Multiple platform build/check report for BioC 3.6 - CHECK report for SWATH2stats on tokay1

Package: SWATH2stats

Version: 1.8.1

Command: rm -rf SWATH2stats.buildbin-libdir SWATH2stats.Rcheck && mkdir SWATH2stats.buildbin-libdir SWATH2stats.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SWATH2stats.buildbin-libdir SWATH2stats_1.8.1.tar.gz >SWATH2stats.Rcheck\00install.out 2>&1 && cp SWATH2stats.Rcheck\00install.out SWATH2stats-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SWATH2stats.buildbin-libdir --install="check:SWATH2stats-install.out" --force-multiarch --no-vignettes --timings SWATH2stats_1.8.1.tar.gz

StartedAt: 2018-04-12 03:30:37 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:32:44 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 127.3 seconds

RetCode: 0

Status: WARNINGS

CheckDir: SWATH2stats.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf SWATH2stats.buildbin-libdir SWATH2stats.Rcheck && mkdir SWATH2stats.buildbin-libdir SWATH2stats.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SWATH2stats.buildbin-libdir SWATH2stats_1.8.1.tar.gz >SWATH2stats.Rcheck\00install.out 2>&1 && cp SWATH2stats.Rcheck\00install.out SWATH2stats-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SWATH2stats.buildbin-libdir --install="check:SWATH2stats-install.out" --force-multiarch --no-vignettes --timings SWATH2stats_1.8.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SWATH2stats.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SWATH2stats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SWATH2stats' version '1.8.1'
* 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 whether package 'SWATH2stats' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi8VKEE/R.INSTALL384c4a1e4bc8/SWATH2stats/man/SWATH2stats-package.Rd:44: missing file link 'aLFQ'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SWATH2stats.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  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 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/SWATH2stats.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'SWATH2stats' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'SWATH2stats'
    finding HTML links ... done
    MSstats_data                            html  
    OpenSWATH_data                          html  
    SWATH2stats-package                     html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi8VKEE/R.INSTALL384c4a1e4bc8/SWATH2stats/man/SWATH2stats-package.Rd:44: missing file link 'aLFQ'
    Spyogenes                               html  
    Study_design                            html  
    assess_decoy_rate                       html  
    assess_fdr_byrun                        html  
    assess_fdr_overall                      html  
    convert4MSstats                         html  
    convert4PECA                            html  
    convert4aLFQ                            html  
    convert4mapDIA                          html  
    convert4pythonscript                    html  
    count_analytes                          html  
    disaggregate                            html  
    filter_all_peptides                     html  
    filter_mscore_all                       html  
    filter_mscore_fdr                       html  
    filter_on_max_peptides                  html  
    filter_on_min_peptides                  html  
    filter_proteotypic_peptides             html  
    import_data                             html  
    mscore4assayfdr                         html  
    mscore4pepfdr                           html  
    mscore4protfdr                          html  
    plot.fdr_cube                           html  
    plot.fdr_table                          html  
    plot_correlation_between_samples        html  
    plot_variation                          html  
    plot_variation_vs_total                 html  
    reduce_OpenSWATH_output                 html  
    removeDecoyProteins                     html  
    sample_annotation                       html  
    transform_MSstats_OpenSWATH             html  
    unifyProteinGroupLabels                 html  
    write_matrix_peptides                   html  
    write_matrix_proteins                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'SWATH2stats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SWATH2stats' as SWATH2stats_1.8.1.zip
* DONE (SWATH2stats)
In R CMD INSTALL
In R CMD INSTALL


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> test_check("SWATH2stats")
Loading required package: SWATH2stats
[1] "peterb_J131223_054"
[1] "peterb_L150425_011_SW"
[1] "peterb_L150514_002_SW"
== testthat results  ===========================================================
OK: 118 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  11.95    0.17   12.20


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> test_check("SWATH2stats")
Loading required package: SWATH2stats
[1] "peterb_J131223_054"
[1] "peterb_L150425_011_SW"
[1] "peterb_L150514_002_SW"
== testthat results  ===========================================================
OK: 118 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  12.93    0.06   13.12

name	user	system	elapsed
assess_decoy_rate	0.31	0.00	0.32
assess_fdr_byrun	0.46	0.00	0.45
assess_fdr_overall	0.37	0.02	0.39
convert4MSstats	1.03	0.00	1.03
convert4PECA	0.42	0.00	0.42
convert4aLFQ	0.67	0.00	0.67
convert4mapDIA	0.69	0.00	0.69
convert4pythonscript	0.30	0.01	0.31
count_analytes	0.28	0.00	0.28
disaggregate	0.50	0.02	0.52
filter_all_peptides	0.28	0.00	0.28
filter_mscore_all	0.33	0.00	0.33
filter_mscore_fdr	0.58	0.00	0.58
filter_on_max_peptides	0.5	0.0	0.5
filter_on_min_peptides	0.32	0.00	0.32
filter_proteotypic_peptides	0.28	0.00	0.28
import_data	0.61	0.02	0.63
mscore4assayfdr	0.5	0.0	0.5
mscore4pepfdr	0.45	0.00	0.45
mscore4protfdr	0.41	0.00	0.40
plot.fdr_cube	0.39	0.00	0.40
plot.fdr_table	0.44	0.00	0.43
plot_correlation_between_samples	1.09	0.00	1.10
plot_variation	1.45	0.00	1.45
plot_variation_vs_total	0.72	0.00	0.72
reduce_OpenSWATH_output	0.25	0.00	0.25
removeDecoyProteins	0.32	0.00	0.31
sample_annotation	0.28	0.00	0.28
transform_MSstats_OpenSWATH	0.01	0.00	0.02
unifyProteinGroupLabels	0.24	0.03	0.26
write_matrix_peptides	0.53	0.00	0.53
write_matrix_proteins	0.36	0.00	0.36

name	user	system	elapsed
assess_decoy_rate	0.20	0.00	0.21
assess_fdr_byrun	0.40	0.00	0.41
assess_fdr_overall	0.31	0.01	0.32
convert4MSstats	0.88	0.00	0.88
convert4PECA	0.39	0.02	0.40
convert4aLFQ	0.65	0.01	0.68
convert4mapDIA	0.67	0.00	0.67
convert4pythonscript	0.23	0.02	0.25
count_analytes	0.25	0.00	0.25
disaggregate	0.47	0.02	0.48
filter_all_peptides	0.23	0.00	0.24
filter_mscore_all	0.25	0.01	0.26
filter_mscore_fdr	0.63	0.00	0.62
filter_on_max_peptides	0.28	0.00	0.29
filter_on_min_peptides	0.28	0.03	0.29
filter_proteotypic_peptides	0.22	0.00	0.22
import_data	0.56	0.00	0.56
mscore4assayfdr	0.49	0.00	0.48
mscore4pepfdr	0.45	0.00	0.45
mscore4protfdr	0.39	0.00	0.39
plot.fdr_cube	0.41	0.00	0.41
plot.fdr_table	0.39	0.00	0.39
plot_correlation_between_samples	1.30	0.03	1.33
plot_variation	1.46	0.00	1.47
plot_variation_vs_total	0.63	0.02	0.64
reduce_OpenSWATH_output	0.23	0.00	0.23
removeDecoyProteins	0.24	0.00	0.24
sample_annotation	0.23	0.00	0.23
transform_MSstats_OpenSWATH	0.01	0.00	0.01
unifyProteinGroupLabels	0.24	0.00	0.24
write_matrix_peptides	0.25	0.01	0.26
write_matrix_proteins	0.22	0.00	0.22

CHECK report for SWATH2stats on tokay1

Summary

Command output

Installation output

Tests output

Example timings