Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1339/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mspms 0.99.7 (landing page) Charlie Bayne
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the mspms package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mspms.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: mspms |
Version: 0.99.7 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:mspms.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings mspms_0.99.7.tar.gz |
StartedAt: 2024-12-24 09:00:45 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 09:15:13 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 868.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: mspms.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:mspms.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings mspms_0.99.7.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/mspms.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mspms/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mspms’ version ‘0.99.7’ * 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 ‘mspms’ 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 ...Warning: program compiled against libxml 212 using older 211 OK * checking code 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 ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed log2fc_t_test 167.302 1.086 168.811 plot_heatmap 29.668 0.219 29.941 prepare_peaks 9.070 0.064 9.161 prepare_fragpipe 7.483 0.084 7.589 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
mspms.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL mspms ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘mspms’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (mspms)
mspms.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(mspms) > > test_check("mspms") Loading required namespace: QFeatures Joining with `by = join_by(quantCols)` Joining with `by = join_by(quantCols)` Joining with `by = join_by(quantCols)` Scale for x is already present. Adding another scale for x, which will replace the existing scale. Scale for x is already present. Adding another scale for x, which will replace the existing scale. Rows: 2444 Columns: 32 -- Column specification -------------------------------------------------------- Delimiter: "," chr (6): Protein Accession, Peptide, Used, Candidate, Sample Profile (Ratio... dbl (25): Protein Group, Protein ID, Quality, Significance, Avg. ppm, Avg. A... lgl (1): PTM 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. 841 peptides were removed because they had a quality score < 0.3 (34%) Rows: 12 Columns: 4 -- Column specification -------------------------------------------------------- Delimiter: "," chr (3): quantCols, group, condition dbl (1): 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. Checking arguments. Loading data as a 'SummarizedExperiment' object. Formatting sample annotations (colData). Formatting data as a 'QFeatures' object. Loading required namespace: imputeLCMD Imputing along margin 2 (samples/columns). Your row data contain missing values. Please read the relevant section(s) in the aggregateFeatures manual page regarding the effects of missing values on data aggregation. Joining with `by = join_by(quantCols)` Joining with `by = join_by(quantCols)` Scale for x is already present. Adding another scale for x, which will replace the existing scale. Scale for x is already present. Adding another scale for x, which will replace the existing scale. Joining with `by = join_by(quantCols)` Joining with `by = join_by(quantCols)` Joining with `by = join_by(quantCols)` Joining with `by = join_by(quantCols)` Joining with `by = join_by(quantCols)` Rows: 1847 Columns: 63 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (19): Peptide Sequence, Prev AA, Next AA, Protein, Protein ID, Entry Nam... dbl (40): Start, End, Peptide Length, CatA_0000_1 Spectral Count, CatA_0000_... num (1): Charges lgl (3): Gene, Mapped Genes, Mapped Proteins 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: 12 Columns: 4 -- Column specification -------------------------------------------------------- Delimiter: "," chr (3): quantCols, group, condition dbl (1): 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. Checking arguments. Loading data as a 'SummarizedExperiment' object. Formatting sample annotations (colData). Formatting data as a 'QFeatures' object. Rows: 2444 Columns: 1 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (1): Protein Group,Protein ID,Protein Accession,Peptide,Used,Candidate,Q... 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: 1207 Columns: 68 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (17): Confidence, Annotated Sequence, Master Protein Accessions, Positio... dbl (48): Peptide Groups Peptide Group ID, Qvality PEP, Qvality q-value, # P... lgl (3): Checked, Modifications, Modifications in Master Proteins 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: 12 Columns: 4 -- Column specification -------------------------------------------------------- Delimiter: "," chr (3): quantCols, group, condition dbl (1): 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. Checking arguments. Loading data as a 'SummarizedExperiment' object. Formatting sample annotations (colData). Formatting data as a 'QFeatures' object. Rows: 1207 Columns: 68 -- Column specification -------------------------------------------------------- Delimiter: "\t" chr (17): Confidence, Annotated Sequence, Master Protein Accessions, Positio... dbl (48): Peptide Groups Peptide Group ID, Qvality PEP, Qvality q-value, # P... lgl (3): Checked, Modifications, Modifications in Master Proteins 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: 12 Columns: 4 -- Column specification -------------------------------------------------------- Delimiter: "," chr (3): quantCols, group, condition dbl (1): 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. Checking arguments. Loading data as a 'SummarizedExperiment' object. Formatting sample annotations (colData). Formatting data as a 'QFeatures' object. Rows: 2444 Columns: 32 -- Column specification -------------------------------------------------------- Delimiter: "," chr (6): Protein Accession, Peptide, Used, Candidate, Sample Profile (Ratio... dbl (25): Protein Group, Protein ID, Quality, Significance, Avg. ppm, Avg. A... lgl (1): PTM 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. 841 peptides were removed because they had a quality score < 0.3 (34%) Rows: 12 Columns: 4 -- Column specification -------------------------------------------------------- Delimiter: "," chr (3): quantCols, group, condition dbl (1): 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. Checking arguments. Loading data as a 'SummarizedExperiment' object. Formatting sample annotations (colData). Formatting data as a 'QFeatures' object. Rows: 2444 Columns: 32 -- Column specification -------------------------------------------------------- Delimiter: "," chr (6): Protein Accession, Peptide, Used, Candidate, Sample Profile (Ratio... dbl (25): Protein Group, Protein ID, Quality, Significance, Avg. ppm, Avg. A... lgl (1): PTM 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: 1 Columns: 1 -- Column specification -------------------------------------------------------- Delimiter: "," chr (1): tests/testdata/ 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. Joining with `by = join_by(quantCols)` Joining with `by = join_by(quantCols)` Checking arguments. Loading data as a 'SummarizedExperiment' object. Formatting sample annotations (colData). Formatting data as a 'QFeatures' object. Imputing along margin 2 (samples/columns). Your row data contain missing values. Please read the relevant section(s) in the aggregateFeatures manual page regarding the effects of missing values on data aggregation. Joining with `by = join_by(quantCols)` Joining with `by = join_by(quantCols)` Joining with `by = join_by(quantCols)` [ FAIL 0 | WARN 7 | SKIP 20 | PASS 97 ] ══ Skipped tests (20) ══════════════════════════════════════════════════════════ • empty test (20): 'test-calc_AA_count_of_motif.R:1:1', 'test-calc_AA_count_of_motif.R:7:1', 'test-calculate_all_cleavages.R:1:1', 'test-log2fc_t_test.R:1:1', 'test-plot_all_icelogos.R:8:1', 'test-plot_all_icelogos.R:15:1', 'test-plot_cleavages_per_pos.R:1:1', 'test-plot_heatmap.R:1:1', 'test-plot_icelogo.R:1:1', 'test-plot_nd_peptides.R:1:1', 'test-plot_pca.R:1:1', 'test-plot_qc_check.R:1:1', 'test-plot_time_course.R:1:1', 'test-plot_volcano.R:1:1', 'test-plotting_helper_functions.R:28:1', 'test-prepare_peaks.R:1:1', 'test-preprocessing_helper_functions.R:515:1', 'test-statistics_helper_functions.R:20:1', 'test-statistics_helper_functions.R:28:1', 'test-statistics_helper_functions.R:46:1' [ FAIL 0 | WARN 7 | SKIP 20 | PASS 97 ] > > proc.time() user system elapsed 578.348 2.727 582.306
mspms.Rcheck/mspms-Ex.timings
name | user | system | elapsed | |
calculate_all_cleavages | 0.012 | 0.004 | 0.015 | |
generate_report | 0 | 0 | 0 | |
log2fc_t_test | 167.302 | 1.086 | 168.811 | |
mspms_tidy | 0.089 | 0.004 | 0.094 | |
plot_all_icelogos | 1.285 | 0.044 | 1.349 | |
plot_cleavages_per_pos | 0.625 | 0.004 | 0.631 | |
plot_heatmap | 29.668 | 0.219 | 29.941 | |
plot_icelogo | 0.593 | 0.000 | 0.594 | |
plot_nd_peptides | 0.414 | 0.000 | 0.414 | |
plot_pca | 4.088 | 0.028 | 4.122 | |
plot_qc_check | 0.968 | 0.000 | 0.970 | |
plot_time_course | 0.018 | 0.000 | 0.018 | |
plot_volcano | 0.534 | 0.004 | 0.539 | |
prepare_fragpipe | 7.483 | 0.084 | 7.589 | |
prepare_pd | 0.002 | 0.000 | 0.002 | |
prepare_peaks | 9.070 | 0.064 | 9.161 | |
process_qf | 1.247 | 0.000 | 1.252 | |