Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-07-30 15:06:00 -0400 (Fri, 30 Jul 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 1204/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnID 1.26.0  (landing page)
Vlad Petyuk
Snapshot Date: 2021-07-29 04:50:02 -0400 (Thu, 29 Jul 2021)
URL: https://git.bioconductor.org/packages/MSnID
Branch: RELEASE_3_13
Last Commit: 542b32c
Last Changed Date: 2021-05-19 12:07:42 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.26.0
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: 2021-07-30 02:37:32 -0400 (Fri, 30 Jul 2021)
EndedAt: 2021-07-30 02:44:56 -0400 (Fri, 30 Jul 2021)
EllapsedTime: 443.7 seconds
RetCode: 0
Status:   OK  
CheckDir: MSnID.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MSnID.Rcheck'
* using R version 4.1.0 (2021-05-18)
* 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  17.08   1.31   22.97
remap_accessions-method  8.06   0.45    8.91
remap_fasta_entry_names  6.97   0.49    7.74
optimize_filter          2.59   0.30   11.63
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
fetch_conversion_table  15.55   1.00   17.42
remap_accessions-method  7.11   0.53    8.12
remap_fasta_entry_names  6.64   0.50    7.45
optimize_filter          2.50   0.23   12.17
* 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.



Installation output

MSnID.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


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

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 71 2620k   71 1861k    0     0  4122k      0 --:--:-- --:--:-- --:--:-- 4117k
100 2620k  100 2620k    0     0  4585k      0 --:--:-- --:--:-- --:--:-- 4589k

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  
REDIRECT:topic	 class:MSnID -> MSnID-class.html [ FAIL ]
REDIRECT:topic	 $<-,MSnID-method -> MSnID-class.html [ FAIL ]
REDIRECT:topic	 [[<-,MSnID,ANY,ANY,ANY-method -> MSnID-class.html [ FAIL ]
REDIRECT:topic	 psms<-,MSnID,data.frame-method -> MSnID-class.html [ FAIL ]
    finding level-2 HTML links ... done

    MSnID-package                           html  
    MSnIDFilter-class                       html  
REDIRECT:topic	 class:MSnIDFilter -> MSnIDFilter-class.html [ FAIL ]
REDIRECT:topic	 $<-,MSnIDFilter-method -> MSnIDFilter-class.html [ FAIL ]
    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  
REDIRECT:topic	 psms<- -> psms.html [ FAIL ]
    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

Tests output

MSnID.Rcheck/tests_i386/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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 Jul 30 02:43:51 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 
  35.85    2.48   47.78 

MSnID.Rcheck/tests_x64/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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 Jul 30 02:44:39 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 
  35.81    0.90   47.09 

Example timings

MSnID.Rcheck/examples_i386/MSnID-Ex.timings

nameusersystemelapsed
MSnID-class000
MSnIDFilter-class0.290.010.31
accessions0.530.000.53
add_mod_symbol0.720.000.73
apply_filter0.210.070.25
assess_missed_cleavages0.170.000.17
assess_termini0.190.010.20
correct_peak_selection0.090.020.11
data0.090.010.11
evaluate_filter0.250.000.25
fetch_conversion_table17.08 1.3122.97
id_quality0.620.030.66
infer_parsimonious_accessions1.470.191.66
map_mod_sites1.190.001.18
mass_measurement_error0.140.000.14
optimize_filter 2.59 0.3011.63
peptides0.140.000.14
psms0.090.010.11
read_mzIDs000
recalibrate0.130.020.14
remap_accessions-method8.060.458.91
remap_fasta_entry_names6.970.497.74
report_mods0.810.000.81

MSnID.Rcheck/examples_x64/MSnID-Ex.timings

nameusersystemelapsed
MSnID-class000
MSnIDFilter-class0.660.050.70
accessions0.090.000.10
add_mod_symbol0.790.010.79
apply_filter0.200.020.22
assess_missed_cleavages0.220.020.24
assess_termini0.220.010.24
correct_peak_selection0.130.000.12
data0.110.000.11
evaluate_filter0.170.060.24
fetch_conversion_table15.55 1.0017.42
id_quality0.090.020.11
infer_parsimonious_accessions1.040.051.10
map_mod_sites1.140.001.14
mass_measurement_error0.080.000.08
optimize_filter 2.50 0.2312.17
peptides0.060.020.08
psms0.10.00.1
read_mzIDs000
recalibrate0.050.030.08
remap_accessions-method7.110.538.12
remap_fasta_entry_names6.640.507.45
report_mods0.910.000.90