BioC 3.4: CHECK report for SWATH2stats on morelia

Package: SWATH2stats

Version: 1.3.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SWATH2stats_1.3.10.tar.gz

StartedAt: 2016-09-20 13:42:50 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 13:43:42 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 52.6 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_1.3.10.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/SWATH2stats.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.3.10’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘imsbInfer’
* 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 ... 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 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-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	0.235	0.004	0.239
assess_fdr_byrun	0.378	0.007	0.384
assess_fdr_overall	0.458	0.007	0.466
convert4MSstats	0.730	0.019	0.749
convert4aLFQ	0.712	0.023	0.736
convert4mapDIA	0.761	0.017	0.779
convert4pythonscript	0.249	0.005	0.254
count_analytes	0.275	0.004	0.279
disaggregate	0.731	0.018	0.749
filter_all_peptides	0.312	0.002	0.314
filter_mscore_all	0.322	0.003	0.325
filter_mscore_fdr	0.613	0.034	0.647
filter_on_max_peptides	0.399	0.003	0.401
filter_on_min_peptides	0.398	0.008	0.407
filter_proteotypic_peptides	0.350	0.004	0.354
import_data	0.527	0.025	0.551
mscore4assayfdr	0.666	0.012	0.679
mscore4pepfdr	0.490	0.003	0.494
mscore4protfdr	0.590	0.017	0.609
plot.fdr_cube	0.452	0.005	0.460
plot.fdr_table	0.255	0.003	0.259
plot_correlation_between_samples	0.426	0.004	0.431
plot_variation	0.841	0.022	0.864
plot_variation_vs_total	0.566	0.012	0.578
reduce_OpenSWATH_output	0.227	0.002	0.229
sample_annotation	0.373	0.002	0.376
transform_MSstats_OpenSWATH	0.007	0.001	0.007
write_matrix_peptides	0.479	0.014	0.495
write_matrix_proteins	0.284	0.002	0.286