BioC 3.3: CHECK report for SWATH2stats on oaxaca

Package: SWATH2stats

Version: 1.2.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SWATH2stats_1.2.3.tar.gz

StartedAt: 2016-10-13 06:45:19 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 06:46:17 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 58.2 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_1.2.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-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 ‘1.2.3’
* 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-3.3-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	0.359	0.006	0.365
assess_fdr_byrun	0.529	0.005	0.534
assess_fdr_overall	0.439	0.007	0.446
convert4MSstats	1.054	0.029	1.087
convert4aLFQ	0.983	0.030	1.014
convert4mapDIA	1.070	0.022	1.094
convert4pythonscript	0.447	0.006	0.453
count_analytes	0.440	0.003	0.444
disaggregate	0.760	0.017	0.778
filter_all_peptides	0.394	0.002	0.396
filter_mscore_all	0.461	0.005	0.467
filter_mscore_fdr	0.819	0.049	0.868
filter_on_max_peptides	0.499	0.006	0.506
filter_on_min_peptides	0.413	0.003	0.416
filter_proteotypic_peptides	0.363	0.007	0.370
import_data	0.532	0.031	0.563
mscore4assayfdr	0.63	0.01	0.64
mscore4pepfdr	0.635	0.010	0.646
mscore4protfdr	0.541	0.004	0.546
plot.fdr_cube	0.310	0.003	0.314
plot.fdr_table	0.413	0.005	0.419
plot_correlation_between_samples	0.681	0.018	0.713
plot_variation	0.816	0.017	0.834
plot_variation_vs_total	0.794	0.019	0.818
reduce_OpenSWATH_output	0.351	0.002	0.353
sample_annotation	0.374	0.001	0.376
transform_MSstats_OpenSWATH	0.007	0.000	0.007
write_matrix_peptides	0.396	0.007	0.402
write_matrix_proteins	0.407	0.002	0.409