BioC 3.5: CHECK report for SWATH2stats on toluca2

Package: SWATH2stats

Version: 1.5.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SWATH2stats_1.5.8.tar.gz

StartedAt: 2017-04-23 10:35:28 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 10:36:53 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 85.1 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_1.5.8.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 r72187)
* 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 ‘1.5.8’
* 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	0.420	0.005	0.508
assess_fdr_byrun	0.495	0.007	0.590
assess_fdr_overall	0.545	0.008	0.674
convert4MSstats	1.193	0.020	1.488
convert4aLFQ	1.045	0.021	1.256
convert4mapDIA	1.133	0.026	1.361
convert4pythonscript	0.374	0.004	0.460
count_analytes	0.371	0.004	0.432
disaggregate	0.759	0.016	0.902
filter_all_peptides	0.353	0.002	0.422
filter_mscore_all	0.432	0.004	0.520
filter_mscore_fdr	0.761	0.006	0.919
filter_on_max_peptides	0.495	0.005	0.582
filter_on_min_peptides	0.439	0.003	0.513
filter_proteotypic_peptides	0.365	0.005	0.427
import_data	0.583	0.026	0.708
mscore4assayfdr	0.623	0.011	0.739
mscore4pepfdr	0.600	0.003	0.695
mscore4protfdr	0.537	0.004	0.631
plot.fdr_cube	0.583	0.003	0.689
plot.fdr_table	0.584	0.006	0.685
plot_correlation_between_samples	1.845	0.007	2.158
plot_variation	2.048	0.022	2.392
plot_variation_vs_total	0.967	0.018	1.121
reduce_OpenSWATH_output	0.339	0.002	0.395
removeDecoyProteins	0.354	0.003	0.418
sample_annotation	0.334	0.002	0.377
transform_MSstats_OpenSWATH	0.007	0.001	0.009
unifyProteinGroupLabels	0.358	0.003	0.419
write_matrix_peptides	0.392	0.009	0.462
write_matrix_proteins	0.364	0.003	0.421