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This page was generated on 2021-12-06 13:05:33 -0500 (Mon, 06 Dec 2021).

CHECK results for MSnID on tokay2

To the developers/maintainers of the MSnID package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSnID.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1223/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnID 1.28.0  (landing page)
Vlad Petyuk
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/MSnID
git_branch: RELEASE_3_14
git_last_commit: 0e6de89
git_last_commit_date: 2021-10-26 12:16:01 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MSnID
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSnID.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MSnID_1.28.0.tar.gz
StartedAt: 2021-12-05 23:57:24 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-06 00:05:08 -0500 (Mon, 06 Dec 2021)
EllapsedTime: 463.5 seconds
RetCode: 0
Status:   OK  
CheckDir: MSnID.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSnID.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MSnID_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MSnID.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.28.0'
* 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  17.22   1.76   24.44
remap_accessions-method  7.40   0.54    8.56
remap_fasta_entry_names  6.70   0.50    7.66
optimize_filter          2.67   0.30   11.64
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
fetch_conversion_table  16.47   1.14   19.11
remap_accessions-method  8.48   0.40    9.44
remap_fasta_entry_names  7.49   0.50    8.40
optimize_filter          2.64   0.25   14.31
* 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-3.14-bioc/meat/MSnID.Rcheck/00check.log'
for details.



Installation output

MSnID.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MSnID_1.28.0.tar.gz && rm -rf MSnID.buildbin-libdir && mkdir MSnID.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSnID.buildbin-libdir MSnID_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MSnID_1.28.0.zip && rm MSnID_1.28.0.tar.gz MSnID_1.28.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 2620k    0  3835    0     0  47503      0  0:00:56 --:--:--  0:00:56 47345
100 2620k  100 2620k    0     0  2968k      0 --:--:-- --:--:-- --:--:-- 2967k

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_1.28.0.zip
* DONE (MSnID)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MSnID' successfully unpacked and MD5 sums checked

Tests output

MSnID.Rcheck/tests_i386/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 -- Mon Dec 06 00:04:07 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 
  34.95    2.68   47.07 

MSnID.Rcheck/tests_x64/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 -- Mon Dec 06 00:04:57 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 
  37.67    0.98   48.76 

Example timings

MSnID.Rcheck/examples_i386/MSnID-Ex.timings

nameusersystemelapsed
MSnID-class000
MSnIDFilter-class0.200.090.29
accessions0.600.000.59
add_mod_symbol0.900.011.00
apply_filter0.290.040.30
assess_missed_cleavages0.250.040.30
assess_termini0.290.000.29
correct_peak_selection0.130.020.14
data0.110.030.14
evaluate_filter0.250.050.28
fetch_conversion_table17.22 1.7624.44
id_quality0.610.000.61
infer_parsimonious_accessions1.440.211.61
map_mod_sites1.080.011.11
mass_measurement_error0.090.000.09
optimize_filter 2.67 0.3011.64
peptides0.140.000.14
psms0.130.000.13
read_mzIDs000
recalibrate0.140.000.14
remap_accessions-method7.400.548.56
remap_fasta_entry_names6.700.507.66
report_mods0.770.040.80

MSnID.Rcheck/examples_x64/MSnID-Ex.timings

nameusersystemelapsed
MSnID-class000
MSnIDFilter-class0.800.030.82
accessions0.130.010.14
add_mod_symbol0.930.021.06
apply_filter0.190.030.20
assess_missed_cleavages0.150.000.16
assess_termini0.160.020.17
correct_peak_selection0.110.000.11
data0.110.000.11
evaluate_filter0.220.030.22
fetch_conversion_table16.47 1.1419.11
id_quality0.10.00.1
infer_parsimonious_accessions1.340.051.37
map_mod_sites1.260.031.29
mass_measurement_error0.10.00.1
optimize_filter 2.64 0.2514.31
peptides0.060.020.08
psms0.080.010.09
read_mzIDs000
recalibrate0.050.040.08
remap_accessions-method8.480.409.44
remap_fasta_entry_names7.490.508.40
report_mods0.930.020.96