| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-02-22 12:48:14 -0500 (Thu, 22 Feb 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4657 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4397 |
| 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 | ||||
| Package 1304/2244 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MQmetrics 1.11.0 (landing page) Alvaro Sanchez-Villalba
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the MQmetrics package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: MQmetrics |
| Version: 1.11.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MQmetrics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MQmetrics_1.11.0.tar.gz |
| StartedAt: 2024-02-22 00:51:12 -0500 (Thu, 22 Feb 2024) |
| EndedAt: 2024-02-22 00:53:35 -0500 (Thu, 22 Feb 2024) |
| EllapsedTime: 142.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MQmetrics.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MQmetrics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MQmetrics_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MQmetrics.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MQmetrics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MQmetrics’ version ‘1.11.0’
* 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 loading without being on the library search path ... 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 5.155 0.731 5.474
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.19-bioc/meat/MQmetrics.Rcheck/00check.log’
for details.
MQmetrics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL MQmetrics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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
5.130 1.572 5.500
MQmetrics.Rcheck/MQmetrics-Ex.timings
| name | user | system | elapsed | |
| MaxQuantAnalysisInfo | 1.399 | 0.816 | 1.718 | |
| PlotAcquisitionCycle | 5.155 | 0.731 | 5.474 | |
| PlotAllDynamicRange | 2.603 | 0.476 | 2.725 | |
| PlotAndromedaScore | 3.053 | 0.430 | 3.132 | |
| PlotCharge | 1.950 | 0.454 | 2.027 | |
| PlotCombinedDynamicRange | 1.496 | 0.466 | 1.589 | |
| PlotHydrophobicity | 2.256 | 0.485 | 2.372 | |
| PlotIntensity | 2.155 | 0.475 | 2.242 | |
| PlotIsotopePattern | 1.467 | 0.463 | 1.543 | |
| PlotMsMs | 1.363 | 0.498 | 1.485 | |
| PlotPCA | 1.301 | 0.445 | 1.368 | |
| PlotPTM | 4.301 | 0.547 | 4.472 | |
| PlotPTMAcrossSamples | 1.322 | 0.430 | 1.389 | |
| PlotPeaks | 1.205 | 0.460 | 1.308 | |
| PlotPeptidesIdentified | 1.413 | 0.382 | 1.414 | |
| PlotProteaseSpecificity | 2.943 | 0.414 | 3.000 | |
| PlotProteinCoverage | 2.669 | 0.429 | 2.733 | |
| PlotProteinOverlap | 1.280 | 0.467 | 1.377 | |
| PlotProteinPeptideRatio | 1.280 | 0.444 | 1.365 | |
| PlotProteinsIdentified | 1.468 | 0.452 | 1.557 | |
| PlotTotalIonCurrent | 1.930 | 0.488 | 2.067 | |
| PlotiRT | 2.135 | 0.419 | 2.187 | |
| PlotiRTScore | 2.124 | 0.471 | 2.237 | |
| ReportTables | 1.451 | 0.580 | 1.555 | |
| generateReport | 0.001 | 0.000 | 0.000 | |
| make_MQCombined | 1.020 | 0.432 | 1.089 | |