BioC 3.5: CHECK report for SWATH2stats on oaxaca

Package: SWATH2stats

Version: 1.5.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SWATH2stats_1.5.7.tar.gz

StartedAt: 2017-03-04 09:50:08 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 09:51:31 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 83.0 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_1.5.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SWATH2stats.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.5.7’
* 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	0.442	0.009	0.451
assess_fdr_byrun	0.411	0.010	0.421
assess_fdr_overall	0.425	0.008	0.432
convert4MSstats	1.179	0.022	1.285
convert4aLFQ	0.974	0.025	1.000
convert4mapDIA	1.197	0.025	1.224
convert4pythonscript	0.366	0.002	0.370
count_analytes	0.361	0.002	0.363
disaggregate	0.717	0.017	0.734
filter_all_peptides	0.357	0.003	0.360
filter_mscore_all	0.401	0.005	0.406
filter_mscore_fdr	0.803	0.014	0.820
filter_on_max_peptides	0.513	0.009	0.522
filter_on_min_peptides	0.404	0.004	0.408
filter_proteotypic_peptides	0.343	0.006	0.349
import_data	0.576	0.026	0.603
mscore4assayfdr	0.653	0.016	0.669
mscore4pepfdr	0.613	0.008	0.621
mscore4protfdr	0.533	0.002	0.536
plot.fdr_cube	0.585	0.004	0.589
plot.fdr_table	0.537	0.005	0.544
plot_correlation_between_samples	1.726	0.006	1.734
plot_variation	1.753	0.025	1.778
plot_variation_vs_total	0.909	0.018	0.927
reduce_OpenSWATH_output	0.363	0.002	0.365
removeDecoyProteins	0.363	0.002	0.366
sample_annotation	0.357	0.002	0.360
transform_MSstats_OpenSWATH	0.008	0.000	0.009
unifyProteinGroupLabels	0.408	0.003	0.411
write_matrix_peptides	0.390	0.010	0.401
write_matrix_proteins	0.358	0.002	0.359