| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-02-22 11:36:07 -0500 (Thu, 22 Feb 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4691 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4444 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4465 |
| 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 1319/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MQmetrics 1.10.0 (landing page) Alvaro Sanchez-Villalba
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.10.0 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MQmetrics.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MQmetrics_1.10.0.tar.gz |
| StartedAt: 2024-02-22 00:17:20 -0500 (Thu, 22 Feb 2024) |
| EndedAt: 2024-02-22 00:19:41 -0500 (Thu, 22 Feb 2024) |
| EllapsedTime: 141.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MQmetrics.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MQmetrics.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MQmetrics_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MQmetrics.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘1.10.0’
* 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 ... NOTE
installed size is 5.3Mb
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 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 5.316 0.597 5.455
* 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 ...
‘MQmetrics.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/MQmetrics.Rcheck/00check.log’
for details.
MQmetrics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL MQmetrics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-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 version 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
Copyright (C) 2023 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
5.323 1.877 5.667
MQmetrics.Rcheck/MQmetrics-Ex.timings
| name | user | system | elapsed | |
| MaxQuantAnalysisInfo | 1.462 | 0.535 | 1.573 | |
| PlotAcquisitionCycle | 5.316 | 0.597 | 5.455 | |
| PlotAllDynamicRange | 2.719 | 0.473 | 2.817 | |
| PlotAndromedaScore | 3.090 | 0.440 | 3.135 | |
| PlotCharge | 2.254 | 0.448 | 2.330 | |
| PlotCombinedDynamicRange | 1.312 | 0.406 | 1.345 | |
| PlotHydrophobicity | 2.025 | 0.449 | 2.107 | |
| PlotIntensity | 2.103 | 0.446 | 2.175 | |
| PlotIsotopePattern | 1.414 | 0.418 | 1.454 | |
| PlotMsMs | 1.197 | 0.437 | 1.273 | |
| PlotPCA | 1.374 | 0.433 | 1.439 | |
| PlotPTM | 4.470 | 0.422 | 4.529 | |
| PlotPTMAcrossSamples | 1.279 | 0.393 | 1.319 | |
| PlotPeaks | 1.166 | 0.394 | 1.194 | |
| PlotPeptidesIdentified | 1.326 | 0.395 | 1.352 | |
| PlotProteaseSpecificity | 2.891 | 0.442 | 2.963 | |
| PlotProteinCoverage | 2.819 | 0.418 | 2.876 | |
| PlotProteinOverlap | 1.508 | 0.385 | 1.527 | |
| PlotProteinPeptideRatio | 1.288 | 0.387 | 1.315 | |
| PlotProteinsIdentified | 1.290 | 0.409 | 1.324 | |
| PlotTotalIonCurrent | 1.994 | 0.451 | 2.072 | |
| PlotiRT | 2.080 | 0.472 | 2.178 | |
| PlotiRTScore | 2.281 | 0.457 | 2.357 | |
| ReportTables | 1.689 | 0.732 | 1.940 | |
| generateReport | 0.000 | 0.000 | 0.001 | |
| make_MQCombined | 0.944 | 0.421 | 1.012 | |