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: 2017-08-16 03:14:17 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 03:16:16 -0400 (Wed, 16 Aug 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 3.4.1 (2017-06-30)
* 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	0.27	0.02	0.28
assess_fdr_byrun	0.45	0.00	0.46
assess_fdr_overall	0.38	0.00	0.38
convert4MSstats	0.98	0.01	1.00
convert4aLFQ	0.71	0.00	0.70
convert4mapDIA	0.92	0.02	0.94
convert4pythonscript	0.47	0.01	0.48
count_analytes	0.53	0.00	0.53
disaggregate	0.91	0.00	0.91
filter_all_peptides	0.29	0.00	0.30
filter_mscore_all	0.42	0.00	0.42
filter_mscore_fdr	0.54	0.00	0.53
filter_on_max_peptides	0.32	0.00	0.33
filter_on_min_peptides	0.61	0.00	0.61
filter_proteotypic_peptides	0.30	0.00	0.29
import_data	0.69	0.00	0.69
mscore4assayfdr	0.53	0.00	0.53
mscore4pepfdr	0.55	0.00	0.55
mscore4protfdr	0.39	0.00	0.39
plot.fdr_cube	0.43	0.00	0.44
plot.fdr_table	0.44	0.00	0.43
plot_correlation_between_samples	1.33	0.02	1.35
plot_variation	1.16	0.00	1.15
plot_variation_vs_total	0.54	0.03	0.58
reduce_OpenSWATH_output	0.25	0.00	0.25
removeDecoyProteins	0.27	0.00	0.27
sample_annotation	0.23	0.00	0.23
transform_MSstats_OpenSWATH	0	0	0
unifyProteinGroupLabels	0.24	0.00	0.28
write_matrix_peptides	0.28	0.00	0.28
write_matrix_proteins	0.25	0.00	0.25

name	user	system	elapsed
assess_decoy_rate	0.25	0.01	0.26
assess_fdr_byrun	0.41	0.02	0.42
assess_fdr_overall	0.33	0.00	0.33
convert4MSstats	1.10	0.02	1.11
convert4aLFQ	0.90	0.01	0.92
convert4mapDIA	0.85	0.00	0.84
convert4pythonscript	0.23	0.00	0.24
count_analytes	0.25	0.00	0.25
disaggregate	0.55	0.00	0.54
filter_all_peptides	0.23	0.00	0.24
filter_mscore_all	0.31	0.00	0.31
filter_mscore_fdr	0.99	0.00	0.98
filter_on_max_peptides	0.64	0.00	0.64
filter_on_min_peptides	0.37	0.00	0.38
filter_proteotypic_peptides	0.3	0.0	0.3
import_data	0.56	0.03	0.59
mscore4assayfdr	0.49	0.00	0.48
mscore4pepfdr	0.53	0.00	0.54
mscore4protfdr	0.45	0.00	0.45
plot.fdr_cube	0.39	0.00	0.39
plot.fdr_table	0.64	0.00	0.64
plot_correlation_between_samples	1.64	0.03	1.67
plot_variation	1.69	0.04	1.72
plot_variation_vs_total	0.72	0.00	0.72
reduce_OpenSWATH_output	0.22	0.00	0.22
removeDecoyProteins	0.22	0.00	0.22
sample_annotation	0.39	0.00	0.40
transform_MSstats_OpenSWATH	0	0	0
unifyProteinGroupLabels	0.31	0.01	0.33
write_matrix_peptides	0.38	0.00	0.38
write_matrix_proteins	0.32	0.00	0.32