BioC 3.5: CHECK report for SWATH2stats on veracruz2

Package: SWATH2stats

Version: 1.6.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SWATH2stats_1.6.1.tar.gz

StartedAt: 2017-10-18 09:34:05 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 09:35:17 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 71.3 seconds

RetCode: 0

Status:  OK

CheckDir: SWATH2stats.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SWATH2stats_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SWATH2stats.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.6.1’
* 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 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-3.5-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	0.371	0.007	0.386
assess_fdr_byrun	0.362	0.009	0.381
assess_fdr_overall	0.289	0.007	0.304
convert4MSstats	0.901	0.019	0.944
convert4aLFQ	0.684	0.016	0.716
convert4mapDIA	0.947	0.027	0.997
convert4pythonscript	0.246	0.004	0.255
count_analytes	0.251	0.004	0.259
disaggregate	0.572	0.017	0.602
filter_all_peptides	0.339	0.005	0.362
filter_mscore_all	0.317	0.009	0.306
filter_mscore_fdr	0.896	0.045	0.641
filter_on_max_peptides	0.388	0.015	0.369
filter_on_min_peptides	0.799	0.170	0.373
filter_proteotypic_peptides	0.656	0.159	0.301
import_data	0.417	0.022	0.448
mscore4assayfdr	0.480	0.007	0.500
mscore4pepfdr	0.406	0.011	0.449
mscore4protfdr	0.342	0.004	0.357
plot.fdr_cube	0.393	0.004	0.406
plot.fdr_table	0.406	0.004	0.421
plot_correlation_between_samples	1.467	0.013	1.538
plot_variation	1.655	0.026	1.741
plot_variation_vs_total	0.813	0.024	0.878
reduce_OpenSWATH_output	0.285	0.002	0.300
removeDecoyProteins	0.295	0.003	0.306
sample_annotation	0.293	0.003	0.316
transform_MSstats_OpenSWATH	0.007	0.001	0.008
unifyProteinGroupLabels	0.301	0.003	0.320
write_matrix_peptides	0.329	0.011	0.358
write_matrix_proteins	0.299	0.003	0.319