BioC 3.5: CHECK report for SWATH2stats on tokay2

Package: SWATH2stats

Version: 1.6.1

Command: rm -rf SWATH2stats.buildbin-libdir SWATH2stats.Rcheck && mkdir SWATH2stats.buildbin-libdir SWATH2stats.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SWATH2stats.buildbin-libdir SWATH2stats_1.6.1.tar.gz >SWATH2stats.Rcheck\00install.out 2>&1 && cp SWATH2stats.Rcheck\00install.out SWATH2stats-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=SWATH2stats.buildbin-libdir --install="check:SWATH2stats-install.out" --force-multiarch --no-vignettes --timings SWATH2stats_1.6.1.tar.gz

StartedAt: 2017-10-18 03:20:09 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 03:22:08 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 119.0 seconds

RetCode: 0

Status:  OK

CheckDir: SWATH2stats.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf SWATH2stats.buildbin-libdir SWATH2stats.Rcheck && mkdir SWATH2stats.buildbin-libdir SWATH2stats.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SWATH2stats.buildbin-libdir SWATH2stats_1.6.1.tar.gz >SWATH2stats.Rcheck\00install.out 2>&1 && cp SWATH2stats.Rcheck\00install.out SWATH2stats-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=SWATH2stats.buildbin-libdir --install="check:SWATH2stats-install.out" --force-multiarch --no-vignettes --timings SWATH2stats_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/SWATH2stats.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SWATH2stats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SWATH2stats' version '1.6.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'imsbInfer' 'MSstats'
* 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 'SWATH2stats' 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: 'MSstats'
* 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' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.R'
 OK
* 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:/Users/biocbuild/bbs-3.5-bioc/meat/SWATH2stats.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'SWATH2stats' ...
** 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 'SWATH2stats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SWATH2stats' as SWATH2stats_1.6.1.zip
* DONE (SWATH2stats)

name	user	system	elapsed
assess_decoy_rate	0.25	0.00	0.25
assess_fdr_byrun	0.39	0.01	0.40
assess_fdr_overall	0.41	0.00	0.40
convert4MSstats	0.91	0.02	0.93
convert4aLFQ	0.65	0.01	0.67
convert4mapDIA	0.85	0.02	0.86
convert4pythonscript	0.26	0.00	0.27
count_analytes	0.27	0.00	0.26
disaggregate	0.70	0.01	0.72
filter_all_peptides	0.27	0.00	0.27
filter_mscore_all	0.33	0.00	0.33
filter_mscore_fdr	0.78	0.00	0.78
filter_on_max_peptides	0.32	0.00	0.33
filter_on_min_peptides	0.32	0.00	0.31
filter_proteotypic_peptides	0.39	0.00	0.39
import_data	0.69	0.01	0.71
mscore4assayfdr	0.56	0.00	0.56
mscore4pepfdr	0.44	0.00	0.44
mscore4protfdr	0.37	0.00	0.37
plot.fdr_cube	0.41	0.00	0.41
plot.fdr_table	0.47	0.02	0.48
plot_correlation_between_samples	1.32	0.00	1.33
plot_variation	1.35	0.01	1.36
plot_variation_vs_total	0.81	0.00	0.81
reduce_OpenSWATH_output	0.36	0.00	0.36
removeDecoyProteins	0.33	0.02	0.35
sample_annotation	0.28	0.00	0.28
transform_MSstats_OpenSWATH	0	0	0
unifyProteinGroupLabels	0.28	0.00	0.28
write_matrix_peptides	0.31	0.00	0.31
write_matrix_proteins	0.28	0.02	0.30

name	user	system	elapsed
assess_decoy_rate	0.23	0.02	0.25
assess_fdr_byrun	0.43	0.00	0.47
assess_fdr_overall	0.41	0.00	0.40
convert4MSstats	1.23	0.03	1.27
convert4aLFQ	0.78	0.00	0.78
convert4mapDIA	0.78	0.00	0.78
convert4pythonscript	0.24	0.00	0.23
count_analytes	0.25	0.00	0.25
disaggregate	0.53	0.00	0.54
filter_all_peptides	0.25	0.00	0.25
filter_mscore_all	0.31	0.00	0.31
filter_mscore_fdr	0.66	0.00	0.65
filter_on_max_peptides	0.37	0.02	0.39
filter_on_min_peptides	0.55	0.04	0.57
filter_proteotypic_peptides	0.30	0.00	0.29
import_data	0.54	0.07	0.61
mscore4assayfdr	0.61	0.00	0.61
mscore4pepfdr	0.8	0.0	0.8
mscore4protfdr	0.59	0.00	0.59
plot.fdr_cube	0.44	0.00	0.44
plot.fdr_table	0.44	0.00	0.44
plot_correlation_between_samples	1.75	0.00	1.75
plot_variation	1.57	0.03	1.60
plot_variation_vs_total	0.64	0.00	0.64
reduce_OpenSWATH_output	0.23	0.00	0.23
removeDecoyProteins	0.20	0.01	0.22
sample_annotation	0.22	0.00	0.22
transform_MSstats_OpenSWATH	0	0	0
unifyProteinGroupLabels	0.23	0.00	0.23
write_matrix_peptides	0.25	0.00	0.25
write_matrix_proteins	0.24	0.00	0.23