Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:41:05 -0400 (Thu, 02 Nov 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
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 1568/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
pmp 1.14.0 (landing page) Gavin Rhys Lloyd
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: pmp |
Version: 1.14.0 |
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:pmp.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings pmp_1.14.0.tar.gz |
StartedAt: 2023-11-02 13:09:30 -0000 (Thu, 02 Nov 2023) |
EndedAt: 2023-11-02 13:13:37 -0000 (Thu, 02 Nov 2023) |
EllapsedTime: 246.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: pmp.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:pmp.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings pmp_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/pmp.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘pmp/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pmp’ version ‘1.14.0’ * 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 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 ... 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 == 0.0091 [2] 75291 - 75291 == 0.0261 [3] 77564 - 77564 == 0.0308 [4] 82382 - 82382 == -0.0816 [5] 84708 - 84708 == -0.1882 [6] 86864 - 86864 == -0.2793 [7] 88757 - 88758 == -0.3103 [8] 90292 - 90292 == -0.2332 [9] 91922 - 91922 == 0.3947 ... [ FAIL 2 | WARN 4 | SKIP 0 | PASS 88 ] Error: Test failures Execution halted * 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 ERROR See ‘/home/biocbuild/bbs-3.18-bioc/meat/pmp.Rcheck/00check.log’ for details.
pmp.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL pmp ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-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 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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(pmp) > > test_check("pmp") NRMSE 0.003560579 <simpleError in qcData[id, ]: incorrect number of dimensions> [ FAIL 2 | WARN 4 | SKIP 0 | PASS 88 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-sbcWrapper.R:17:3'): sbcWrapper returns expected output ────── `out` not equal to testData$sbcWrapper. 149/172 mismatches (average diff: 0.00352) [24] 12340 - 12340 == -0.003928 [25] 12430 - 12430 == -0.003422 [26] 12520 - 12520 == -0.002908 [27] 12611 - 12611 == -0.002386 [28] 12702 - 12702 == -0.001856 [29] 12794 - 12794 == -0.001319 [30] 12887 - 12887 == -0.000777 [31] 12981 - 12981 == -0.000246 [32] 13075 - 13075 == 0.000254 ... ── Failure ('test-splineSmoother.R:11:3'): splineSmoother returns expected output ── `out` not equal to testData$splineSmoother. 16/16 mismatches (average diff: 0.894) [1] 73277 - 73277 == 0.0091 [2] 75291 - 75291 == 0.0261 [3] 77564 - 77564 == 0.0308 [4] 82382 - 82382 == -0.0816 [5] 84708 - 84708 == -0.1882 [6] 86864 - 86864 == -0.2793 [7] 88757 - 88758 == -0.3103 [8] 90292 - 90292 == -0.2332 [9] 91922 - 91922 == 0.3947 ... [ FAIL 2 | WARN 4 | SKIP 0 | PASS 88 ] Error: Test failures Execution halted
pmp.Rcheck/pmp-Ex.timings
name | user | system | elapsed | |
QCRSC | 0.309 | 0.000 | 0.309 | |
filter_peaks_by_blank | 0.141 | 0.000 | 0.142 | |
filter_peaks_by_fraction | 1.781 | 0.084 | 1.869 | |
filter_peaks_by_rsd | 0.043 | 0.000 | 0.043 | |
filter_samples_by_mv | 0.037 | 0.004 | 0.041 | |
glog_plot_optimised_lambda | 1.091 | 0.004 | 1.096 | |
glog_transformation | 0.479 | 0.000 | 0.480 | |
mv_imputation | 0.19 | 0.00 | 0.19 | |
normalise_to_sum | 0.046 | 0.000 | 0.046 | |
pqn_normalisation | 0.201 | 0.000 | 0.202 | |
processing_history | 0.095 | 0.000 | 0.096 | |
remove_peaks | 0.020 | 0.000 | 0.021 | |
sbc_plot | 0.663 | 0.000 | 0.665 | |