Multiple platform build/check report for BioC 3.13 - CHECK results for MSnID on tokay2

Package: MSnID

Version: 1.26.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSnID.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MSnID_1.26.0.tar.gz

StartedAt: 2021-10-15 02:21:27 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 02:28:54 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 446.7 seconds

RetCode: 0

Status: OK

CheckDir: MSnID.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSnID.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MSnID_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MSnID.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSnID/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSnID' version '1.26.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 'MSnID' 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 ... NOTE
Namespaces in Imports field not imported from:
  'BiocGenerics' 'BiocStyle' 'RUnit' 'ggplot2' 'msmsTests' 'xtable'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable 'peptideRef'
Undefined global functions or variables:
  peptideRef
* 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 LazyData ... 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
fetch_conversion_table  16.18   1.47   26.66
remap_accessions-method  7.23   0.58    8.34
remap_fasta_entry_names  6.89   0.50    7.80
optimize_filter          2.47   0.24   11.32
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
fetch_conversion_table  16.27   1.19   19.02
remap_accessions-method  7.47   0.48    8.59
remap_fasta_entry_names  7.03   0.47    7.92
optimize_filter          2.67   0.24   12.93
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/MSnID.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MSnID_1.26.0.tar.gz && rm -rf MSnID.buildbin-libdir && mkdir MSnID.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSnID.buildbin-libdir MSnID_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MSnID_1.26.0.zip && rm MSnID_1.26.0.tar.gz MSnID_1.26.0.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
  3 2620k    3   98k    0     0   518k      0  0:00:05 --:--:--  0:00:05  517k
 82 2620k   82 2163k    0     0  1827k      0  0:00:01  0:00:01 --:--:-- 1827k
100 2620k  100 2620k    0     0  1966k      0  0:00:01  0:00:01 --:--:-- 1967k

install for i386

* installing *source* package 'MSnID' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MSnID'
    finding HTML links ... done
    MSnID-class                             html  
    finding level-2 HTML links ... done

    MSnID-package                           html  
    MSnIDFilter-class                       html  
    accessions                              html  
    add_mod_symbol                          html  
    apply_filter                            html  
    assess_missed_cleavages                 html  
    assess_termini                          html  
    correct_peak_selection                  html  
    data                                    html  
    evaluate_filter                         html  
    fetch_conversion_table                  html  
    id_quality                              html  
    infer_parsimonious_accessions           html  
    map_mod_sites                           html  
    mass_measurement_error                  html  
    optimize_filter                         html  
    peptides                                html  
    psms                                    html  
    read_mzIDs                              html  
    recalibrate                             html  
    remap_accessions-method                 html  
    remap_fasta_entry_names                 html  
    report_mods                             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 'MSnID' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSnID' as MSnID_1.26.0.zip
* DONE (MSnID)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'MSnID' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> BiocGenerics:::testPackage("MSnID")
Note, the anticipated/suggested columns in the
peptide-to-spectrum matching results are:
-----------------------------------------------
accession
calculatedMassToCharge
chargeState
experimentalMassToCharge
isDecoy
peptide
spectrumFile
spectrumID
Reading from mzIdentMLs ...

reading c_elegans.mzid.gz... DONE!
Reading from mzIdentMLs ...



RUNIT TEST PROTOCOL -- Fri Oct 15 02:27:54 2021 
*********************************************** 
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MSnID RUnit Tests - 19 test functions, 0 errors, 0 failures
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 
There were 12 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
  33.98    2.01   45.86


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> BiocGenerics:::testPackage("MSnID")
Note, the anticipated/suggested columns in the
peptide-to-spectrum matching results are:
-----------------------------------------------
accession
calculatedMassToCharge
chargeState
experimentalMassToCharge
isDecoy
peptide
spectrumFile
spectrumID
Reading from mzIdentMLs ...

reading c_elegans.mzid.gz... DONE!
Reading from mzIdentMLs ...



RUNIT TEST PROTOCOL -- Fri Oct 15 02:28:42 2021 
*********************************************** 
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MSnID RUnit Tests - 19 test functions, 0 errors, 0 failures
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 
There were 12 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
  36.04    1.14   48.03

name	user	system	elapsed
MSnID-class	0	0	0
MSnIDFilter-class	0.31	0.01	0.31
accessions	0.55	0.02	0.56
add_mod_symbol	0.77	0.00	0.77
apply_filter	0.25	0.06	0.29
assess_missed_cleavages	0.23	0.05	0.28
assess_termini	0.33	0.05	0.38
correct_peak_selection	0.13	0.03	0.15
data	0.12	0.01	0.15
evaluate_filter	0.27	0.01	0.28
fetch_conversion_table	16.18	1.47	26.66
id_quality	0.63	0.00	0.62
infer_parsimonious_accessions	1.11	0.10	1.19
map_mod_sites	1.06	0.03	1.09
mass_measurement_error	0.06	0.01	0.08
optimize_filter	2.47	0.24	11.32
peptides	0.10	0.00	0.09
psms	0.07	0.01	0.09
read_mzIDs	0	0	0
recalibrate	0.13	0.00	0.13
remap_accessions-method	7.23	0.58	8.34
remap_fasta_entry_names	6.89	0.50	7.80
report_mods	0.71	0.00	0.70

name	user	system	elapsed
MSnID-class	0	0	0
MSnIDFilter-class	0.82	0.01	0.85
accessions	0.12	0.02	0.14
add_mod_symbol	0.94	0.01	0.95
apply_filter	0.22	0.00	0.22
assess_missed_cleavages	0.16	0.02	0.18
assess_termini	0.17	0.01	0.18
correct_peak_selection	0.09	0.02	0.11
data	0.10	0.02	0.11
evaluate_filter	0.20	0.01	0.22
fetch_conversion_table	16.27	1.19	19.02
id_quality	0.09	0.00	0.09
infer_parsimonious_accessions	1.31	0.08	1.39
map_mod_sites	1.45	0.03	1.48
mass_measurement_error	0.10	0.01	0.11
optimize_filter	2.67	0.24	12.93
peptides	0.03	0.03	0.06
psms	0.10	0.00	0.09
read_mzIDs	0	0	0
recalibrate	0.09	0.00	0.10
remap_accessions-method	7.47	0.48	8.59
remap_fasta_entry_names	7.03	0.47	7.92
report_mods	0.93	0.02	0.93

CHECK results for MSnID on tokay2

Summary

Command output

Installation output

Tests output

Example timings