Back to Multiple platform build/check report for BioC 3.13
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2021-10-15 15:06:12 -0400 (Fri, 15 Oct 2021).

CHECK results for MQmetrics on tokay2

To the developers/maintainers of the MQmetrics package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MQmetrics.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 1190/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MQmetrics 1.0.0  (landing page)
Alvaro Sanchez-Villalba
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/MQmetrics
git_branch: RELEASE_3_13
git_last_commit: f3e2d25
git_last_commit_date: 2021-05-19 13:03:06 -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: MQmetrics
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MQmetrics.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MQmetrics_1.0.0.tar.gz
StartedAt: 2021-10-15 02:16:43 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 02:20:40 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 236.2 seconds
RetCode: 0
Status:   OK  
CheckDir: MQmetrics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MQmetrics.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MQmetrics_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MQmetrics.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 'MQmetrics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MQmetrics' version '1.0.0'
* package encoding: UTF-8
* 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 'MQmetrics' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
    help      1.6Mb
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
PlotAcquisitionCycle 7.82   0.43    6.89
PlotPTM              5.49   0.17    5.04
PlotTotalIonCurrent  5.09   0.27    3.40
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
PlotAcquisitionCycle 9.68   0.14    7.15
PlotTotalIonCurrent  6.14   0.32    3.72
PlotPTM              5.25   0.09    5.00
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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-3.13-bioc/meat/MQmetrics.Rcheck/00check.log'
for details.



Installation output

MQmetrics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MQmetrics_1.0.0.tar.gz && rm -rf MQmetrics.buildbin-libdir && mkdir MQmetrics.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MQmetrics.buildbin-libdir MQmetrics_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MQmetrics_1.0.0.zip && rm MQmetrics_1.0.0.tar.gz MQmetrics_1.0.0.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
  5 2899k    5  165k    0     0   650k      0  0:00:04 --:--:--  0:00:04  650k
 86 2899k   86 2512k    0     0  2044k      0  0:00:01  0:00:01 --:--:-- 2044k
100 2899k  100 2899k    0     0  2137k      0  0:00:01  0:00:01 --:--:-- 2137k

install for i386

* installing *source* package 'MQmetrics' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MQmetrics'
    finding HTML links ... done
    MaxQuantAnalysisInfo                    html  
    PlotAcquisitionCycle                    html  
    PlotAllDynamicRange                     html  
    PlotAndromedaScore                      html  
    PlotCharge                              html  
    PlotCombinedDynamicRange                html  
    PlotHydrophobicity                      html  
    PlotIdentificationType                  html  
    PlotIntensity                           html  
    PlotIsotopePattern                      html  
    PlotMsMs                                html  
    PlotPCA                                 html  
    PlotPTM                                 html  
    PlotPeaks                               html  
    PlotPeptidesIdentified                  html  
    PlotProteaseSpecificity                 html  
    PlotProteinCoverage                     html  
    PlotProteinOverlap                      html  
    PlotProteinPeptideRatio                 html  
    PlotProteinsIdentified                  html  
    PlotTotalIonCurrent                     html  
    PlotiRT                                 html  
    PlotiRTScore                            html  
    ReportTables                            html  
    generateReport                          html  
    make_MQCombined                         html  
*** copying figures
** 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 'MQmetrics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MQmetrics' as MQmetrics_1.0.0.zip
* DONE (MQmetrics)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'MQmetrics' successfully unpacked and MD5 sums checked

Tests output

MQmetrics.Rcheck/tests_i386/testthat.Rout


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.

> library(testthat)
> library(MQmetrics)
> 
> test_check("MQmetrics")
Rows: 7 Columns: 52
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (8): Raw file, Experiment, Enzyme, Enzyme mode, Variable modifications,...
dbl (34): Multiplicity, Max. missed cleavages, MS, MS/MS, MS3, MS/MS Submitt...
lgl (10): Enzyme first search, Enzyme mode first search, Use enzyme first se...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 2638 Columns: 65
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (16): Sequence, Identification type QC02_210326, Identification type QC0...
dbl (48): Missed cleavages, Experiment QC02_210326, Experiment QC02_210331, ...
lgl  (1): Reverse

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 13161 Columns: 9
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (3): Experiment, Potential contaminant, Sequence
dbl (5): Charge, m/z, Retention time, Calibrated retention time, Intensity
lgl (1): Reverse

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 32418 Columns: 4
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (1): Experiment
dbl (3): Retention time, Cycle time, MS/MS count

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 29621 Columns: 4
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): Experiment, Reverse
dbl (2): Retention time, Total ion current

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 4751 Columns: 32
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (10): Identification type QC02_210326, Identification type QC02_210331, ...
dbl (22): Intensity, Intensity QC02_210326, Intensity QC02_210331, Intensity...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 2803 Columns: 16
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (4): Modifications, Proteins, Potential contaminant, Reverse
dbl (12): Intensity QC02_210326, Intensity QC02_210331, Intensity QC02_21040...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 108 Columns: 2
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): Parameter, Value

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 53 Columns: 6
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (3): Job, Start date, End date
dbl  (1): Running time [min]
time (2): Start time, End time

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 7 Columns: 52
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (8): Raw file, Experiment, Enzyme, Enzyme mode, Variable modifications,...
dbl (34): Multiplicity, Max. missed cleavages, MS, MS/MS, MS3, MS/MS Submitt...
lgl (10): Enzyme first search, Enzyme mode first search, Use enzyme first se...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 2638 Columns: 65
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (16): Sequence, Identification type QC02_210326, Identification type QC0...
dbl (48): Missed cleavages, Experiment QC02_210326, Experiment QC02_210331, ...
lgl  (1): Reverse

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 13161 Columns: 9
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (3): Experiment, Potential contaminant, Sequence
dbl (5): Charge, m/z, Retention time, Calibrated retention time, Intensity
lgl (1): Reverse

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 32418 Columns: 4
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (1): Experiment
dbl (3): Retention time, Cycle time, MS/MS count

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 29621 Columns: 4
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): Experiment, Reverse
dbl (2): Retention time, Total ion current

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 4751 Columns: 32
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (10): Identification type QC02_210326, Identification type QC02_210331, ...
dbl (22): Intensity, Intensity QC02_210326, Intensity QC02_210331, Intensity...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 2803 Columns: 16
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (4): Modifications, Proteins, Potential contaminant, Reverse
dbl (12): Intensity QC02_210326, Intensity QC02_210331, Intensity QC02_21040...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 108 Columns: 2
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): Parameter, Value

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 53 Columns: 6
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (3): Job, Start date, End date
dbl  (1): Running time [min]
time (2): Start time, End time

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 4751 Columns: 32
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (10): Identification type QC02_210326, Identification type QC02_210331, ...
dbl (22): Intensity, Intensity QC02_210326, Intensity QC02_210331, Intensity...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 7 Columns: 52
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (8): Raw file, Experiment, Enzyme, Enzyme mode, Variable modifications,...
dbl (34): Multiplicity, Max. missed cleavages, MS, MS/MS, MS3, MS/MS Submitt...
lgl (10): Enzyme first search, Enzyme mode first search, Use enzyme first se...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Using Charge as value column: use value.var to override.
Aggregation function missing: defaulting to length
Rows: 7 Columns: 52
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (8): Raw file, Experiment, Enzyme, Enzyme mode, Variable modifications,...
dbl (34): Multiplicity, Max. missed cleavages, MS, MS/MS, MS3, MS/MS Submitt...
lgl (10): Enzyme first search, Enzyme mode first search, Use enzyme first se...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 2638 Columns: 65
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (16): Sequence, Identification type QC02_210326, Identification type QC0...
dbl (48): Missed cleavages, Experiment QC02_210326, Experiment QC02_210331, ...
lgl  (1): Reverse

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 13161 Columns: 9
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (3): Experiment, Potential contaminant, Sequence
dbl (5): Charge, m/z, Retention time, Calibrated retention time, Intensity
lgl (1): Reverse

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 32418 Columns: 4
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (1): Experiment
dbl (3): Retention time, Cycle time, MS/MS count

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 29621 Columns: 4
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): Experiment, Reverse
dbl (2): Retention time, Total ion current

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 4751 Columns: 32
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (10): Identification type QC02_210326, Identification type QC02_210331, ...
dbl (22): Intensity, Intensity QC02_210326, Intensity QC02_210331, Intensity...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 2803 Columns: 16
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (4): Modifications, Proteins, Potential contaminant, Reverse
dbl (12): Intensity QC02_210326, Intensity QC02_210331, Intensity QC02_21040...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 108 Columns: 2
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): Parameter, Value

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 53 Columns: 6
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (3): Job, Start date, End date
dbl  (1): Running time [min]
time (2): Start time, End time

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
   9.59    0.78    8.95 

MQmetrics.Rcheck/tests_x64/testthat.Rout


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.

> library(testthat)
> library(MQmetrics)
> 
> test_check("MQmetrics")
Rows: 7 Columns: 52
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (8): Raw file, Experiment, Enzyme, Enzyme mode, Variable modifications,...
dbl (34): Multiplicity, Max. missed cleavages, MS, MS/MS, MS3, MS/MS Submitt...
lgl (10): Enzyme first search, Enzyme mode first search, Use enzyme first se...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 2638 Columns: 65
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (16): Sequence, Identification type QC02_210326, Identification type QC0...
dbl (48): Missed cleavages, Experiment QC02_210326, Experiment QC02_210331, ...
lgl  (1): Reverse

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 13161 Columns: 9
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (3): Experiment, Potential contaminant, Sequence
dbl (5): Charge, m/z, Retention time, Calibrated retention time, Intensity
lgl (1): Reverse

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 32418 Columns: 4
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (1): Experiment
dbl (3): Retention time, Cycle time, MS/MS count

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 29621 Columns: 4
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): Experiment, Reverse
dbl (2): Retention time, Total ion current

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 4751 Columns: 32
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (10): Identification type QC02_210326, Identification type QC02_210331, ...
dbl (22): Intensity, Intensity QC02_210326, Intensity QC02_210331, Intensity...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 2803 Columns: 16
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (4): Modifications, Proteins, Potential contaminant, Reverse
dbl (12): Intensity QC02_210326, Intensity QC02_210331, Intensity QC02_21040...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 108 Columns: 2
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): Parameter, Value

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 53 Columns: 6
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (3): Job, Start date, End date
dbl  (1): Running time [min]
time (2): Start time, End time

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 7 Columns: 52
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (8): Raw file, Experiment, Enzyme, Enzyme mode, Variable modifications,...
dbl (34): Multiplicity, Max. missed cleavages, MS, MS/MS, MS3, MS/MS Submitt...
lgl (10): Enzyme first search, Enzyme mode first search, Use enzyme first se...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 2638 Columns: 65
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (16): Sequence, Identification type QC02_210326, Identification type QC0...
dbl (48): Missed cleavages, Experiment QC02_210326, Experiment QC02_210331, ...
lgl  (1): Reverse

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 13161 Columns: 9
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (3): Experiment, Potential contaminant, Sequence
dbl (5): Charge, m/z, Retention time, Calibrated retention time, Intensity
lgl (1): Reverse

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 32418 Columns: 4
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (1): Experiment
dbl (3): Retention time, Cycle time, MS/MS count

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 29621 Columns: 4
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): Experiment, Reverse
dbl (2): Retention time, Total ion current

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 4751 Columns: 32
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (10): Identification type QC02_210326, Identification type QC02_210331, ...
dbl (22): Intensity, Intensity QC02_210326, Intensity QC02_210331, Intensity...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 2803 Columns: 16
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (4): Modifications, Proteins, Potential contaminant, Reverse
dbl (12): Intensity QC02_210326, Intensity QC02_210331, Intensity QC02_21040...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 108 Columns: 2
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): Parameter, Value

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 53 Columns: 6
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (3): Job, Start date, End date
dbl  (1): Running time [min]
time (2): Start time, End time

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 4751 Columns: 32
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (10): Identification type QC02_210326, Identification type QC02_210331, ...
dbl (22): Intensity, Intensity QC02_210326, Intensity QC02_210331, Intensity...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 7 Columns: 52
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (8): Raw file, Experiment, Enzyme, Enzyme mode, Variable modifications,...
dbl (34): Multiplicity, Max. missed cleavages, MS, MS/MS, MS3, MS/MS Submitt...
lgl (10): Enzyme first search, Enzyme mode first search, Use enzyme first se...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Using Charge as value column: use value.var to override.
Aggregation function missing: defaulting to length
Rows: 7 Columns: 52
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (8): Raw file, Experiment, Enzyme, Enzyme mode, Variable modifications,...
dbl (34): Multiplicity, Max. missed cleavages, MS, MS/MS, MS3, MS/MS Submitt...
lgl (10): Enzyme first search, Enzyme mode first search, Use enzyme first se...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 2638 Columns: 65
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (16): Sequence, Identification type QC02_210326, Identification type QC0...
dbl (48): Missed cleavages, Experiment QC02_210326, Experiment QC02_210331, ...
lgl  (1): Reverse

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 13161 Columns: 9
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (3): Experiment, Potential contaminant, Sequence
dbl (5): Charge, m/z, Retention time, Calibrated retention time, Intensity
lgl (1): Reverse

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 32418 Columns: 4
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (1): Experiment
dbl (3): Retention time, Cycle time, MS/MS count

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 29621 Columns: 4
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): Experiment, Reverse
dbl (2): Retention time, Total ion current

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 4751 Columns: 32
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (10): Identification type QC02_210326, Identification type QC02_210331, ...
dbl (22): Intensity, Intensity QC02_210326, Intensity QC02_210331, Intensity...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 2803 Columns: 16
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (4): Modifications, Proteins, Potential contaminant, Reverse
dbl (12): Intensity QC02_210326, Intensity QC02_210331, Intensity QC02_21040...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 108 Columns: 2
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (2): Parameter, Value

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 53 Columns: 6
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr  (3): Job, Start date, End date
dbl  (1): Running time [min]
time (2): Start time, End time

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
   8.85    0.67    8.32 

Example timings

MQmetrics.Rcheck/examples_i386/MQmetrics-Ex.timings

nameusersystemelapsed
MaxQuantAnalysisInfo2.000.173.28
PlotAcquisitionCycle7.820.436.89
PlotAllDynamicRange3.420.183.21
PlotAndromedaScore4.670.224.35
PlotCharge2.190.102.14
PlotCombinedDynamicRange1.720.201.39
PlotHydrophobicity3.120.192.72
PlotIdentificationType2.960.082.75
PlotIntensity3.450.122.98
PlotIsotopePattern1.700.111.50
PlotMsMs1.820.161.75
PlotPCA2.390.292.28
PlotPTM5.490.175.04
PlotPeaks2.040.111.68
PlotPeptidesIdentified2.050.101.76
PlotProteaseSpecificity3.730.223.63
PlotProteinCoverage2.040.201.67
PlotProteinOverlap2.030.251.72
PlotProteinPeptideRatio2.420.191.79
PlotProteinsIdentified2.050.151.93
PlotTotalIonCurrent5.090.273.40
PlotiRT2.800.192.56
PlotiRTScore2.500.152.47
ReportTables3.390.362.82
generateReport000
make_MQCombined2.240.111.72

MQmetrics.Rcheck/examples_x64/MQmetrics-Ex.timings

nameusersystemelapsed
MaxQuantAnalysisInfo2.660.192.10
PlotAcquisitionCycle9.680.147.15
PlotAllDynamicRange3.490.083.43
PlotAndromedaScore4.400.114.26
PlotCharge2.580.172.53
PlotCombinedDynamicRange2.240.131.80
PlotHydrophobicity3.620.183.37
PlotIdentificationType2.360.112.02
PlotIntensity2.830.242.73
PlotIsotopePattern1.690.151.68
PlotMsMs2.060.131.82
PlotPCA2.160.112.05
PlotPTM5.250.095.00
PlotPeaks1.960.111.89
PlotPeptidesIdentified2.020.221.66
PlotProteaseSpecificity4.250.204.00
PlotProteinCoverage1.810.111.56
PlotProteinOverlap2.020.081.88
PlotProteinPeptideRatio2.230.062.12
PlotProteinsIdentified2.070.181.91
PlotTotalIonCurrent6.140.323.72
PlotiRT3.060.182.65
PlotiRTScore2.20.12.1
ReportTables3.280.432.89
generateReport000
make_MQCombined1.880.181.64