Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-10-18 20:38 -0400 (Fri, 18 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 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 1491/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
orthos 1.2.0 (landing page) Panagiotis Papasaikas
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | 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 | OK | OK | |||||||||
To the developers/maintainers of the orthos package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/orthos.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: orthos |
Version: 1.2.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:orthos.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings orthos_1.2.0.tar.gz |
StartedAt: 2024-10-17 03:22:33 -0400 (Thu, 17 Oct 2024) |
EndedAt: 2024-10-17 03:43:23 -0400 (Thu, 17 Oct 2024) |
EllapsedTime: 1250.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: orthos.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:orthos.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings orthos_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/orthos.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.5 LTS * using session charset: UTF-8 * checking for file ‘orthos/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘orthos’ version ‘1.2.0’ * 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 ‘orthos’ can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See ‘/home/biocbuild/bbs-3.19-bioc/meat/orthos.Rcheck/00install.out’ for details. * 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 ... 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 line endings in shell scripts ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotQueryResultsManh 71.256 55.484 210.828 plotQueryResultsViolin 62.249 18.921 89.740 decomposeVar 49.216 12.721 83.041 queryWithContrasts 34.544 16.395 38.574 loadContrastDatabase 7.832 0.921 14.261 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/orthos.Rcheck/00check.log’ for details.
orthos.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL orthos ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘orthos’ ... ** using non-staged installation via StagedInstall field ** 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 * DONE (orthos)
orthos.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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(orthos) Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats 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 Loading required package: GenomicRanges Loading required package: stats4 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, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors 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: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > > test_check("orthos") demo_decomposed_contrasts_mouse_rds already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/mouse_v212_NDF_c100_DEMOse.rds demo_decomposed_contrasts_mouse_hdf5 already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/mouse_v212_NDF_c100_DEMOassays.h5 demo_decomposed_contrasts_human_rds already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds demo_decomposed_contrasts_human_hdf5 already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5 demo_decomposed_contrasts_mouse_rds already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/mouse_v212_NDF_c100_DEMOse.rds demo_decomposed_contrasts_mouse_hdf5 already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/mouse_v212_NDF_c100_DEMOassays.h5 demo_decomposed_contrasts_human_rds already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds demo_decomposed_contrasts_human_hdf5 already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5 demo_decomposed_contrasts_mouse_rds already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/mouse_v212_NDF_c100_DEMOse.rds demo_decomposed_contrasts_mouse_hdf5 already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/mouse_v212_NDF_c100_DEMOassays.h5 demo_decomposed_contrasts_human_rds already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds demo_decomposed_contrasts_human_hdf5 already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5 2024-10-17 03:37:51.945242: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: SSE4.1 SSE4.2 AVX AVX2 AVX512F AVX512_VNNI FMA To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags. 2024-10-17 03:37:52.435022: I tensorflow/core/util/util.cc:169] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`. see ?orthosData and browseVignettes('orthosData') for documentation loading from cache require("keras") 2024-10-17 03:38:04.670393: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: SSE4.1 SSE4.2 AVX AVX2 AVX512F AVX512_VNNI FMA To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags. WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 476ms/step see ?orthosData and browseVignettes('orthosData') for documentation loading from cache WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually. see ?orthosData and browseVignettes('orthosData') for documentation loading from cache WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 419ms/step 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 276ms/step see ?orthosData and browseVignettes('orthosData') for documentation loading from cache WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 57ms/step see ?orthosData and browseVignettes('orthosData') for documentation loading from cache WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually. see ?orthosData and browseVignettes('orthosData') for documentation loading from cache WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually. WARNING:tensorflow:5 out of the last 5 calls to <function Model.make_predict_function.<locals>.predict_function at 0x7fe3ac4dc700> triggered tf.function retracing. Tracing is expensive and the excessive number of tracings could be due to (1) creating @tf.function repeatedly in a loop, (2) passing tensors with different shapes, (3) passing Python objects instead of tensors. For (1), please define your @tf.function outside of the loop. For (2), @tf.function has reduce_retracing=True option that can avoid unnecessary retracing. For (3), please refer to https://www.tensorflow.org/guide/function#controlling_retracing and https://www.tensorflow.org/api_docs/python/tf/function for more details. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 249ms/step WARNING:tensorflow:6 out of the last 6 calls to <function Model.make_predict_function.<locals>.predict_function at 0x7fe3ac4dc040> triggered tf.function retracing. Tracing is expensive and the excessive number of tracings could be due to (1) creating @tf.function repeatedly in a loop, (2) passing tensors with different shapes, (3) passing Python objects instead of tensors. For (1), please define your @tf.function outside of the loop. For (2), @tf.function has reduce_retracing=True option that can avoid unnecessary retracing. For (3), please refer to https://www.tensorflow.org/guide/function#controlling_retracing and https://www.tensorflow.org/api_docs/python/tf/function for more details. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 70ms/step Checking input... demo_decomposed_contrasts_human_rds already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds demo_decomposed_contrasts_human_hdf5 already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5 Detecting feature ids-type... Feature ids-type detected: GENE_SYMBOL 18051/18051 provided input features mapped against a total of 20411 model features. 2360 missing features will be set to 0. --> Missing features corresponding to non/lowly expressed genes in your context(s) are of no consequence. --> The model is robust to small fractions (<10%) of missing genes that are expressed in your context(s). --> Increased numbers of missing expressed genes in your input might result in model performance decline. Preparing input... Encoding context... see ?orthosData and browseVignettes('orthosData') for documentation loading from cache WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 59ms/step Encoding and decoding contrasts... see ?orthosData and browseVignettes('orthosData') for documentation loading from cache WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually. see ?orthosData and browseVignettes('orthosData') for documentation loading from cache WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 70ms/step 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 58ms/step Preparing output... Done! Checking input... demo_decomposed_contrasts_mouse_rds already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/mouse_v212_NDF_c100_DEMOse.rds demo_decomposed_contrasts_mouse_hdf5 already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/mouse_v212_NDF_c100_DEMOassays.h5 Detecting feature ids-type... Feature ids-type detected: GENE_SYMBOL 19774/19776 provided input features mapped against a total of 20339 model features. 565 missing features will be set to 0. --> Missing features corresponding to non/lowly expressed genes in your context(s) are of no consequence. --> The model is robust to small fractions (<10%) of missing genes that are expressed in your context(s). --> Increased numbers of missing expressed genes in your input might result in model performance decline. Preparing input... Encoding context... see ?orthosData and browseVignettes('orthosData') for documentation loading from cache WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 59ms/step Encoding and decoding contrasts... see ?orthosData and browseVignettes('orthosData') for documentation loading from cache WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually. see ?orthosData and browseVignettes('orthosData') for documentation loading from cache WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 369ms/step 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 73ms/step Preparing output... Done! demo_decomposed_contrasts_human_rds already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds demo_decomposed_contrasts_human_hdf5 already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5 demo_decomposed_contrasts_mouse_rds already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/mouse_v212_NDF_c100_DEMOse.rds demo_decomposed_contrasts_mouse_hdf5 already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/mouse_v212_NDF_c100_DEMOassays.h5 demo_decomposed_contrasts_human_rds already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds demo_decomposed_contrasts_human_hdf5 already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5 see ?orthosData and browseVignettes('orthosData') for documentation loading from cache WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 61ms/step see ?orthosData and browseVignettes('orthosData') for documentation loading from cache WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually. see ?orthosData and browseVignettes('orthosData') for documentation loading from cache WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually. 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 380ms/step 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 66ms/step demo_decomposed_contrasts_human_rds already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds demo_decomposed_contrasts_human_hdf5 already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5 provided contrast: INPUT_CONTRASTS provided contrast: DECODED_CONTRASTS provided contrast: RESIDUAL_CONTRASTS Loading contrast database... demo_decomposed_contrasts_human_rds already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds demo_decomposed_contrasts_human_hdf5 already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5 Thresholding genes... Querying contrast database with INPUT_CONTRASTS... | | | 0% | |=================================== | 50% | |======================================================================| 100% Querying contrast database with DECODED_CONTRASTS... | | | 0% | |=================================== | 50% | |======================================================================| 100% Querying contrast database with RESIDUAL_CONTRASTS... | | | 0% | |=================================== | 50% | |======================================================================| 100% Compiling query statistics... Done! [ FAIL 0 | WARN 2 | SKIP 1 | PASS 216 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • cannot test `mustWork` when data is available (1): 'test-decomposeVar.R:66:5' [ FAIL 0 | WARN 2 | SKIP 1 | PASS 216 ] > > proc.time() user system elapsed 160.439 87.814 254.938
orthos.Rcheck/orthos-Ex.timings
name | user | system | elapsed | |
decomposeVar | 49.216 | 12.721 | 83.041 | |
loadContrastDatabase | 7.832 | 0.921 | 14.261 | |
plotQueryResultsManh | 71.256 | 55.484 | 210.828 | |
plotQueryResultsViolin | 62.249 | 18.921 | 89.740 | |
queryWithContrasts | 34.544 | 16.395 | 38.574 | |
testOrthosEnv | 0.004 | 0.004 | 0.008 | |