| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:21:52 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1241/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MQmetrics 1.4.0 (landing page) Alvaro Sanchez-Villalba
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: MQmetrics |
| Version: 1.4.0 |
| Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MQmetrics.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MQmetrics_1.4.0.tar.gz |
| StartedAt: 2022-10-19 02:06:10 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 02:08:56 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 166.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MQmetrics.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MQmetrics.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MQmetrics_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/MQmetrics.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MQmetrics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MQmetrics' version '1.4.0'
* 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 5.2Mb
sub-directories of 1Mb or more:
extdata 4.9Mb
* 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
* 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 ... NOTE
PlotAndromedaScore: no visible binding for global variable
'median(Score)'
Undefined global functions or variables:
median(Score)
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PlotAcquisitionCycle 6.42 0.95 6.89
PlotPTM 6.28 0.94 6.50
PlotProteaseSpecificity 4.59 1.00 4.84
PlotAndromedaScore 4.73 0.81 4.97
PlotProteinCoverage 4.53 0.79 4.74
PlotiRT 3.94 1.09 4.12
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
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: 2 NOTEs
See
'F:/biocbuild/bbs-3.15-bioc/meat/MQmetrics.Rcheck/00check.log'
for details.
MQmetrics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MQmetrics ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'MQmetrics' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** 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 * DONE (MQmetrics)
MQmetrics.Rcheck/tests/testthat.Rout
R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
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)
> 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
9.23 3.73 10.17
MQmetrics.Rcheck/MQmetrics-Ex.timings
| name | user | system | elapsed | |
| MaxQuantAnalysisInfo | 2.24 | 0.86 | 2.95 | |
| PlotAcquisitionCycle | 6.42 | 0.95 | 6.89 | |
| PlotAllDynamicRange | 3.97 | 0.97 | 4.28 | |
| PlotAndromedaScore | 4.73 | 0.81 | 4.97 | |
| PlotCharge | 2.95 | 0.93 | 3.28 | |
| PlotCombinedDynamicRange | 2.47 | 1.06 | 2.77 | |
| PlotHydrophobicity | 3.39 | 1.11 | 3.81 | |
| PlotIntensity | 2.64 | 1.01 | 3.00 | |
| PlotIsotopePattern | 2.55 | 0.80 | 2.84 | |
| PlotMsMs | 2.27 | 0.89 | 2.53 | |
| PlotPCA | 2.14 | 0.84 | 2.43 | |
| PlotPTM | 6.28 | 0.94 | 6.50 | |
| PlotPTMAcrossSamples | 2.37 | 1.08 | 2.79 | |
| PlotPeaks | 2.29 | 1.08 | 2.67 | |
| PlotPeptidesIdentified | 2.55 | 0.83 | 2.83 | |
| PlotProteaseSpecificity | 4.59 | 1.00 | 4.84 | |
| PlotProteinCoverage | 4.53 | 0.79 | 4.74 | |
| PlotProteinOverlap | 2.30 | 0.91 | 2.46 | |
| PlotProteinPeptideRatio | 2.22 | 1.06 | 2.61 | |
| PlotProteinsIdentified | 2.58 | 1.02 | 2.89 | |
| PlotTotalIonCurrent | 3.48 | 0.92 | 3.90 | |
| PlotiRT | 3.94 | 1.09 | 4.12 | |
| PlotiRTScore | 3.64 | 0.99 | 3.94 | |
| ReportTables | 3.25 | 1.40 | 3.56 | |
| generateReport | 0 | 0 | 0 | |
| make_MQCombined | 1.95 | 0.97 | 2.22 | |