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 11:40:05 -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. |
Package: SVMDO |
Version: 1.4.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SVMDO_1.4.0.tar.gz |
StartedAt: 2024-05-04 01:19:09 -0400 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 01:24:41 -0400 (Sat, 04 May 2024) |
EllapsedTime: 332.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SVMDO.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SVMDO_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SVMDO.Rcheck’ * using R version 4.4.0 beta (2024-04-14 r86421) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * 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 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 (2024-04-14 r86421) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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: 5618,6532,1650,3479,341,138050 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 192343,1329,486,1270,2308,2559 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1347,6526,7097,10965,6392,64900 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7498,5291,1113,6948,2642,5820 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6927,4988,3687,353500,1327,3559 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 51,4852,7031,84557,8659,1277 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5329,5594,23101,3570,9965,494324 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2244,367,7026,3952,779,4548 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 196743,867,84061,7200,3766,3099 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 790,593,23479,27329,80201,10522 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4009,4716,56458,6999,112817,27329 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1608,10560,2776,25801,1363,1118 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3593,6868,5116,51167,2791,23411 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 79796,7252,92667,6383,55024,5116 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7056,6289,3577,217,5584,6093 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1435,3645,5176,56606,246,1605 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 477,51167,409,7840,2590,1340 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9377,6524,54796,10020,1019,3034 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 60386,4035,100529063,1672,9588,6093 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6301,1601,22845,5581,7046,100529063 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7097,6531,2147,23178,80309,6659 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1345,23410,2026,790,2168,1737 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 55163,54577,1401,4650,55600,197322 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5741,51703,3074,5192,2762,316 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6794,5193,4319,1394,3768,796 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 64116,165,1080,29079,64788,5662 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3119,5095,2954,4311,2702,5745 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7389,6770,7021,726,1428,836 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 56729,22933,54704,5444,23576,1056 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1029,2169,6720,3738,4522,4758 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 84833,132158,5053,493753,6550,825 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5467,54539,4312,551,10457,3958 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 81788,6340,5245,8029,27010,23706 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 27097,4160,2948,3995,885,9380 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4151,7226,5581,84701,7049,4137 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 81570,27089,5625,4318,3576,796 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4548,107075310,5621,51106,4233,7295 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 191,6571,54796,1906,29947,2746 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4627,5589,10682,406991,148713,8609 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6280,57061,51119,134,5320,9572 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5621,84705,10013,5139,5468,84062 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9526,8813,148713,4126,5274,2034 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 104,2702,26762,1582,5087,2161 --> return NULL... No gene sets have size between 10 and 500 ... --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 407021,664,2903,9382,7137,8856 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 29881,6678,8639,3098,4160,5771 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4283,1043,6338,89823,4712,2591 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 55805,7057,2592,6337,2875,4556 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 54931,10379,493856,1208,5837,104909134 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 648998,3767,51649,4792,642489,1348 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4151,958,796,353500,2137,53345 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4357,84868,200205,4720,3762,55885 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 104909134,55630,87178,1312,57620,487 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4143,4276,91942,1558,9021,594 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10134,26119,26291,4968,4650,7471 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 38,33,7124,9969,5962,6341 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3383,5291,2203,4149,29881,196385 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5743,84061,64788,3932,132,115286 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10497,1910,4723,7248,3763,1537 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6009,3586,2194,132158,3291,5264 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7421,25915,341,825,10886,2998 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 54600,26873,65985,27344,9056,7498 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1634,387,1268,2266,29880,100131801 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3676,51,5321,9663,10874,100133941 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5598,3958,5321,8932,909,1329 --> return NULL... No gene sets have size between 10 and 500 ... --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 59340,2161,55867,3630,4319,6514 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 129787,22852,5730,406903,6868,3418 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 217,875,138050,5020,102,5830 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1022,2731,3423,3577,10549,55600 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 25813,57001,3383,407024,509,4842 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2517,440503,6609,5193,57761,5742 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 84868,3576,8639,10559,3766,4282 --> return NULL... No gene sets have size between 10 and 500 ... --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1636,857,875,5515,3953,57761 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 567,9317,53947,3988,549,6342 --> return NULL... No gene sets have size between 10 and 500 ... --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 268,84342,5741,1716,3356,1968 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6311,6093,65993,3688,4843,5161 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 116519,200205,387787,2767,249,64432 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1118,26227,84649,48,7486,9927 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1043,54205,79133,5365,4337,4009 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4041,3995,768239,55805,3674,4088 --> return NULL... 2024-05-04 01:24:32.420 R[41568:1727723262] XType: com.apple.fonts is not accessible. 2024-05-04 01:24:32.421 R[41568:1727723262] XType: XTFontStaticRegistry is enabled. [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ] > > proc.time() user system elapsed 54.813 1.590 56.877
SVMDO.Rcheck/SVMDO-Ex.timings
name | user | system | elapsed | |
runGUI | 0.770 | 0.037 | 0.828 | |