BioC 3.5: CHECK report for SWATH2stats on malbec2

Package: SWATH2stats

Version: 1.6.1

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings SWATH2stats_1.6.1.tar.gz

StartedAt: 2017-10-18 02:48:15 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:49:14 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 59.1 seconds

RetCode: 0

Status:  OK

CheckDir: SWATH2stats.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings SWATH2stats_1.6.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/SWATH2stats.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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 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
  ‘/home/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	0.288	0.000	0.288
assess_fdr_byrun	0.324	0.004	0.328
assess_fdr_overall	0.304	0.000	0.302
convert4MSstats	0.888	0.004	0.894
convert4aLFQ	0.992	0.000	0.996
convert4mapDIA	0.756	0.008	0.762
convert4pythonscript	0.232	0.004	0.236
count_analytes	0.288	0.000	0.286
disaggregate	0.468	0.004	0.472
filter_all_peptides	0.236	0.000	0.234
filter_mscore_all	0.352	0.000	0.344
filter_mscore_fdr	0.472	0.004	0.476
filter_on_max_peptides	0.404	0.000	0.300
filter_on_min_peptides	0.456	0.000	0.356
filter_proteotypic_peptides	0.352	0.000	0.355
import_data	0.524	0.004	0.528
mscore4assayfdr	0.420	0.000	0.423
mscore4pepfdr	0.396	0.000	0.396
mscore4protfdr	0.332	0.000	0.334
plot.fdr_cube	0.352	0.004	0.353
plot.fdr_table	0.352	0.008	0.360
plot_correlation_between_samples	1.180	0.008	1.188
plot_variation	1.620	0.004	1.624
plot_variation_vs_total	0.548	0.000	0.548
reduce_OpenSWATH_output	0.212	0.000	0.210
removeDecoyProteins	0.220	0.004	0.223
sample_annotation	0.204	0.004	0.209
transform_MSstats_OpenSWATH	0.004	0.000	0.005
unifyProteinGroupLabels	0.204	0.004	0.210
write_matrix_peptides	0.236	0.004	0.239
write_matrix_proteins	0.224	0.000	0.221