Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
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 1512/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
OUTRIDER 1.26.3 (landing page) Christian Mertes
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the OUTRIDER package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OUTRIDER.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: OUTRIDER |
Version: 1.26.3 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OUTRIDER_1.26.3.tar.gz |
StartedAt: 2025-10-14 12:16:37 -0000 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 12:26:37 -0000 (Tue, 14 Oct 2025) |
EllapsedTime: 600.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: OUTRIDER.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OUTRIDER_1.26.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/OUTRIDER.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * 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-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘OUTRIDER/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OUTRIDER’ version ‘1.26.3’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 22 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘OUTRIDER’ can be installed ... OK * used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ * 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: 'ggbio:::.buildFacetsFromArgs' See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: 'checkOutriderDataSet' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE estimateBestQ: no visible binding for global variable ‘oht’ plotEncDimSearch.OUTRIDER: no visible binding for global variable ‘oht’ plotEncDimSearch.OUTRIDER: no visible binding for global variable ‘singular_values’ plotEncDimSearch,OutriderDataSet: no visible binding for global variable ‘oht’ plotEncDimSearch,OutriderDataSet: no visible binding for global variable ‘singular_values’ Undefined global functions or variables: oht singular_values * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Non-topic package-anchored link(s) in Rd file 'getter_setter_functions.Rd': ‘[DESeq2]{estimateDispersions}’ Non-topic package-anchored link(s) in Rd file 'sizeFactors.Rd': ‘[DESeq2]{estimateSizeFactors}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘OUTRIDER-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: OUTRIDER > ### Title: OUTRIDER - Finding expression outlier events > ### Aliases: OUTRIDER > > ### ** Examples > > ods <- makeExampleOutriderDataSet() > implementation <- 'autoencoder' > ## Don't show: > ods <- ods[1:10,1:10] > implementation <- 'pca' > ## End(Don't show) > ods <- OUTRIDER(ods, implementation=implementation) Tue Oct 14 12:24:39 2025: SizeFactor estimation ... Tue Oct 14 12:24:39 2025: Controlling for confounders ... Using provided q with: 10 Tue Oct 14 12:24:39 2025: Using the pca implementation for controlling. Tue Oct 14 12:24:40 2025: Used the pca implementation for controlling. Tue Oct 14 12:24:40 2025: Fitting the data ... Tue Oct 14 12:24:44 2025: P-value calculation ... Tue Oct 14 12:24:45 2025: Zscore calculation ... > > pValue(ods)[1:10,1:10] sample_1 sample_2 sample_3 sample_4 sample_5 sample_6 feature_1 0.9708112 0.9673898 1.0000000 1.0000000 0.9682199 0.9715971 feature_2 1.0000000 0.9645359 0.9956326 0.9691272 0.9565509 1.0000000 feature_3 0.9956214 1.0000000 0.9817906 0.9714409 0.9874758 1.0000000 feature_4 0.9172160 1.0000000 0.8531784 0.9520697 0.9681790 0.9964730 feature_5 0.9341059 0.9465044 0.8974455 0.9659065 1.0000000 1.0000000 feature_6 0.9589618 0.9899073 0.8672567 1.0000000 1.0000000 0.8466523 feature_7 0.9996636 0.9941701 0.9987946 0.9951733 0.9949322 0.9736942 feature_8 1.0000000 0.9589015 0.8852728 1.0000000 0.9101463 0.8960677 feature_9 0.9944175 0.9819508 0.9432241 1.0000000 0.9670230 1.0000000 feature_10 1.0000000 0.9713634 1.0000000 0.9862026 0.9942747 0.9858947 sample_7 sample_8 sample_9 sample_10 feature_1 0.9654920 1.0000000 0.9479204 0.9599123 feature_2 1.0000000 0.9600617 0.9691272 0.9950102 feature_3 0.9944387 0.9835739 1.0000000 1.0000000 feature_4 0.9738876 0.9834010 0.9285130 0.9901875 feature_5 0.9985055 1.0000000 0.9314466 1.0000000 feature_6 0.9361394 0.9962628 0.9703490 0.9706844 feature_7 1.0000000 1.0000000 0.9939868 0.9878672 feature_8 0.9879651 0.9976097 0.9930988 0.9906877 feature_9 1.0000000 0.9898412 0.9810968 1.0000000 feature_10 0.9773213 0.9988272 1.0000000 1.0000000 > res <- results(ods, all=TRUE) > res Key: <geneID, sampleID> geneID sampleID pValue padjust zScore l2fc rawcounts <char> <char> <num> <num> <num> <num> <int> 1: feature_1 sample_1 0.9708112 1 -0.26 -0.02 58 2: feature_1 sample_10 0.9599123 1 -0.99 -0.04 35 3: feature_1 sample_2 0.9673898 1 -0.46 -0.03 49 4: feature_1 sample_3 1.0000000 1 0.74 0.00 434 5: feature_1 sample_4 1.0000000 1 0.83 0.00 1052 6: feature_1 sample_5 0.9682199 1 -0.41 -0.03 51 7: feature_1 sample_6 0.9715971 1 0.88 0.00 4121 8: feature_1 sample_7 0.9654920 1 0.89 0.00 5031 9: feature_1 sample_8 1.0000000 1 0.80 0.00 691 10: feature_1 sample_9 0.9479204 1 -2.03 -0.06 22 11: feature_10 sample_1 1.0000000 1 0.54 0.00 1449 12: feature_10 sample_10 1.0000000 1 0.66 0.00 2818 13: feature_10 sample_2 0.9713634 1 0.77 0.00 27702 14: feature_10 sample_3 1.0000000 1 0.57 0.00 1673 15: feature_10 sample_4 0.9862026 1 -0.71 -0.01 238 16: feature_10 sample_5 0.9942747 1 0.17 0.00 580 17: feature_10 sample_6 0.9858947 1 -0.75 -0.01 231 18: feature_10 sample_7 0.9773213 1 -2.37 -0.01 112 19: feature_10 sample_8 0.9988272 1 0.44 0.00 1036 20: feature_10 sample_9 1.0000000 1 0.67 0.00 2984 21: feature_2 sample_1 1.0000000 1 0.76 0.00 1033 22: feature_2 sample_10 0.9950102 1 0.50 -0.01 241 23: feature_2 sample_2 0.9645359 1 -1.10 -0.03 42 24: feature_2 sample_3 0.9956326 1 0.79 0.00 1592 25: feature_2 sample_4 0.9691272 1 -0.74 -0.03 52 26: feature_2 sample_5 0.9565509 1 -1.84 -0.05 30 27: feature_2 sample_6 1.0000000 1 0.78 0.00 1247 28: feature_2 sample_7 1.0000000 1 0.76 0.00 1041 29: feature_2 sample_8 0.9600617 1 0.83 0.00 5113 30: feature_2 sample_9 0.9691272 1 -0.74 -0.03 52 31: feature_3 sample_1 0.9956214 1 -0.04 0.00 404 32: feature_3 sample_10 1.0000000 1 0.59 0.00 1238 33: feature_3 sample_2 1.0000000 1 0.67 0.00 1690 34: feature_3 sample_3 0.9817906 1 -1.96 -0.01 130 35: feature_3 sample_4 0.9714409 1 0.84 0.00 8658 36: feature_3 sample_5 0.9874758 1 0.80 0.00 4329 37: feature_3 sample_6 1.0000000 1 0.32 0.00 657 38: feature_3 sample_7 0.9944387 1 -0.14 0.00 363 39: feature_3 sample_8 0.9835739 1 -1.62 -0.01 148 40: feature_3 sample_9 1.0000000 1 0.54 0.00 1062 41: feature_4 sample_1 0.9172160 1 -0.67 -0.17 7 42: feature_4 sample_10 0.9901875 1 0.39 -0.03 48 43: feature_4 sample_2 1.0000000 1 0.57 -0.01 235 44: feature_4 sample_3 0.8531784 1 -2.53 -0.42 2 45: feature_4 sample_4 0.9520697 1 0.59 0.00 541 46: feature_4 sample_5 0.9681790 1 0.59 0.00 427 47: feature_4 sample_6 0.9964730 1 0.57 -0.01 278 48: feature_4 sample_7 0.9738876 1 0.58 0.00 392 49: feature_4 sample_8 0.9834010 1 0.34 -0.04 39 50: feature_4 sample_9 0.9285130 1 -0.43 -0.14 9 51: feature_5 sample_1 0.9341059 1 0.88 0.00 336 52: feature_5 sample_10 1.0000000 1 0.73 -0.01 120 53: feature_5 sample_2 0.9465044 1 -1.33 -0.12 11 54: feature_5 sample_3 0.8974455 1 0.91 0.00 497 55: feature_5 sample_4 0.9659065 1 -0.58 -0.08 17 56: feature_5 sample_5 1.0000000 1 0.29 -0.03 41 57: feature_5 sample_6 1.0000000 1 0.45 -0.03 54 58: feature_5 sample_7 0.9985055 1 0.22 -0.04 37 59: feature_5 sample_8 1.0000000 1 0.47 -0.03 56 60: feature_5 sample_9 0.9314466 1 -2.05 -0.15 8 61: feature_6 sample_1 0.9589618 1 0.35 -0.04 39 62: feature_6 sample_10 0.9706844 1 0.45 -0.02 74 63: feature_6 sample_2 0.9899073 1 0.56 0.00 398 64: feature_6 sample_3 0.8672567 1 -1.54 -0.32 3 65: feature_6 sample_4 1.0000000 1 0.58 0.00 2050 66: feature_6 sample_5 1.0000000 1 0.58 0.00 2075 67: feature_6 sample_6 0.8466523 1 -2.16 -0.42 2 68: feature_6 sample_7 0.9361394 1 0.04 -0.08 16 69: feature_6 sample_8 0.9962628 1 0.57 0.00 939 70: feature_6 sample_9 0.9703490 1 0.58 0.00 59866 71: feature_7 sample_1 0.9996636 1 0.27 0.00 1095 72: feature_7 sample_10 0.9878672 1 -2.29 -0.01 275 73: feature_7 sample_2 0.9941701 1 0.99 0.00 6690 74: feature_7 sample_3 0.9987946 1 0.16 0.00 980 75: feature_7 sample_4 0.9951733 1 -0.39 0.00 623 76: feature_7 sample_5 0.9949322 1 -0.43 0.00 605 77: feature_7 sample_6 0.9736942 1 1.09 0.00 23938 78: feature_7 sample_7 1.0000000 1 0.67 0.00 2051 79: feature_7 sample_8 1.0000000 1 0.56 0.00 1647 80: feature_7 sample_9 0.9939868 1 -0.62 0.00 540 81: feature_8 sample_1 1.0000000 1 0.56 -0.01 217 82: feature_8 sample_10 0.9906877 1 0.46 -0.02 90 83: feature_8 sample_2 0.9589015 1 0.09 -0.05 26 84: feature_8 sample_3 0.8852728 1 -2.08 -0.26 4 85: feature_8 sample_4 1.0000000 1 0.58 0.00 323 86: feature_8 sample_5 0.9101463 1 0.62 0.00 3174 87: feature_8 sample_6 0.8960677 1 -1.66 -0.22 5 88: feature_8 sample_7 0.9879651 1 0.44 -0.02 80 89: feature_8 sample_8 0.9976097 1 0.51 -0.01 122 90: feature_8 sample_9 0.9930988 1 0.48 -0.01 100 91: feature_9 sample_1 0.9944175 1 0.34 0.00 503 92: feature_9 sample_10 1.0000000 1 0.45 0.00 2206 93: feature_9 sample_2 0.9819508 1 0.02 -0.01 152 94: feature_9 sample_3 0.9432241 1 -2.80 -0.07 20 95: feature_9 sample_4 1.0000000 1 0.44 0.00 1830 96: feature_9 sample_5 0.9670230 1 0.47 0.00 22553 97: feature_9 sample_6 1.0000000 1 0.41 0.00 1030 98: feature_9 sample_7 1.0000000 1 0.44 0.00 1934 99: feature_9 sample_8 0.9898412 1 0.25 0.00 310 100: feature_9 sample_9 0.9810968 1 -0.01 -0.01 142 geneID sampleID pValue padjust zScore l2fc rawcounts meanRawcounts normcounts meanCorrected theta aberrant AberrantBySample <num> <num> <num> <num> <lgcl> <num> 1: 1154.4 242.52 243.43 120191.17 FALSE 0 2: 1154.4 239.85 243.43 120191.17 FALSE 0 3: 1154.4 241.77 243.43 120191.17 FALSE 0 4: 1154.4 246.13 243.43 120191.17 FALSE 0 5: 1154.4 246.47 243.43 120191.17 FALSE 0 6: 1154.4 241.96 243.43 120191.17 FALSE 0 7: 1154.4 246.64 243.43 120191.17 FALSE 0 8: 1154.4 246.65 243.43 120191.17 FALSE 0 9: 1154.4 246.35 243.43 120191.17 FALSE 0 10: 1154.4 235.98 243.43 120191.17 FALSE 0 11: 3882.3 1078.11 1076.47 244289.23 FALSE 0 12: 3882.3 1078.47 1076.47 244289.23 FALSE 0 13: 3882.3 1078.81 1076.47 244289.23 FALSE 0 14: 3882.3 1078.21 1076.47 244289.23 FALSE 0 15: 3882.3 1074.34 1076.47 244289.23 FALSE 0 16: 3882.3 1076.99 1076.47 244289.23 FALSE 0 17: 3882.3 1074.20 1076.47 244289.23 FALSE 0 18: 3882.3 1069.30 1076.47 244289.23 FALSE 0 19: 3882.3 1077.81 1076.47 244289.23 FALSE 0 20: 3882.3 1078.49 1076.47 244289.23 FALSE 0 21: 1044.3 315.69 312.80 124394.23 FALSE 0 22: 1044.3 314.69 312.80 124394.23 FALSE 0 23: 1044.3 308.64 312.80 124394.23 FALSE 0 24: 1044.3 315.79 312.80 124394.23 FALSE 0 25: 1044.3 310.03 312.80 124394.23 FALSE 0 26: 1044.3 305.80 312.80 124394.23 FALSE 0 27: 1044.3 315.74 312.80 124394.23 FALSE 0 28: 1044.3 315.69 312.80 124394.23 FALSE 0 29: 1044.3 315.93 312.80 124394.23 FALSE 0 30: 1044.3 310.03 312.80 124394.23 FALSE 0 31: 1867.9 829.51 829.59 144900.44 FALSE 0 32: 1867.9 830.89 829.59 144900.44 FALSE 0 33: 1867.9 831.07 829.59 144900.44 FALSE 0 34: 1867.9 825.21 829.59 144900.44 FALSE 0 35: 1867.9 831.47 829.59 144900.44 FALSE 0 36: 1867.9 831.37 829.59 144900.44 FALSE 0 37: 1867.9 830.30 829.59 144900.44 FALSE 0 38: 1867.9 829.28 829.59 144900.44 FALSE 0 39: 1867.9 825.98 829.59 144900.44 FALSE 0 40: 1867.9 830.78 829.59 144900.44 FALSE 0 41: 197.8 61.25 65.67 102654.97 FALSE 0 42: 197.8 68.57 65.67 102654.97 FALSE 0 43: 197.8 69.70 65.67 102654.97 FALSE 0 44: 197.8 46.66 65.67 102654.97 FALSE 0 45: 197.8 69.87 65.67 102654.97 FALSE 0 46: 197.8 69.83 65.67 102654.97 FALSE 0 47: 197.8 69.75 65.67 102654.97 FALSE 0 48: 197.8 69.82 65.67 102654.97 FALSE 0 49: 197.8 68.25 65.67 102654.97 FALSE 0 50: 197.8 63.00 65.67 102654.97 FALSE 0 51: 117.7 53.49 51.78 64681.51 FALSE 0 52: 117.7 53.21 51.78 64681.51 FALSE 0 53: 117.7 49.18 51.78 64681.51 FALSE 0 54: 117.7 53.54 51.78 64681.51 FALSE 0 55: 117.7 50.67 51.78 64681.51 FALSE 0 56: 117.7 52.37 51.78 64681.51 FALSE 0 57: 117.7 52.67 51.78 64681.51 FALSE 0 58: 117.7 52.24 51.78 64681.51 FALSE 0 59: 117.7 52.71 51.78 64681.51 FALSE 0 60: 117.7 47.69 51.78 64681.51 FALSE 0 61: 6546.2 184.39 176.16 153439.14 FALSE 0 62: 6546.2 186.59 176.16 153439.14 FALSE 0 63: 6546.2 188.64 176.16 153439.14 FALSE 0 64: 6546.2 141.84 176.16 153439.14 FALSE 0 65: 6546.2 189.02 176.16 153439.14 FALSE 0 66: 6546.2 189.02 176.16 153439.14 FALSE 0 67: 6546.2 126.08 176.16 153439.14 FALSE 0 68: 6546.2 177.99 176.16 153439.14 FALSE 0 69: 6546.2 188.91 176.16 153439.14 FALSE 0 70: 6546.2 189.11 176.16 153439.14 FALSE 0 71: 3844.4 1416.78 1416.38 107550.29 FALSE 0 72: 3844.4 1412.93 1416.38 107550.29 FALSE 0 73: 3844.4 1417.86 1416.38 107550.29 FALSE 0 74: 3844.4 1416.62 1416.38 107550.29 FALSE 0 75: 3844.4 1415.80 1416.38 107550.29 FALSE 0 76: 3844.4 1415.73 1416.38 107550.29 FALSE 0 77: 3844.4 1418.01 1416.38 107550.29 FALSE 0 78: 3844.4 1417.38 1416.38 107550.29 FALSE 0 79: 3844.4 1417.21 1416.38 107550.29 FALSE 0 80: 3844.4 1415.45 1416.38 107550.29 FALSE 0 81: 414.1 83.20 79.79 176319.66 FALSE 0 82: 414.1 82.66 79.79 176319.66 FALSE 0 83: 414.1 80.48 79.79 176319.66 FALSE 0 84: 414.1 66.86 79.79 176319.66 FALSE 0 85: 414.1 83.32 79.79 176319.66 FALSE 0 86: 414.1 83.55 79.79 176319.66 FALSE 0 87: 414.1 69.65 79.79 176319.66 FALSE 0 88: 414.1 82.55 79.79 176319.66 FALSE 0 89: 414.1 82.90 79.79 176319.66 FALSE 0 90: 414.1 82.75 79.79 176319.66 FALSE 0 91: 3068.0 646.91 643.74 201806.58 FALSE 0 92: 3068.0 647.91 643.74 201806.58 FALSE 0 93: 3068.0 643.96 643.74 201806.58 FALSE 0 94: 3068.0 617.33 643.74 201806.58 FALSE 0 95: 3068.0 647.85 643.74 201806.58 FALSE 0 96: 3068.0 648.17 643.74 201806.58 FALSE 0 97: 3068.0 647.57 643.74 201806.58 FALSE 0 98: 3068.0 647.87 643.74 201806.58 FALSE 0 99: 3068.0 646.12 643.74 201806.58 FALSE 0 100: 3068.0 643.67 643.74 201806.58 FALSE 0 meanRawcounts normcounts meanCorrected theta aberrant AberrantBySample AberrantByGene padj_rank <num> <num> 1: 0 5.5 2: 0 5.5 3: 0 5.5 4: 0 5.5 5: 0 5.5 6: 0 5.5 7: 0 5.5 8: 0 5.5 9: 0 5.5 10: 0 5.5 11: 0 5.5 12: 0 5.5 13: 0 5.5 14: 0 5.5 15: 0 5.5 16: 0 5.5 17: 0 5.5 18: 0 5.5 19: 0 5.5 20: 0 5.5 21: 0 5.5 22: 0 5.5 23: 0 5.5 24: 0 5.5 25: 0 5.5 26: 0 5.5 27: 0 5.5 28: 0 5.5 29: 0 5.5 30: 0 5.5 31: 0 5.5 32: 0 5.5 33: 0 5.5 34: 0 5.5 35: 0 5.5 36: 0 5.5 37: 0 5.5 38: 0 5.5 39: 0 5.5 40: 0 5.5 41: 0 5.5 42: 0 5.5 43: 0 5.5 44: 0 5.5 45: 0 5.5 46: 0 5.5 47: 0 5.5 48: 0 5.5 49: 0 5.5 50: 0 5.5 51: 0 5.5 52: 0 5.5 53: 0 5.5 54: 0 5.5 55: 0 5.5 56: 0 5.5 57: 0 5.5 58: 0 5.5 59: 0 5.5 60: 0 5.5 61: 0 5.5 62: 0 5.5 63: 0 5.5 64: 0 5.5 65: 0 5.5 66: 0 5.5 67: 0 5.5 68: 0 5.5 69: 0 5.5 70: 0 5.5 71: 0 5.5 72: 0 5.5 73: 0 5.5 74: 0 5.5 75: 0 5.5 76: 0 5.5 77: 0 5.5 78: 0 5.5 79: 0 5.5 80: 0 5.5 81: 0 5.5 82: 0 5.5 83: 0 5.5 84: 0 5.5 85: 0 5.5 86: 0 5.5 87: 0 5.5 88: 0 5.5 89: 0 5.5 90: 0 5.5 91: 0 5.5 92: 0 5.5 93: 0 5.5 94: 0 5.5 95: 0 5.5 96: 0 5.5 97: 0 5.5 98: 0 5.5 99: 0 5.5 100: 0 5.5 AberrantByGene padj_rank > > plotAberrantPerSample(ods) Warning in scale_y_log10(limits = c(oneOffset, NA)) : log-10 transformation introduced infinite values. Warning: Removed 10 rows containing missing values or values outside the scale range (`geom_bar()`). > plotVolcano(ods, 1) Error in pm[[2]] : subscript out of bounds Calls: plotVolcano ... plotVolcano -> .local -> ggplotly -> ggplotly.ggplot -> gg2list Execution halted * 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: Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test_plotting.R:21:5 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─OUTRIDER::plotVolcano(ods, 30) 5. └─OUTRIDER::plotVolcano(ods, 30) 6. └─OUTRIDER (local) .local(object, ...) 7. ├─plotly::ggplotly(p, tooltip = "text") 8. └─plotly:::ggplotly.ggplot(p, tooltip = "text") 9. └─plotly::gg2list(...) [ FAIL 1 | WARN 2 | SKIP 0 | PASS 99 ] 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: 2 ERRORs, 4 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/OUTRIDER.Rcheck/00check.log’ for details.
OUTRIDER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL OUTRIDER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘OUTRIDER’ ... ** this is package ‘OUTRIDER’ version ‘1.26.3’ ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_DONT_USE_OPENMP -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_DONT_USE_OPENMP -fPIC -g -O2 -Wall -Werror=format-security -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -L/home/biocbuild/R/R/lib -lRlapack -L/home/biocbuild/R/R/lib -lRblas -lgfortran -lm -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-OUTRIDER/00new/OUTRIDER/libs ** R ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (OUTRIDER)
OUTRIDER.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" Copyright (C) 2025 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. > library(testthat) > library(OUTRIDER) Loading required package: BiocParallel Loading required package: GenomicFeatures Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars The following object is masked from 'package:Biobase': rowMedians Loading required package: data.table Attaching package: 'data.table' The following object is masked from 'package:SummarizedExperiment': shift The following object is masked from 'package:GenomicRanges': shift The following object is masked from 'package:IRanges': shift The following objects are masked from 'package:S4Vectors': first, second > > register(SerialParam()) > > test_check("OUTRIDER") [1] "Tue Oct 14 12:25:12 2025: Initial PCA loss: 6.269466444026" [1] "Tue Oct 14 12:25:14 2025: Iteration: 1 loss: 4.61577601938473" [1] "Tue Oct 14 12:25:15 2025: Iteration: 2 loss: 4.55515474101613" [1] "Tue Oct 14 12:25:16 2025: Iteration: 3 loss: 4.51373526295885" [1] "Tue Oct 14 12:25:17 2025: Iteration: 4 loss: 4.48283487981497" [1] "Tue Oct 14 12:25:17 2025: Iteration: 5 loss: 4.46743909110935" [1] "Tue Oct 14 12:25:18 2025: Iteration: 6 loss: 4.46542241472605" Time difference of 5.551991 secs [1] "Tue Oct 14 12:25:18 2025: 6 Final nb-AE loss: 4.46542241472605" [1] "Tue Oct 14 12:25:20 2025: Initial PCA loss: 6.269466444026" [1] "Tue Oct 14 12:25:21 2025: Iteration: 1 loss: 4.61577601938473" [1] "Tue Oct 14 12:25:22 2025: Iteration: 2 loss: 4.55515474101613" [1] "Tue Oct 14 12:25:23 2025: Iteration: 3 loss: 4.51373526295885" [1] "Tue Oct 14 12:25:24 2025: Iteration: 4 loss: 4.48283487981497" [1] "Tue Oct 14 12:25:25 2025: Iteration: 5 loss: 4.46743909110935" [1] "Tue Oct 14 12:25:26 2025: Iteration: 6 loss: 4.46542241472605" Time difference of 5.365014 secs [1] "Tue Oct 14 12:25:26 2025: 6 Final nb-AE loss: 4.46542241472605" class: OutriderDataSet class: RangedSummarizedExperiment dim: 100 50 metadata(1): version assays(1): counts rownames(100): ENSG00000223972.4 ENSG00000227232.4 ... ENSG00000107404.13 ENSG00000162576.12 rowData names(0): colnames(50): GTEX.UPK5.0426.SM.3GAEK GTEX.WFG7.2026.SM.3GIL7 ... GTEX.11UD2.2526.SM.5CVNU GTEX.13O61.1426.SM.5KM3D colData names(1): sampleID [1] "Tue Oct 14 12:25:34 2025: Initial PCA loss: 4.45497702648287" [1] "Tue Oct 14 12:25:36 2025: Iteration: 1 loss: 4.10212714917902" [1] "Tue Oct 14 12:25:37 2025: Iteration: 2 loss: 4.08520151065717" Time difference of 1.875806 secs [1] "Tue Oct 14 12:25:37 2025: 2 Final nb-AE loss: 4.08520151065717" [1] "Evaluation loss: 0.409365624668786 for q=3" [1] "Tue Oct 14 12:25:38 2025: Initial PCA loss: 4.42698071615731" [1] "Tue Oct 14 12:25:40 2025: Iteration: 1 loss: 4.02209565570526" [1] "Tue Oct 14 12:25:41 2025: Iteration: 2 loss: 4.00839830497134" Time difference of 1.933573 secs [1] "Tue Oct 14 12:25:41 2025: 2 Final nb-AE loss: 4.00839830497134" [1] "Evaluation loss: 0.422585264564871 for q=4" [1] "Tue Oct 14 12:25:42 2025: Initial PCA loss: 4.40759694007152" [1] "Tue Oct 14 12:25:43 2025: Iteration: 1 loss: 3.94101914633159" [1] "Tue Oct 14 12:25:44 2025: Iteration: 2 loss: 3.92229871820955" Time difference of 1.899659 secs [1] "Tue Oct 14 12:25:44 2025: 2 Final nb-AE loss: 3.92229871820955" [1] "Evaluation loss: 0.380595225546335 for q=5" Optimal encoding dimension: 4 Optimal encoding dimension: 50 Optimal encoding dimension: 20 Optimal encoding dimension: 2 Optimal encoding dimension: 4 [1] "Tue Oct 14 12:26:22 2025: Initial PCA loss: 7.16457134714849" [1] "Tue Oct 14 12:26:24 2025: Iteration: 1 loss: 6.82913931405131" [1] "Tue Oct 14 12:26:25 2025: Iteration: 2 loss: 6.82749008590827" Time difference of 2.423867 secs [1] "Tue Oct 14 12:26:25 2025: 2 Final nb-AE loss: 6.82749008590827" [ FAIL 1 | WARN 2 | SKIP 0 | PASS 99 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_plotting.R:21:5'): plotting ──────────────────────────────────── <subscriptOutOfBoundsError/error/condition> Error in `pm[[2]]`: subscript out of bounds Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test_plotting.R:21:5 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─OUTRIDER::plotVolcano(ods, 30) 5. └─OUTRIDER::plotVolcano(ods, 30) 6. └─OUTRIDER (local) .local(object, ...) 7. ├─plotly::ggplotly(p, tooltip = "text") 8. └─plotly:::ggplotly.ggplot(p, tooltip = "text") 9. └─plotly::gg2list(...) [ FAIL 1 | WARN 2 | SKIP 0 | PASS 99 ] Error: Test failures Execution halted
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
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