Multiple platform build/check report for BioC 3.11 - CHECK report for SWATH2stats on tokay2

Package: SWATH2stats

Version: 1.18.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SWATH2stats.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SWATH2stats_1.18.0.tar.gz

StartedAt: 2020-10-17 08:44:30 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 08:51:02 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 391.9 seconds

RetCode: 0

Status: OK

CheckDir: SWATH2stats.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SWATH2stats.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SWATH2stats_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/SWATH2stats.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.18.0'
* 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 (user + system) or elapsed time > 5s
                     user system elapsed
convert_protein_ids 12.55   0.03   16.86
load_mart           10.94   0.01   14.48
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
convert_protein_ids 9.69   0.04   13.97
load_mart           7.86   0.00   11.50
* 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-3.11-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/3.11/bioc/src/contrib/SWATH2stats_1.18.0.tar.gz && rm -rf SWATH2stats.buildbin-libdir && mkdir SWATH2stats.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SWATH2stats.buildbin-libdir SWATH2stats_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL SWATH2stats_1.18.0.zip && rm SWATH2stats_1.18.0.tar.gz SWATH2stats_1.18.0.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  25.7M      0 --:--:-- --:--:-- --:--:-- 27.4M

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_1.18.0.zip
* DONE (SWATH2stats)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'SWATH2stats' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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: 13 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  27.31    0.45   37.15


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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: 13 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  21.70    0.40   30.54

name	user	system	elapsed
JPP_update	0.17	0.00	0.17
add_genesymbol	0.02	0.00	0.01
assess_decoy_rate	0.11	0.00	0.11
assess_fdr_byrun	0.19	0.06	0.25
assess_fdr_overall	0.20	0.02	0.22
convert4MSstats	0.46	0.00	0.45
convert4PECA	0.21	0.00	0.22
convert4aLFQ	0.46	0.00	0.45
convert4mapDIA	0.75	0.00	0.75
convert4pythonscript	0.12	0.00	0.13
convert_protein_ids	12.55	0.03	16.86
count_analytes	0.22	0.01	0.23
disaggregate	0.81	0.00	0.81
filter_all_peptides	0.16	0.00	0.16
filter_mscore_all	0.2	0.0	0.2
filter_mscore_fdr	0.77	0.00	0.77
filter_on_max_peptides	0.26	0.02	0.28
filter_on_min_peptides	0.25	0.01	0.27
filter_proteotypic_peptides	0.17	0.00	0.17
import_data	0.80	0.02	0.81
load_mart	10.94	0.01	14.48
mscore4assayfdr	0.81	0.00	0.82
mscore4pepfdr	0.28	0.00	0.28
mscore4protfdr	0.25	0.00	0.25
plot.fdr_cube	0.14	0.02	0.15
plot.fdr_table	0.17	0.00	0.43
plot_correlation_between_samples	0.59	0.00	0.60
plot_variation	0.74	0.02	0.75
plot_variation_vs_total	0.40	0.01	0.42
reduce_OpenSWATH_output	0.13	0.00	0.12
removeDecoyProteins	0.11	0.00	0.11
sample_annotation	0.11	0.02	0.13
transform_MSstats_OpenSWATH	0	0	0
unifyProteinGroupLabels	0.12	0.00	0.12
write_matrix_peptides	0.12	0.01	0.14
write_matrix_proteins	0.14	0.00	0.14

name	user	system	elapsed
JPP_update	0.16	0.00	0.15
add_genesymbol	0	0	0
assess_decoy_rate	0.13	0.00	0.12
assess_fdr_byrun	0.36	0.01	0.47
assess_fdr_overall	0.25	0.02	0.27
convert4MSstats	0.96	0.03	1.00
convert4PECA	0.25	0.02	0.26
convert4aLFQ	0.93	0.01	0.94
convert4mapDIA	0.43	0.02	0.45
convert4pythonscript	0.14	0.00	0.14
convert_protein_ids	9.69	0.04	13.97
count_analytes	0.22	0.00	0.22
disaggregate	1.08	0.00	1.07
filter_all_peptides	0.23	0.00	0.24
filter_mscore_all	0.27	0.00	0.26
filter_mscore_fdr	0.59	0.00	0.60
filter_on_max_peptides	0.27	0.00	0.26
filter_on_min_peptides	0.26	0.00	0.27
filter_proteotypic_peptides	0.22	0.00	0.22
import_data	0.69	0.03	0.72
load_mart	7.86	0.00	11.50
mscore4assayfdr	0.41	0.01	0.42
mscore4pepfdr	0.32	0.00	0.33
mscore4protfdr	0.24	0.00	0.23
plot.fdr_cube	0.17	0.00	0.17
plot.fdr_table	0.17	0.00	0.18
plot_correlation_between_samples	0.36	0.00	0.35
plot_variation	0.44	0.00	0.44
plot_variation_vs_total	0.50	0.02	0.52
reduce_OpenSWATH_output	0.14	0.00	0.14
removeDecoyProteins	0.14	0.00	0.14
sample_annotation	0.14	0.00	0.15
transform_MSstats_OpenSWATH	0	0	0
unifyProteinGroupLabels	0.14	0.01	0.15
write_matrix_peptides	0.14	0.00	0.14
write_matrix_proteins	0.12	0.00	0.13

CHECK report for SWATH2stats on tokay2

Summary

Command output

Installation output

Tests output

Example timings