Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-09 11:40:49 -0400 (Thu, 09 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4748 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
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 680/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
escape 2.0.0 (landing page) Nick Borcherding
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the escape package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/escape.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: escape |
Version: 2.0.0 |
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:escape.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings escape_2.0.0.tar.gz |
StartedAt: 2024-05-09 07:15:39 -0000 (Thu, 09 May 2024) |
EndedAt: 2024-05-09 07:25:01 -0000 (Thu, 09 May 2024) |
EllapsedTime: 562.0 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: escape.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:escape.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings escape_2.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/escape.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * 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 ‘escape/DESCRIPTION’ ... OK * this is package ‘escape’ version ‘2.0.0’ * 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 ‘escape’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 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 getGeneSets 6.753 0.144 6.91 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: • pcaEnrichment/pcaenrichment-facetby-plot.svg • pcaEnrichment/pcaenrichment-hex-plot.svg • ridgeEnrichment/ridgeenrichment-facet-plot.svg • ridgeEnrichment/ridgeenrichment-gradient-facet-plot.svg • ridgeEnrichment/ridgeenrichment-gradient-plot.svg • ridgeEnrichment/ridgeenrichment-gradient-reorder-plot.svg • ridgeEnrichment/ridgeenrichment-order-plot.svg • ridgeEnrichment/ridgeenrichment-rugadded-plot.svg • scatterEnrichment/scatterenrichment-facet-plot.svg • scatterEnrichment/scatterenrichment-hex-plot.svg • scatterEnrichment/scatterenrichment-scale-plot.svg • splitEnrichment/splitenrichment-facet-plot.svg • splitEnrichment/splitenrichment-mean-plot.svg 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, 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/escape.Rcheck/00check.log’ for details.
escape.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL escape ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘escape’ ... ** using staged installation ** R ** data ** inst ** 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 (escape)
escape.Rcheck/tests/spelling.Rout
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 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. > if(requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.211 0.021 0.221
escape.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(escape) > > test_check("escape") [1] "Calculating features per cell..." [1] "Normalizing enrichment scores per cell..." [1] "Calculating features per cell..." [1] "Normalizing enrichment scores per cell..." Picking joint bandwidth of 9.72 [1] "Using sets of 1000 cells. Running 1 times." [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." [1] "Using sets of 1000 cells. Running 1 times." [1] "Using sets of 1000 cells. Running 1 times." [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." Notch went outside hinges ℹ Do you want `notch = FALSE`? Notch went outside hinges ℹ Do you want `notch = FALSE`? [ FAIL 1 | WARN 0 | SKIP 7 | PASS 17 ] ══ Skipped tests (7) ═══════════════════════════════════════════════════════════ • On CRAN (7): 'test-densityEnrichment.R:9:3', 'test-geyserEnrichment.R:8:3', 'test-heatmapEnrichment.R:7:3', 'test-pcaEnrichment.R:9:3', 'test-ridgeEnrichment.R:8:3', 'test-scatterEnrichment.R:7:3', 'test-splitEnrichment.R:7:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-performPCA.R:13:3'): performPCA works ──────────────────────── output$PCA not equal to getdata("performPCA", "performPCA_PCAvalues"). 68/170 mismatches (average diff: 2.59) [69] -0.408 - 0.408 == -0.817 [70] 2.435 - -2.435 == 4.870 [71] 0.745 - -0.745 == 1.490 [72] 4.293 - -4.293 == 8.586 [73] -1.497 - 1.497 == -2.993 [74] 2.343 - -2.343 == 4.686 [75] -1.769 - 1.769 == -3.538 [76] 0.568 - -0.568 == 1.136 [77] -1.935 - 1.935 == -3.870 ... [ FAIL 1 | WARN 0 | SKIP 7 | PASS 17 ] Deleting unused snapshots: • densityEnrichment/denistyenrichment-group-by-plot.svg • geyserEnrichment/geyserenrichment-facet-plot.svg • geyserEnrichment/geyserenrichment-gradient-facet-plot.svg • geyserEnrichment/geyserenrichment-gradient-plot.svg • geyserEnrichment/geyserenrichment-gradient-reorder-plot.svg • geyserEnrichment/geyserenrichment-order-plot.svg • geyserEnrichment/geyserenrichment-scale-plot.svg • heatmapEnrichment/heatmapenrichment-clustercolumns-plot.svg • heatmapEnrichment/heatmapenrichment-clusterrows-plot.svg • heatmapEnrichment/heatmapenrichment-facet-plot.svg • heatmapEnrichment/heatmapenrichment-scale-plot.svg • pcaEnrichment/pcaenrichment-addfactors-plot.svg • pcaEnrichment/pcaenrichment-facetby-addfactors-plot.svg • pcaEnrichment/pcaenrichment-facetby-plot.svg • pcaEnrichment/pcaenrichment-hex-plot.svg • ridgeEnrichment/ridgeenrichment-facet-plot.svg • ridgeEnrichment/ridgeenrichment-gradient-facet-plot.svg • ridgeEnrichment/ridgeenrichment-gradient-plot.svg • ridgeEnrichment/ridgeenrichment-gradient-reorder-plot.svg • ridgeEnrichment/ridgeenrichment-order-plot.svg • ridgeEnrichment/ridgeenrichment-rugadded-plot.svg • scatterEnrichment/scatterenrichment-facet-plot.svg • scatterEnrichment/scatterenrichment-hex-plot.svg • scatterEnrichment/scatterenrichment-scale-plot.svg • splitEnrichment/splitenrichment-facet-plot.svg • splitEnrichment/splitenrichment-mean-plot.svg Error: Test failures Execution halted
escape.Rcheck/escape-Ex.timings
name | user | system | elapsed | |
densityEnrichment | 0.987 | 0.011 | 1.003 | |
escape.matrix | 0.507 | 0.020 | 0.528 | |
getGeneSets | 6.753 | 0.144 | 6.910 | |
geyserEnrichment | 1.254 | 0.064 | 1.321 | |
heatmapEnrichment | 0.702 | 0.028 | 0.732 | |
pcaEnrichment | 0.702 | 0.000 | 0.704 | |
performNormalization | 0.533 | 0.000 | 0.533 | |
performPCA | 0.496 | 0.004 | 0.500 | |
ridgeEnrichment | 1.037 | 0.028 | 1.068 | |
runEscape | 0.459 | 0.016 | 0.475 | |
scatterEnrichment | 0.690 | 0.000 | 0.692 | |
splitEnrichment | 1.006 | 0.000 | 1.009 | |