Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:43 -0400 (Fri, 15 Oct 2021).
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. |
Package 1190/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MQmetrics 1.0.0 (landing page) Alvaro Sanchez-Villalba
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: MQmetrics |
Version: 1.0.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MQmetrics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MQmetrics_1.0.0.tar.gz |
StartedAt: 2021-10-14 21:24:48 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 21:27:24 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 156.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MQmetrics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MQmetrics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MQmetrics_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/MQmetrics.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (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 ‘1.0.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘MQmetrics’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.6Mb sub-directories of 1Mb or more: extdata 4.9Mb help 1.5Mb * 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 ... 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed PlotAcquisitionCycle 7.259 0.406 6.564 PlotPTM 6.847 0.239 6.897 PlotAndromedaScore 5.312 0.211 5.360 * 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 ‘/Users/biocbuild/bbs-3.13-bioc/meat/MQmetrics.Rcheck/00check.log’ for details.
MQmetrics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MQmetrics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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 8.486 0.917 8.721
MQmetrics.Rcheck/MQmetrics-Ex.timings
name | user | system | elapsed | |
MaxQuantAnalysisInfo | 2.264 | 0.274 | 2.421 | |
PlotAcquisitionCycle | 7.259 | 0.406 | 6.564 | |
PlotAllDynamicRange | 3.750 | 0.261 | 3.885 | |
PlotAndromedaScore | 5.312 | 0.211 | 5.360 | |
PlotCharge | 2.810 | 0.184 | 2.855 | |
PlotCombinedDynamicRange | 1.945 | 0.192 | 2.018 | |
PlotHydrophobicity | 3.504 | 0.252 | 3.490 | |
PlotIdentificationType | 2.879 | 0.187 | 2.950 | |
PlotIntensity | 2.917 | 0.224 | 2.901 | |
PlotIsotopePattern | 2.111 | 0.195 | 2.188 | |
PlotMsMs | 1.964 | 0.200 | 2.047 | |
PlotPCA | 2.118 | 0.203 | 2.146 | |
PlotPTM | 6.847 | 0.239 | 6.897 | |
PlotPeaks | 1.862 | 0.177 | 1.925 | |
PlotPeptidesIdentified | 1.808 | 0.189 | 1.885 | |
PlotProteaseSpecificity | 4.609 | 0.210 | 4.662 | |
PlotProteinCoverage | 1.850 | 0.208 | 1.892 | |
PlotProteinOverlap | 1.959 | 0.179 | 1.963 | |
PlotProteinPeptideRatio | 2.246 | 0.203 | 2.266 | |
PlotProteinsIdentified | 1.875 | 0.191 | 1.886 | |
PlotTotalIonCurrent | 4.505 | 0.252 | 3.860 | |
PlotiRT | 3.151 | 0.228 | 3.264 | |
PlotiRTScore | 2.526 | 0.194 | 2.596 | |
ReportTables | 2.783 | 0.316 | 2.691 | |
generateReport | 0 | 0 | 0 | |
make_MQCombined | 1.700 | 0.188 | 1.798 | |