Multiple platform build/check report for BioC 3.14 - CHECK results for SWATH2stats on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

Package: SWATH2stats

Version: 1.24.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SWATH2stats.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SWATH2stats_1.24.0.tar.gz

StartedAt: 2022-04-13 03:47:51 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 03:55:36 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 464.8 seconds

RetCode: 1

Status: ERROR

CheckDir: SWATH2stats.Rcheck

Warnings: NA

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SWATH2stats.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SWATH2stats_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/SWATH2stats.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.24.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: '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' ... ERROR
Running examples in 'SWATH2stats-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: load_mart
> ### Title: Establish connection to biomaRt database
> ### Aliases: load_mart
> 
> ### ** Examples
> 
> {
+  data_table <- data.frame(Protein = c("Q01581", "P49327", "2/P63261/P60709"),
+                           Abundance = c(100, 3390, 43423))
+  mart <- convert_protein_ids(data_table)
+  }
Warning: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://"
Ensembl site unresponsive, trying uswest mirror
Ensembl site unresponsive, trying asia mirror
Error: Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
load_mart 4.88   0.08   55.29
* 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 ERROR, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/SWATH2stats.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/SWATH2stats_1.24.0.tar.gz && rm -rf SWATH2stats.buildbin-libdir && mkdir SWATH2stats.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SWATH2stats.buildbin-libdir SWATH2stats_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL SWATH2stats_1.24.0.zip && rm SWATH2stats_1.24.0.tar.gz SWATH2stats_1.24.0.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
 19 2667k   19  523k    0     0   606k      0  0:00:04 --:--:--  0:00:04  606k
 74 2667k   74 1995k    0     0  1068k      0  0:00:02  0:00:01  0:00:01 1068k
100 2667k  100 2667k    0     0  1222k      0  0:00:02  0:00:02 --:--:-- 1223k

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  
    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                           html  
    filter_mscore_condition                 html  
    filter_mscore_fdr                       html  
    filter_mscore_freqobs                   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  
    rmDecoyProt                             html  
    sample_annotation                       html  
    transform_MSstats_OpenSWATH             html  
    unifyProteinGroupLabels                 html  
    validate_columns                        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_1.24.0.zip
* DONE (SWATH2stats)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'SWATH2stats' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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"
[ FAIL 0 | WARN 74 | SKIP 0 | PASS 113 ]

[ FAIL 0 | WARN 74 | SKIP 0 | PASS 113 ]
> 
> proc.time()
   user  system elapsed 
  23.39    0.75   73.95


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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"
[ FAIL 0 | WARN 74 | SKIP 0 | PASS 113 ]

[ FAIL 0 | WARN 74 | SKIP 0 | PASS 113 ]
> 
> proc.time()
   user  system elapsed 
  20.60    0.37   47.03

name	user	system	elapsed
JPP_update	0.11	0.00	0.11
add_genesymbol	0	0	0
assess_decoy_rate	0.1	0.0	0.1
assess_fdr_byrun	0.15	0.00	0.15
assess_fdr_overall	0.13	0.03	0.16
convert4MSstats	0.53	0.02	0.55
convert4PECA	0.12	0.00	0.12
convert4aLFQ	0.52	0.01	0.53
convert4mapDIA	0.30	0.02	0.32
convert4pythonscript	0.12	0.02	0.14
convert_protein_ids	0	0	0
count_analytes	0.11	0.00	0.11
disaggregate	0.19	0.01	0.20
filter_all_peptides	0.11	0.00	0.11
filter_mscore	0.14	0.02	0.16
filter_mscore_condition	0.14	0.00	0.14
filter_mscore_fdr	0.33	0.01	0.34
filter_mscore_freqobs	0.12	0.00	0.12
filter_on_max_peptides	0.13	0.00	0.13
filter_on_min_peptides	0.14	0.00	0.14
filter_proteotypic_peptides	0.11	0.00	0.11
import_data	0.57	0.03	0.59

name	user	system	elapsed
JPP_update	0.10	0.02	0.11
add_genesymbol	0.01	0.00	0.01
assess_decoy_rate	0.11	0.00	0.11
assess_fdr_byrun	0.22	0.00	0.21
assess_fdr_overall	0.51	0.00	0.52
convert4MSstats	0.61	0.01	0.62
convert4PECA	0.14	0.00	0.14
convert4aLFQ	0.63	0.00	0.63
convert4mapDIA	0.30	0.02	0.31
convert4pythonscript	0.12	0.00	0.13
convert_protein_ids	0	0	0
count_analytes	0.14	0.00	0.14
disaggregate	0.19	0.00	0.19
filter_all_peptides	0.14	0.00	0.14
filter_mscore	0.16	0.00	0.15
filter_mscore_condition	0.15	0.00	0.16
filter_mscore_fdr	0.36	0.01	0.38
filter_mscore_freqobs	0.16	0.00	0.15
filter_on_max_peptides	0.19	0.00	0.19
filter_on_min_peptides	0.15	0.00	0.16
filter_proteotypic_peptides	0.13	0.00	0.12
import_data	0.58	0.00	0.57
load_mart	4.88	0.08	55.29
mscore4assayfdr	0.44	0.00	0.43
mscore4pepfdr	0.25	0.02	0.27
mscore4protfdr	0.23	0.00	0.23
plot.fdr_cube	0.14	0.01	0.16
plot.fdr_table	0.17	0.00	0.17
plot_correlation_between_samples	0.33	0.03	0.36
plot_variation	0.41	0.00	0.41
plot_variation_vs_total	0.34	0.00	0.34
reduce_OpenSWATH_output	0.11	0.00	0.11
removeDecoyProteins	0.12	0.00	0.12
sample_annotation	0.56	0.02	0.58
transform_MSstats_OpenSWATH	0	0	0
unifyProteinGroupLabels	0.13	0.00	0.12
validate_columns	0	0	0
write_matrix_peptides	0.12	0.00	0.13
write_matrix_proteins	0.11	0.00	0.11

CHECK results for SWATH2stats on tokay2

Summary

Command output

Installation output

Tests output

Example timings