Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:41:12 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 2112/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SVMDO 1.4.0 (landing page) Mustafa Erhan Ozer
| 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 | OK | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the SVMDO package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SVMDO.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: SVMDO |
Version: 1.4.0 |
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings SVMDO_1.4.0.tar.gz |
StartedAt: 2024-05-04 12:35:17 -0000 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 12:41:21 -0000 (Sat, 04 May 2024) |
EllapsedTime: 363.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SVMDO.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings SVMDO_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SVMDO.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 ‘SVMDO/DESCRIPTION’ ... OK * this is package ‘SVMDO’ version ‘1.4.0’ * 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 ‘SVMDO’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
SVMDO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘SVMDO’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading `shiny::dataTableOutput()` is deprecated as of shiny 1.8.1. Please use `DT::DTOutput()` instead. Since you have a suitable version of DT (>= v0.32.1), shiny::dataTableOutput() will automatically use DT::DTOutput() under-the-hood. If this happens to break your app, set `options(shiny.legacy.datatable = TRUE)` to get the legacy datatable implementation (or `FALSE` to squelch this message). See <https://rstudio.github.io/DT/shiny.html> for more information. ** 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 (SVMDO)
SVMDO.Rcheck/tests/testthat.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. > # 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(SVMDO) Loading required package: shiny > > test_check("SVMDO") 'select()' returned 1:1 mapping between keys and columns --> No gene can be mapped.... --> Expected input gene ID: 6348,28976,7297,7054,5092,3725 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 567,57505,3303,494324,3482,4036 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2064,91574,3767,23576,3122,2696 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4842,5080,3598,4323,4544,4137 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 84701,4217,7450,4171,4792,8772 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2852,22877,435,57215,773,4247 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 50507,5019,56606,90480,10166,341 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2597,2752,35,367,6446,6566 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10874,2109,3131,3240,6356,57104 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 84572,162417,91647,405,29947,26873 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1524,6999,1281,51099,4716,6319 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 125988,5970,5925,2588,35,6248 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5069,51703,2712,3667,729238,22901 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8682,8560,3651,3106,51024,2555 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 51703,55331,2584,6696,126328,4773 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 27235,1056,538,339,4000,718 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9514,8842,10643,90865,92935,4255 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 648998,23365,29926,522,216,5194 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8462,4255,4718,10020,1806,644096 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5697,1585,635,5029,7442,4306 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 56652,51083,5802,9572,5189,164656 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3802,5195,4595,3077,5054,4722 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1738,5230,2200,7351,7289,1312 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 116085,5644,35,4232,6340,347411 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8202,64900,4688,5290,1513,10365 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 91949,517,5728,7421,4124,51099 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2788,29881,6343,3574,116228,2937 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 197322,7099,3929,51601,5291,22797 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5369,2280,5467,92609,2936,55243 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8854,54578,5315,1444,2152,51181 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10845,4276,3643,3032,23274,51548 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 949,119559,5023,522,3098,100126861 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10221,4283,1559,92935,56606,3122 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7919,6342,9512,729238,3416,407040 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 374291,3293,345,2701,366,54331 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 114814,6505,5662,113235,406982,79602 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 51548,23389,5825,1244,6772,8743 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 308,7167,3418,3482,867,648998 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5328,1565,2752,150379,5325,3489 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8195,712,1201,2885,10599,4695 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5328,3815,10128,55937,285,401 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 27232,79602,2244,4535,25915,3458 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 116085,5241,55630,3980,256297,29078 --> return NULL... No gene sets have size between 10 and 500 ... --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 617,54577,84649,2006,3703,2864 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 497231,266,648998,1351,2159,2760 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2992,3658,148738,3645,5742,84572 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5193,1605,4286,4128,2639,1201 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2778,2793,64801,728642,8691,5053 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6097,79191,6715,55343,6339,65993 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1376,79944,6941,885,23474,4351 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 125988,5193,2653,93587,6555,3060 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10,1956,80724,4886,3503,3101 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2572,10841,6582,374291,4536,1356 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4217,6532,4543,1339,2919,5122 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 57554,1869,7916,255231,1493,3503 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3640,10423,231,93587,63892,5108 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7369,6616,7030,30061,619373,2876 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1565,7124,145741,221895,3684,4171 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 64087,759,92667,7048,4128,1815 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 50814,55005,8218,388962,3033,102 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7167,5592,4055,2056,407008,53346 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10295,100131801,270,2713,66036,3670 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6362,4012,1728,1645,8218,55005 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4049,4012,26191,1203,4489,11222 --> return NULL... No gene sets have size between 10 and 500 ... --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 84340,84447,6777,55867,409,116931 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3676,10599,56945,27232,7098,23236 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1595,4714,51094,840,1716,3640 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5288,10320,4521,7369,5295,4773 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6519,115286,1376,3157,22877,2694 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 33,55867,5029,54806,5168,718 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 149775,8773,2026,65080,7538,79144 --> return NULL... No gene sets have size between 10 and 500 ... --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 632,3565,10845,8772,406922,7097 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7032,1489,253827,7422,56244,5962 --> return NULL... No gene sets have size between 10 and 500 ... --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5662,3329,3663,3600,6183,55163 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3691,4803,1734,155,6402,3485 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4162,7385,10628,100506742,6403,5451 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5507,4724,25813,84889,3945,80339 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 148738,5621,2167,2146,5091,2713 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 90865,6341,364,4323,599,7019 --> return NULL... [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ] > > proc.time() user system elapsed 65.351 1.802 67.253
SVMDO.Rcheck/SVMDO-Ex.timings
name | user | system | elapsed | |
runGUI | 0.752 | 0.032 | 0.785 | |