BioC 3.6: CHECK report for SWATH2stats on veracruz1

Package: SWATH2stats

Version: 1.7.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SWATH2stats_1.7.2.tar.gz

StartedAt: 2017-08-16 09:02:04 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 09:03:14 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 69.6 seconds

RetCode: 0

Status:  OK

CheckDir: SWATH2stats.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SWATH2stats_1.7.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/SWATH2stats.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SWATH2stats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SWATH2stats’ version ‘1.7.2’
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/SWATH2stats.Rcheck/00check.log’
for details.

* 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
* DONE (SWATH2stats)

name	user	system	elapsed
assess_decoy_rate	0.323	0.005	0.340
assess_fdr_byrun	0.420	0.007	0.453
assess_fdr_overall	0.392	0.009	0.407
convert4MSstats	1.055	0.021	1.108
convert4aLFQ	0.925	0.025	0.978
convert4mapDIA	1.055	0.022	1.128
convert4pythonscript	0.355	0.003	0.372
count_analytes	0.342	0.004	0.355
disaggregate	0.756	0.019	0.793
filter_all_peptides	0.345	0.004	0.350
filter_mscore_all	0.405	0.005	0.423
filter_mscore_fdr	0.722	0.009	0.740
filter_on_max_peptides	0.401	0.002	0.451
filter_on_min_peptides	0.513	0.018	0.507
filter_proteotypic_peptides	0.361	0.009	0.361
import_data	0.534	0.020	0.567
mscore4assayfdr	0.487	0.005	0.522
mscore4pepfdr	0.498	0.008	0.513
mscore4protfdr	0.430	0.005	0.455
plot.fdr_cube	0.431	0.003	0.440
plot.fdr_table	0.415	0.003	0.423
plot_correlation_between_samples	1.405	0.005	1.464
plot_variation	1.497	0.014	1.541
plot_variation_vs_total	0.732	0.014	0.768
reduce_OpenSWATH_output	0.270	0.002	0.271
removeDecoyProteins	0.267	0.001	0.271
sample_annotation	0.264	0.002	0.283
transform_MSstats_OpenSWATH	0.007	0.001	0.007
unifyProteinGroupLabels	0.297	0.001	0.304
write_matrix_peptides	0.321	0.008	0.334
write_matrix_proteins	0.249	0.001	0.254