Multiple platform build/check report for BioC 3.9 - CHECK report for SWATH2stats on tokay2

Package: SWATH2stats

Version: 1.14.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SWATH2stats.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SWATH2stats_1.14.0.tar.gz

StartedAt: 2019-10-16 07:27:37 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:31:02 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 204.6 seconds

RetCode: 0

Status: OK

CheckDir: SWATH2stats.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SWATH2stats.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SWATH2stats_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SWATH2stats.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.14.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'imsbInfer', 'aLFQ'
* 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 ... 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
* 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
* 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
convert_protein_ids  0.8      0   10.17
** 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/SWATH2stats.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/SWATH2stats_1.14.0.tar.gz && rm -rf SWATH2stats.buildbin-libdir && mkdir SWATH2stats.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SWATH2stats.buildbin-libdir SWATH2stats_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SWATH2stats_1.14.0.zip && rm SWATH2stats_1.14.0.tar.gz SWATH2stats_1.14.0.zip
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2646k  100 2646k    0     0  28.6M      0 --:--:-- --:--:-- --:--:-- 31.1M

install for i386

* installing *source* package 'SWATH2stats' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SWATH2stats'
    finding HTML links ... done
    JPP_update                              html  
    MSstats_data                            html  
    OpenSWATH_data                          html  
    SWATH2stats-package                     html  
    Spyogenes                               html  
    Study_design                            html  
    add_genesymbol                          html  
    assess_decoy_rate                       html  
    assess_fdr_byrun                        html  
    assess_fdr_overall                      html  
    convert4MSstats                         html  
    convert4PECA                            html  
    convert4aLFQ                            html  
    convert4mapDIA                          html  
    convert4pythonscript                    html  
    convert_protein_ids                     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  
    load_mart                               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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'SWATH2stats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SWATH2stats' as SWATH2stats_1.14.0.zip
* DONE (SWATH2stats)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SWATH2stats' successfully unpacked and MD5 sums checked


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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: 113 | SKIPPED: 0 | WARNINGS: 11 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  10.42    0.60   15.90


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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: 113 | SKIPPED: 0 | WARNINGS: 11 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  14.21    0.40   17.62

name	user	system	elapsed
JPP_update	0.19	0.00	0.18
add_genesymbol	0.00	0.02	0.02
assess_decoy_rate	0.14	0.02	0.16
assess_fdr_byrun	0.29	0.01	0.31
assess_fdr_overall	0.22	0.02	0.24
convert4MSstats	0.42	0.00	0.42
convert4PECA	0.22	0.01	0.23
convert4aLFQ	0.69	0.00	0.69
convert4mapDIA	1.03	0.00	1.03
convert4pythonscript	0.22	0.00	0.22
convert_protein_ids	0.80	0.00	10.17
count_analytes	0.18	0.00	0.19
disaggregate	0.69	0.00	0.69
filter_all_peptides	0.2	0.0	0.2
filter_mscore_all	0.19	0.00	0.19
filter_mscore_fdr	0.56	0.00	0.56
filter_on_max_peptides	0.25	0.02	0.27
filter_on_min_peptides	0.22	0.05	0.26
filter_proteotypic_peptides	0.19	0.00	0.19
import_data	0.74	0.03	0.77
load_mart	0.64	0.00	2.51
mscore4assayfdr	0.45	0.00	0.45
mscore4pepfdr	0.28	0.00	0.29
mscore4protfdr	0.27	0.00	0.26
plot.fdr_cube	0.15	0.01	0.17
plot.fdr_table	0.16	0.00	0.16
plot_correlation_between_samples	0.53	0.00	0.53
plot_variation	0.44	0.02	0.45
plot_variation_vs_total	0.36	0.01	0.38
reduce_OpenSWATH_output	0.11	0.02	0.12
removeDecoyProteins	0.17	0.00	0.18
sample_annotation	0.22	0.00	0.21
transform_MSstats_OpenSWATH	0.01	0.00	0.02
unifyProteinGroupLabels	0.17	0.00	0.17
write_matrix_peptides	0.22	0.00	0.22
write_matrix_proteins	0.19	0.00	0.19

name	user	system	elapsed
JPP_update	0.09	0.00	0.10
add_genesymbol	0.02	0.00	0.01
assess_decoy_rate	0.11	0.00	0.11
assess_fdr_byrun	0.22	0.02	0.23
assess_fdr_overall	0.14	0.00	0.15
convert4MSstats	0.61	0.02	0.62
convert4PECA	0.23	0.00	0.23
convert4aLFQ	0.66	0.00	0.66
convert4mapDIA	0.46	0.00	0.47
convert4pythonscript	0.40	0.00	0.39
convert_protein_ids	0.71	0.01	3.22
count_analytes	0.19	0.02	0.20
disaggregate	0.44	0.01	0.46
filter_all_peptides	0.12	0.00	0.12
filter_mscore_all	0.19	0.00	0.18
filter_mscore_fdr	0.39	0.00	0.39
filter_on_max_peptides	0.17	0.03	0.19
filter_on_min_peptides	0.19	0.00	0.19
filter_proteotypic_peptides	0.15	0.02	0.17
import_data	0.63	0.00	0.63
load_mart	0.59	0.01	2.50
mscore4assayfdr	0.41	0.00	0.40
mscore4pepfdr	0.28	0.00	0.28
mscore4protfdr	0.22	0.02	0.24
plot.fdr_cube	0.17	0.00	0.17
plot.fdr_table	0.19	0.02	0.20
plot_correlation_between_samples	0.59	0.00	0.60
plot_variation	0.52	0.01	0.53
plot_variation_vs_total	0.45	0.02	0.47
reduce_OpenSWATH_output	0.13	0.00	0.13
removeDecoyProteins	0.14	0.00	0.14
sample_annotation	0.11	0.02	0.12
transform_MSstats_OpenSWATH	0.00	0.01	0.02
unifyProteinGroupLabels	0.10	0.04	0.14
write_matrix_peptides	0.16	0.00	0.16
write_matrix_proteins	0.2	0.0	0.2

CHECK report for SWATH2stats on tokay2

Summary

Command output

Installation output

Tests output

Example timings