| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:20:33 -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: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:MQmetrics.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings MQmetrics_1.4.0.tar.gz |
| StartedAt: 2022-10-18 20:43:01 -0400 (Tue, 18 Oct 2022) |
| EndedAt: 2022-10-18 20:45:00 -0400 (Tue, 18 Oct 2022) |
| EllapsedTime: 118.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MQmetrics.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:MQmetrics.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings MQmetrics_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/MQmetrics.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (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 for sufficient/correct file permissions ... OK
* checking whether package ‘MQmetrics’ 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
* 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
PlotPTM 5.481 0.553 5.519
PlotAcquisitionCycle 5.364 0.460 5.380
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.15-bioc/meat/MQmetrics.Rcheck/00check.log’
for details.
MQmetrics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL MQmetrics ### ############################################################################## ############################################################################## * installing to library ‘/home/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) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
7.222 1.779 7.438
MQmetrics.Rcheck/MQmetrics-Ex.timings
| name | user | system | elapsed | |
| MaxQuantAnalysisInfo | 1.843 | 0.585 | 1.963 | |
| PlotAcquisitionCycle | 5.364 | 0.460 | 5.380 | |
| PlotAllDynamicRange | 3.277 | 0.483 | 3.305 | |
| PlotAndromedaScore | 4.194 | 0.463 | 4.179 | |
| PlotCharge | 2.572 | 0.526 | 2.552 | |
| PlotCombinedDynamicRange | 2.091 | 0.508 | 2.115 | |
| PlotHydrophobicity | 2.788 | 0.440 | 2.765 | |
| PlotIntensity | 2.393 | 0.448 | 2.417 | |
| PlotIsotopePattern | 2.058 | 0.387 | 2.011 | |
| PlotMsMs | 1.736 | 0.449 | 1.690 | |
| PlotPCA | 2.040 | 0.477 | 2.047 | |
| PlotPTM | 5.481 | 0.553 | 5.519 | |
| PlotPTMAcrossSamples | 1.898 | 0.531 | 1.936 | |
| PlotPeaks | 1.681 | 0.583 | 1.735 | |
| PlotPeptidesIdentified | 1.784 | 0.437 | 1.750 | |
| PlotProteaseSpecificity | 3.686 | 0.520 | 3.703 | |
| PlotProteinCoverage | 3.810 | 0.401 | 3.795 | |
| PlotProteinOverlap | 1.923 | 0.477 | 2.039 | |
| PlotProteinPeptideRatio | 1.763 | 0.492 | 1.785 | |
| PlotProteinsIdentified | 1.881 | 0.509 | 1.861 | |
| PlotTotalIonCurrent | 2.717 | 0.577 | 2.828 | |
| PlotiRT | 2.785 | 0.514 | 2.789 | |
| PlotiRTScore | 2.794 | 0.524 | 2.888 | |
| ReportTables | 2.124 | 0.707 | 2.287 | |
| generateReport | 0 | 0 | 0 | |
| make_MQCombined | 1.577 | 0.528 | 1.661 | |