BioC 3.4: CHECK report for SWATH2stats on morelia

Package: SWATH2stats

Version: 1.4.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SWATH2stats_1.4.1.tar.gz

StartedAt: 2017-04-15 08:43:14 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 08:44:18 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 64.0 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_1.4.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/SWATH2stats.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.4.1’
* 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-3.4-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	0.351	0.005	0.356
assess_fdr_byrun	0.458	0.005	0.465
assess_fdr_overall	0.404	0.008	0.415
convert4MSstats	1.006	0.027	1.035
convert4aLFQ	0.869	0.021	0.892
convert4mapDIA	0.896	0.021	0.918
convert4pythonscript	0.341	0.002	0.343
count_analytes	0.410	0.004	0.415
disaggregate	0.646	0.019	0.666
filter_all_peptides	0.331	0.002	0.332
filter_mscore_all	0.514	0.009	0.525
filter_mscore_fdr	0.765	0.030	0.798
filter_on_max_peptides	0.408	0.008	0.416
filter_on_min_peptides	0.378	0.004	0.384
filter_proteotypic_peptides	0.366	0.002	0.368
import_data	0.564	0.027	0.591
mscore4assayfdr	0.545	0.007	0.551
mscore4pepfdr	0.637	0.006	0.644
mscore4protfdr	0.581	0.018	0.599
plot.fdr_cube	0.385	0.006	0.391
plot.fdr_table	0.377	0.004	0.381
plot_correlation_between_samples	0.624	0.005	0.629
plot_variation	0.602	0.013	0.615
plot_variation_vs_total	0.597	0.014	0.610
reduce_OpenSWATH_output	0.238	0.001	0.239
sample_annotation	0.244	0.002	0.247
transform_MSstats_OpenSWATH	0.005	0.001	0.005
write_matrix_peptides	0.352	0.005	0.358
write_matrix_proteins	0.296	0.002	0.299