Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1573/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
pmp 1.18.0 (landing page) Gavin Rhys Lloyd
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
To the developers/maintainers of the pmp package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pmp.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: pmp |
Version: 1.18.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pmp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pmp_1.18.0.tar.gz |
StartedAt: 2024-12-21 05:00:40 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 05:03:59 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 199.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: pmp.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pmp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pmp_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/pmp.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘pmp/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pmp’ version ‘1.18.0’ * 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 ‘pmp’ 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 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 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 16/16 mismatches (average diff: 0.894) [1] 73277 - 73277 == 0.00918 [2] 75291 - 75291 == 0.02623 [3] 77564 - 77564 == 0.03082 [4] 82382 - 82382 == -0.08162 [5] 84708 - 84708 == -0.18823 [6] 86864 - 86864 == -0.27938 [7] 88757 - 88758 == -0.31029 [8] 90292 - 90292 == -0.23323 [9] 91922 - 91922 == 0.39465 ... [ FAIL 3 | WARN 0 | SKIP 0 | PASS 87 ] Error: Test failures Execution halted * 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: 1 ERROR See ‘/Users/biocbuild/bbs-3.20-bioc/meat/pmp.Rcheck/00check.log’ for details.
pmp.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pmp ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘pmp’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (pmp)
pmp.Rcheck/tests/testthat.Rout.fail
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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(pmp) > > test_check("pmp") NRMSE 0.003724107 <simpleError in qcData[id, ]: incorrect number of dimensions> [ FAIL 3 | WARN 0 | SKIP 0 | PASS 87 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-glog_transformation.R:9:3'): Glog function returns expected output ── lambda == as.integer(attributes(out)$processing_history$glog_transformation$lambda_opt) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-sbcWrapper.R:17:3'): sbcWrapper returns expected output ────── `out` not equal to testData$sbcWrapper. 149/172 mismatches (average diff: 0.00325) [24] 12340 - 12340 == -0.004236 [25] 12430 - 12430 == -0.003694 [26] 12520 - 12520 == -0.003143 [27] 12611 - 12611 == -0.002584 [28] 12702 - 12702 == -0.002017 [29] 12794 - 12794 == -0.001441 [30] 12887 - 12887 == -0.000860 [31] 12981 - 12981 == -0.000291 [32] 13075 - 13075 == 0.000245 ... ── Failure ('test-splineSmoother.R:11:3'): splineSmoother returns expected output ── `out` not equal to testData$splineSmoother. 16/16 mismatches (average diff: 0.894) [1] 73277 - 73277 == 0.00918 [2] 75291 - 75291 == 0.02623 [3] 77564 - 77564 == 0.03082 [4] 82382 - 82382 == -0.08162 [5] 84708 - 84708 == -0.18823 [6] 86864 - 86864 == -0.27938 [7] 88757 - 88758 == -0.31029 [8] 90292 - 90292 == -0.23323 [9] 91922 - 91922 == 0.39465 ... [ FAIL 3 | WARN 0 | SKIP 0 | PASS 87 ] Error: Test failures Execution halted
pmp.Rcheck/pmp-Ex.timings
name | user | system | elapsed | |
QCRSC | 0.301 | 0.008 | 0.311 | |
filter_peaks_by_blank | 0.075 | 0.001 | 0.076 | |
filter_peaks_by_fraction | 1.276 | 0.051 | 1.335 | |
filter_peaks_by_rsd | 0.020 | 0.000 | 0.022 | |
filter_samples_by_mv | 0.016 | 0.001 | 0.018 | |
glog_plot_optimised_lambda | 0.371 | 0.041 | 0.416 | |
glog_transformation | 0.172 | 0.013 | 0.186 | |
mv_imputation | 0.059 | 0.002 | 0.061 | |
normalise_to_sum | 0.019 | 0.000 | 0.020 | |
pqn_normalisation | 0.106 | 0.003 | 0.110 | |
processing_history | 0.030 | 0.000 | 0.031 | |
remove_peaks | 0.009 | 0.000 | 0.009 | |
sbc_plot | 0.282 | 0.004 | 0.288 | |