Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:19 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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To the developers/maintainers of the OUTRIDER package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1409/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
OUTRIDER 1.17.1 (landing page) Christian Mertes
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: OUTRIDER |
Version: 1.17.1 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings OUTRIDER_1.17.1.tar.gz |
StartedAt: 2023-02-07 10:33:14 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 10:44:25 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 670.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: OUTRIDER.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings OUTRIDER_1.17.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/OUTRIDER.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘OUTRIDER/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OUTRIDER’ version ‘1.17.1’ * 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 ‘OUTRIDER’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ * 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 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 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 ... NOTE padjOnSubset: no visible global function definition for ‘bpmapply’ Undefined global functions or variables: bpmapply * 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 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 Feb 7 10:40:43 2023: SizeFactor estimation ... Tue Feb 7 10:40:43 2023: Controlling for confounders ... Using provided q with: 10 Tue Feb 7 10:40:43 2023: Using the pca implementation for controlling. Tue Feb 7 10:40:43 2023: Used the pca implementation for controlling. Tue Feb 7 10:40:43 2023: Fitting the data ... Tue Feb 7 10:40:49 2023: P-value calculation ... Tue Feb 7 10:40:50 2023: 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 0.9956328 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 0.9899074 0.8672567 1.0000000 1.0000000 0.8466524 feature_7 0.9996621 0.9941735 0.9987931 0.9951721 0.9949311 0.9736960 feature_8 1.0000000 0.9589016 0.8852729 1.0000000 0.9101461 0.8960677 feature_9 0.9944175 0.9819508 0.9432241 1.0000000 0.9670230 1.0000000 feature_10 1.0000000 0.9714403 1.0000000 0.9861801 0.9942400 0.9858725 sample_7 sample_8 sample_9 sample_10 feature_1 0.9654920 1.0000000 0.9479204 0.9599123 feature_2 1.0000000 0.9600618 0.9691272 0.9950101 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 0.9962630 0.9703483 0.9706845 feature_7 1.0000000 1.0000000 0.9939857 0.9878664 feature_8 0.9879652 0.9976097 0.9930989 0.9906877 feature_9 1.0000000 0.9898412 0.9810968 1.0000000 feature_10 0.9773058 0.9987815 1.0000000 1.0000000 > res <- results(ods, all=TRUE) > res geneID sampleID pValue padjust zScore l2fc rawcounts normcounts 1: feature_1 sample_1 0.9708112 1 -0.26 -0.02 58 242.52 2: feature_2 sample_1 1.0000000 1 0.76 0.00 1033 315.69 3: feature_3 sample_1 0.9956214 1 -0.04 0.00 404 829.51 4: feature_4 sample_1 0.9172160 1 -0.67 -0.17 7 61.25 5: feature_5 sample_1 0.9341059 1 0.88 0.00 336 53.49 6: feature_6 sample_1 0.9589618 1 0.35 -0.04 39 184.39 7: feature_7 sample_1 0.9996621 1 0.27 0.00 1095 1416.78 8: feature_8 sample_1 1.0000000 1 0.56 -0.01 217 83.20 9: feature_9 sample_1 0.9944175 1 0.34 0.00 503 646.91 10: feature_10 sample_1 1.0000000 1 0.54 0.00 1449 1078.11 11: feature_1 sample_2 0.9673898 1 -0.46 -0.03 49 241.77 12: feature_2 sample_2 0.9645359 1 -1.10 -0.03 42 308.64 13: feature_3 sample_2 1.0000000 1 0.67 0.00 1690 831.07 14: feature_4 sample_2 1.0000000 1 0.57 -0.01 235 69.70 15: feature_5 sample_2 0.9465044 1 -1.33 -0.12 11 49.18 16: feature_6 sample_2 0.9899074 1 0.56 0.00 398 188.64 17: feature_7 sample_2 0.9941735 1 0.99 0.00 6690 1417.86 18: feature_8 sample_2 0.9589016 1 0.09 -0.05 26 80.48 19: feature_9 sample_2 0.9819508 1 0.02 -0.01 152 643.96 20: feature_10 sample_2 0.9714403 1 0.77 0.00 27702 1078.81 21: feature_1 sample_3 1.0000000 1 0.74 0.00 434 246.13 22: feature_2 sample_3 0.9956328 1 0.79 0.00 1592 315.79 23: feature_3 sample_3 0.9817906 1 -1.96 -0.01 130 825.21 24: feature_4 sample_3 0.8531784 1 -2.53 -0.42 2 46.66 25: feature_5 sample_3 0.8974455 1 0.91 0.00 497 53.54 26: feature_6 sample_3 0.8672567 1 -1.54 -0.32 3 141.84 27: feature_7 sample_3 0.9987931 1 0.16 0.00 980 1416.62 28: feature_8 sample_3 0.8852729 1 -2.08 -0.26 4 66.86 29: feature_9 sample_3 0.9432241 1 -2.80 -0.07 20 617.33 30: feature_10 sample_3 1.0000000 1 0.57 0.00 1673 1078.21 31: feature_1 sample_4 1.0000000 1 0.83 0.00 1052 246.47 32: feature_2 sample_4 0.9691272 1 -0.74 -0.03 52 310.03 33: feature_3 sample_4 0.9714409 1 0.84 0.00 8658 831.47 34: feature_4 sample_4 0.9520697 1 0.59 0.00 541 69.87 35: feature_5 sample_4 0.9659065 1 -0.58 -0.08 17 50.67 36: feature_6 sample_4 1.0000000 1 0.58 0.00 2050 189.02 37: feature_7 sample_4 0.9951721 1 -0.39 0.00 623 1415.80 38: feature_8 sample_4 1.0000000 1 0.58 0.00 323 83.32 39: feature_9 sample_4 1.0000000 1 0.44 0.00 1830 647.85 40: feature_10 sample_4 0.9861801 1 -0.71 -0.01 238 1074.34 41: feature_1 sample_5 0.9682199 1 -0.41 -0.03 51 241.96 42: feature_2 sample_5 0.9565509 1 -1.84 -0.05 30 305.80 43: feature_3 sample_5 0.9874758 1 0.80 0.00 4329 831.37 44: feature_4 sample_5 0.9681790 1 0.59 0.00 427 69.83 45: feature_5 sample_5 1.0000000 1 0.29 -0.03 41 52.37 46: feature_6 sample_5 1.0000000 1 0.58 0.00 2075 189.02 47: feature_7 sample_5 0.9949311 1 -0.43 0.00 605 1415.73 48: feature_8 sample_5 0.9101461 1 0.62 0.00 3174 83.55 49: feature_9 sample_5 0.9670230 1 0.47 0.00 22553 648.17 50: feature_10 sample_5 0.9942400 1 0.17 0.00 580 1076.99 51: feature_1 sample_6 0.9715971 1 0.88 0.00 4121 246.64 52: feature_2 sample_6 1.0000000 1 0.78 0.00 1247 315.74 53: feature_3 sample_6 1.0000000 1 0.32 0.00 657 830.30 54: feature_4 sample_6 0.9964730 1 0.57 -0.01 278 69.75 55: feature_5 sample_6 1.0000000 1 0.45 -0.03 54 52.67 56: feature_6 sample_6 0.8466524 1 -2.16 -0.42 2 126.08 57: feature_7 sample_6 0.9736960 1 1.09 0.00 23938 1418.01 58: feature_8 sample_6 0.8960677 1 -1.66 -0.22 5 69.65 59: feature_9 sample_6 1.0000000 1 0.41 0.00 1030 647.57 60: feature_10 sample_6 0.9858725 1 -0.75 -0.01 231 1074.20 61: feature_1 sample_7 0.9654920 1 0.89 0.00 5031 246.65 62: feature_2 sample_7 1.0000000 1 0.76 0.00 1041 315.69 63: feature_3 sample_7 0.9944387 1 -0.14 0.00 363 829.28 64: feature_4 sample_7 0.9738876 1 0.58 0.00 392 69.82 65: feature_5 sample_7 0.9985055 1 0.22 -0.04 37 52.24 66: feature_6 sample_7 0.9361394 1 0.04 -0.08 16 177.99 67: feature_7 sample_7 1.0000000 1 0.67 0.00 2051 1417.38 68: feature_8 sample_7 0.9879652 1 0.44 -0.02 80 82.55 69: feature_9 sample_7 1.0000000 1 0.44 0.00 1934 647.87 70: feature_10 sample_7 0.9773058 1 -2.37 -0.01 112 1069.30 71: feature_1 sample_8 1.0000000 1 0.80 0.00 691 246.35 72: feature_2 sample_8 0.9600618 1 0.83 0.00 5113 315.93 73: feature_3 sample_8 0.9835739 1 -1.62 -0.01 148 825.98 74: feature_4 sample_8 0.9834010 1 0.34 -0.04 39 68.25 75: feature_5 sample_8 1.0000000 1 0.47 -0.03 56 52.71 76: feature_6 sample_8 0.9962630 1 0.57 0.00 939 188.91 77: feature_7 sample_8 1.0000000 1 0.56 0.00 1647 1417.21 78: feature_8 sample_8 0.9976097 1 0.51 -0.01 122 82.90 79: feature_9 sample_8 0.9898412 1 0.25 0.00 310 646.12 80: feature_10 sample_8 0.9987815 1 0.44 0.00 1036 1077.81 81: feature_1 sample_9 0.9479204 1 -2.03 -0.06 22 235.98 82: feature_2 sample_9 0.9691272 1 -0.74 -0.03 52 310.03 83: feature_3 sample_9 1.0000000 1 0.54 0.00 1062 830.78 84: feature_4 sample_9 0.9285130 1 -0.43 -0.14 9 63.00 85: feature_5 sample_9 0.9314466 1 -2.05 -0.15 8 47.69 86: feature_6 sample_9 0.9703483 1 0.58 0.00 59866 189.11 87: feature_7 sample_9 0.9939857 1 -0.62 0.00 540 1415.45 88: feature_8 sample_9 0.9930989 1 0.48 -0.01 100 82.75 89: feature_9 sample_9 0.9810968 1 -0.01 -0.01 142 643.67 90: feature_10 sample_9 1.0000000 1 0.67 0.00 2984 1078.49 91: feature_1 sample_10 0.9599123 1 -0.99 -0.04 35 239.85 92: feature_2 sample_10 0.9950101 1 0.50 -0.01 241 314.69 93: feature_3 sample_10 1.0000000 1 0.59 0.00 1238 830.89 94: feature_4 sample_10 0.9901875 1 0.39 -0.03 48 68.57 95: feature_5 sample_10 1.0000000 1 0.73 -0.01 120 53.21 96: feature_6 sample_10 0.9706845 1 0.45 -0.02 74 186.59 97: feature_7 sample_10 0.9878664 1 -2.29 -0.01 275 1412.93 98: feature_8 sample_10 0.9906877 1 0.46 -0.02 90 82.66 99: feature_9 sample_10 1.0000000 1 0.45 0.00 2206 647.91 100: feature_10 sample_10 1.0000000 1 0.66 0.00 2818 1078.47 geneID sampleID pValue padjust zScore l2fc rawcounts normcounts meanCorrected theta aberrant AberrantBySample AberrantByGene padj_rank 1: 243.43 120193.2 FALSE 0 0 5.5 2: 312.80 124437.3 FALSE 0 0 5.5 3: 829.59 144900.2 FALSE 0 0 5.5 4: 65.67 102654.8 FALSE 0 0 5.5 5: 51.78 64681.5 FALSE 0 0 5.5 6: 176.16 153410.4 FALSE 0 0 5.5 7: 1416.38 107763.6 FALSE 0 0 5.5 8: 79.79 176265.5 FALSE 0 0 5.5 9: 643.74 201805.4 FALSE 0 0 5.5 10: 1076.47 271486.9 FALSE 0 0 5.5 11: 243.43 120193.2 FALSE 0 0 5.5 12: 312.80 124437.3 FALSE 0 0 5.5 13: 829.59 144900.2 FALSE 0 0 5.5 14: 65.67 102654.8 FALSE 0 0 5.5 15: 51.78 64681.5 FALSE 0 0 5.5 16: 176.16 153410.4 FALSE 0 0 5.5 17: 1416.38 107763.6 FALSE 0 0 5.5 18: 79.79 176265.5 FALSE 0 0 5.5 19: 643.74 201805.4 FALSE 0 0 5.5 20: 1076.47 271486.9 FALSE 0 0 5.5 21: 243.43 120193.2 FALSE 0 0 5.5 22: 312.80 124437.3 FALSE 0 0 5.5 23: 829.59 144900.2 FALSE 0 0 5.5 24: 65.67 102654.8 FALSE 0 0 5.5 25: 51.78 64681.5 FALSE 0 0 5.5 26: 176.16 153410.4 FALSE 0 0 5.5 27: 1416.38 107763.6 FALSE 0 0 5.5 28: 79.79 176265.5 FALSE 0 0 5.5 29: 643.74 201805.4 FALSE 0 0 5.5 30: 1076.47 271486.9 FALSE 0 0 5.5 31: 243.43 120193.2 FALSE 0 0 5.5 32: 312.80 124437.3 FALSE 0 0 5.5 33: 829.59 144900.2 FALSE 0 0 5.5 34: 65.67 102654.8 FALSE 0 0 5.5 35: 51.78 64681.5 FALSE 0 0 5.5 36: 176.16 153410.4 FALSE 0 0 5.5 37: 1416.38 107763.6 FALSE 0 0 5.5 38: 79.79 176265.5 FALSE 0 0 5.5 39: 643.74 201805.4 FALSE 0 0 5.5 40: 1076.47 271486.9 FALSE 0 0 5.5 41: 243.43 120193.2 FALSE 0 0 5.5 42: 312.80 124437.3 FALSE 0 0 5.5 43: 829.59 144900.2 FALSE 0 0 5.5 44: 65.67 102654.8 FALSE 0 0 5.5 45: 51.78 64681.5 FALSE 0 0 5.5 46: 176.16 153410.4 FALSE 0 0 5.5 47: 1416.38 107763.6 FALSE 0 0 5.5 48: 79.79 176265.5 FALSE 0 0 5.5 49: 643.74 201805.4 FALSE 0 0 5.5 50: 1076.47 271486.9 FALSE 0 0 5.5 51: 243.43 120193.2 FALSE 0 0 5.5 52: 312.80 124437.3 FALSE 0 0 5.5 53: 829.59 144900.2 FALSE 0 0 5.5 54: 65.67 102654.8 FALSE 0 0 5.5 55: 51.78 64681.5 FALSE 0 0 5.5 56: 176.16 153410.4 FALSE 0 0 5.5 57: 1416.38 107763.6 FALSE 0 0 5.5 58: 79.79 176265.5 FALSE 0 0 5.5 59: 643.74 201805.4 FALSE 0 0 5.5 60: 1076.47 271486.9 FALSE 0 0 5.5 61: 243.43 120193.2 FALSE 0 0 5.5 62: 312.80 124437.3 FALSE 0 0 5.5 63: 829.59 144900.2 FALSE 0 0 5.5 64: 65.67 102654.8 FALSE 0 0 5.5 65: 51.78 64681.5 FALSE 0 0 5.5 66: 176.16 153410.4 FALSE 0 0 5.5 67: 1416.38 107763.6 FALSE 0 0 5.5 68: 79.79 176265.5 FALSE 0 0 5.5 69: 643.74 201805.4 FALSE 0 0 5.5 70: 1076.47 271486.9 FALSE 0 0 5.5 71: 243.43 120193.2 FALSE 0 0 5.5 72: 312.80 124437.3 FALSE 0 0 5.5 73: 829.59 144900.2 FALSE 0 0 5.5 74: 65.67 102654.8 FALSE 0 0 5.5 75: 51.78 64681.5 FALSE 0 0 5.5 76: 176.16 153410.4 FALSE 0 0 5.5 77: 1416.38 107763.6 FALSE 0 0 5.5 78: 79.79 176265.5 FALSE 0 0 5.5 79: 643.74 201805.4 FALSE 0 0 5.5 80: 1076.47 271486.9 FALSE 0 0 5.5 81: 243.43 120193.2 FALSE 0 0 5.5 82: 312.80 124437.3 FALSE 0 0 5.5 83: 829.59 144900.2 FALSE 0 0 5.5 84: 65.67 102654.8 FALSE 0 0 5.5 85: 51.78 64681.5 FALSE 0 0 5.5 86: 176.16 153410.4 FALSE 0 0 5.5 87: 1416.38 107763.6 FALSE 0 0 5.5 88: 79.79 176265.5 FALSE 0 0 5.5 89: 643.74 201805.4 FALSE 0 0 5.5 90: 1076.47 271486.9 FALSE 0 0 5.5 91: 243.43 120193.2 FALSE 0 0 5.5 92: 312.80 124437.3 FALSE 0 0 5.5 93: 829.59 144900.2 FALSE 0 0 5.5 94: 65.67 102654.8 FALSE 0 0 5.5 95: 51.78 64681.5 FALSE 0 0 5.5 96: 176.16 153410.4 FALSE 0 0 5.5 97: 1416.38 107763.6 FALSE 0 0 5.5 98: 79.79 176265.5 FALSE 0 0 5.5 99: 643.74 201805.4 FALSE 0 0 5.5 100: 1076.47 271486.9 FALSE 0 0 5.5 meanCorrected theta aberrant AberrantBySample AberrantByGene padj_rank FDR_set 1: transcriptome-wide 2: transcriptome-wide 3: transcriptome-wide 4: transcriptome-wide 5: transcriptome-wide 6: transcriptome-wide 7: transcriptome-wide 8: transcriptome-wide 9: transcriptome-wide 10: transcriptome-wide 11: transcriptome-wide 12: transcriptome-wide 13: transcriptome-wide 14: transcriptome-wide 15: transcriptome-wide 16: transcriptome-wide 17: transcriptome-wide 18: transcriptome-wide 19: transcriptome-wide 20: transcriptome-wide 21: transcriptome-wide 22: transcriptome-wide 23: transcriptome-wide 24: transcriptome-wide 25: transcriptome-wide 26: transcriptome-wide 27: transcriptome-wide 28: transcriptome-wide 29: transcriptome-wide 30: transcriptome-wide 31: transcriptome-wide 32: transcriptome-wide 33: transcriptome-wide 34: transcriptome-wide 35: transcriptome-wide 36: transcriptome-wide 37: transcriptome-wide 38: transcriptome-wide 39: transcriptome-wide 40: transcriptome-wide 41: transcriptome-wide 42: transcriptome-wide 43: transcriptome-wide 44: transcriptome-wide 45: transcriptome-wide 46: transcriptome-wide 47: transcriptome-wide 48: transcriptome-wide 49: transcriptome-wide 50: transcriptome-wide 51: transcriptome-wide 52: transcriptome-wide 53: transcriptome-wide 54: transcriptome-wide 55: transcriptome-wide 56: transcriptome-wide 57: transcriptome-wide 58: transcriptome-wide 59: transcriptome-wide 60: transcriptome-wide 61: transcriptome-wide 62: transcriptome-wide 63: transcriptome-wide 64: transcriptome-wide 65: transcriptome-wide 66: transcriptome-wide 67: transcriptome-wide 68: transcriptome-wide 69: transcriptome-wide 70: transcriptome-wide 71: transcriptome-wide 72: transcriptome-wide 73: transcriptome-wide 74: transcriptome-wide 75: transcriptome-wide 76: transcriptome-wide 77: transcriptome-wide 78: transcriptome-wide 79: transcriptome-wide 80: transcriptome-wide 81: transcriptome-wide 82: transcriptome-wide 83: transcriptome-wide 84: transcriptome-wide 85: transcriptome-wide 86: transcriptome-wide 87: transcriptome-wide 88: transcriptome-wide 89: transcriptome-wide 90: transcriptome-wide 91: transcriptome-wide 92: transcriptome-wide 93: transcriptome-wide 94: transcriptome-wide 95: transcriptome-wide 96: transcriptome-wide 97: transcriptome-wide 98: transcriptome-wide 99: transcriptome-wide 100: transcriptome-wide FDR_set > > plotAberrantPerSample(ods) Warning: Transformation introduced infinite values in continuous y-axis Warning: Removed 10 rows containing missing values (`geom_bar()`). > plotVolcano(ods, 1) > > # example of restricting FDR correction to subsets of genes of interest > genesOfInterest <- list("sample_1"=sample(rownames(ods), 3), + "sample_2"=sample(rownames(ods), 8), + "sample_6"=sample(rownames(ods), 5)) > genesOfInterest $sample_1 [1] "feature_10" "feature_1" "feature_6" $sample_2 [1] "feature_8" "feature_10" "feature_4" "feature_3" "feature_6" [6] "feature_1" "feature_2" "feature_9" $sample_6 [1] "feature_5" "feature_6" "feature_8" "feature_10" "feature_7" > ods <- OUTRIDER(ods, subsets=list("exampleSubset"=genesOfInterest)) Tue Feb 7 10:40:53 2023: SizeFactor estimation ... Tue Feb 7 10:40:53 2023: Controlling for confounders ... Using provided q with: 10 Tue Feb 7 10:40:54 2023: Using the autoencoder implementation for controlling. [1] "Tue Feb 7 10:40:56 2023: Initial PCA loss: 6.95599736916101" Killed * 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: [1] "Tue Feb 7 10:42:19 2023: 2 Final nb-AE loss: 4.14004814419489" [1] "Evaluation loss: 0.517781423170479 for q=3" [1] "Tue Feb 7 10:42:21 2023: Initial PCA loss: 4.4572558295302" [1] "Tue Feb 7 10:42:24 2023: Iteration: 1 loss: 4.07122946861174" [1] "Tue Feb 7 10:42:26 2023: Iteration: 2 loss: 4.05826513752563" Time difference of 3.442074 secs [1] "Tue Feb 7 10:42:26 2023: 2 Final nb-AE loss: 4.05826513752563" [1] "Evaluation loss: 0.454717572219274 for q=4" [1] "Tue Feb 7 10:42:27 2023: Initial PCA loss: 4.4282762368912" [1] "Tue Feb 7 10:42:29 2023: Iteration: 1 loss: 3.9973349377491" [1] "Tue Feb 7 10:42:30 2023: Iteration: 2 loss: 3.96432433728888" Time difference of 2.703483 secs [1] "Tue Feb 7 10:42:30 2023: 2 Final nb-AE loss: 3.96432433728888" [1] "Evaluation loss: 0.426020105666412 for q=5" Killed * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘OUTRIDER.Rnw’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘OUTRIDER.Rnw’ using knitr The magick package is required to crop "figure/deVsOutlier-1.png" but not available. Killed * checking PDF version of manual ... OK * DONE Status: 3 ERRORs, 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/OUTRIDER.Rcheck/00check.log’ for details.
OUTRIDER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL OUTRIDER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘OUTRIDER’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_DONT_USE_OPENMP -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_DONT_USE_OPENMP -fPIC -g -O2 -Wall -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -llapack -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRblas -lgfortran -lm -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/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) (2023-01-14 r83615) -- "Unsuffered Consequences" 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(OUTRIDER) Loading required package: BiocParallel Loading required package: GenomicFeatures Loading required package: BiocGenerics 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, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' 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 Feb 7 10:41:35 2023: Initial PCA loss: 6.23443546871152" [1] "Tue Feb 7 10:41:38 2023: Iteration: 1 loss: 4.48133717042354" [1] "Tue Feb 7 10:41:40 2023: Iteration: 2 loss: 4.42404695782621" [1] "Tue Feb 7 10:41:41 2023: Iteration: 3 loss: 4.38477899522259" [1] "Tue Feb 7 10:41:42 2023: Iteration: 4 loss: 4.36539405165039" [1] "Tue Feb 7 10:41:43 2023: Iteration: 5 loss: 4.35942745103864" [1] "Tue Feb 7 10:41:44 2023: Iteration: 6 loss: 4.35611040440345" Time difference of 8.072001 secs [1] "Tue Feb 7 10:41:44 2023: 6 Final nb-AE loss: 4.35611040440345" [1] "Tue Feb 7 10:41:46 2023: Initial PCA loss: 6.23443546871152" [1] "Tue Feb 7 10:41:48 2023: Iteration: 1 loss: 4.48133717042354" [1] "Tue Feb 7 10:41:49 2023: Iteration: 2 loss: 4.42404695782621" [1] "Tue Feb 7 10:41:50 2023: Iteration: 3 loss: 4.38477899522259" [1] "Tue Feb 7 10:41:51 2023: Iteration: 4 loss: 4.36539405165039" [1] "Tue Feb 7 10:41:52 2023: Iteration: 5 loss: 4.35942745103864" [1] "Tue Feb 7 10:41:53 2023: Iteration: 6 loss: 4.35611040440345" Time difference of 6.006369 secs [1] "Tue Feb 7 10:41:53 2023: 6 Final nb-AE loss: 4.35611040440345" 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 Feb 7 10:42:15 2023: Initial PCA loss: 4.4885467635678" [1] "Tue Feb 7 10:42:18 2023: Iteration: 1 loss: 4.15953916852321" [1] "Tue Feb 7 10:42:19 2023: Iteration: 2 loss: 4.14004814419489" Time difference of 3.183209 secs [1] "Tue Feb 7 10:42:19 2023: 2 Final nb-AE loss: 4.14004814419489" [1] "Evaluation loss: 0.517781423170479 for q=3" [1] "Tue Feb 7 10:42:21 2023: Initial PCA loss: 4.4572558295302" [1] "Tue Feb 7 10:42:24 2023: Iteration: 1 loss: 4.07122946861174" [1] "Tue Feb 7 10:42:26 2023: Iteration: 2 loss: 4.05826513752563" Time difference of 3.442074 secs [1] "Tue Feb 7 10:42:26 2023: 2 Final nb-AE loss: 4.05826513752563" [1] "Evaluation loss: 0.454717572219274 for q=4" [1] "Tue Feb 7 10:42:27 2023: Initial PCA loss: 4.4282762368912" [1] "Tue Feb 7 10:42:29 2023: Iteration: 1 loss: 3.9973349377491" [1] "Tue Feb 7 10:42:30 2023: Iteration: 2 loss: 3.96432433728888" Time difference of 2.703483 secs [1] "Tue Feb 7 10:42:30 2023: 2 Final nb-AE loss: 3.96432433728888" [1] "Evaluation loss: 0.426020105666412 for q=5" Killed
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
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