.22	0.00	0.22
replace_non_null_elements	0.23	0.00	0.23
seed_correction	0.57	0.01	0.58
seed_correction_pooled	0.54	0.02	0.56
seed_removal	0.39	0.01	0.40
seeds_analysis	1.44	0.02	1.47
sortInner	0.23	0.00	0.24
split_df	0.25	0.00	0.25
transcribe_seqs	0.25	0.00	0.25