Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:03:17 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SVMDO_1.4.0.tar.gz |
StartedAt: 2024-05-31 08:50:52 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 08:55:44 -0400 (Fri, 31 May 2024) |
EllapsedTime: 291.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SVMDO.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --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 (2024-04-24) * 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 22.04.4 LTS * using session charset: UTF-8 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
SVMDO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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 (2024-04-24) -- "Puppy Cup" 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(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: 800,80201,10724,2101,84063,64919 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 26517,1497,4846,5257,51548,10559 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 55885,1604,6522,6272,1337,140803 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 567,3811,8694,7021,142,3426 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2806,4792,57570,389692,10295,1514 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2932,2944,494324,1444,10560,5068 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 11132,6649,90070,54809,5080,3172 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 857,3074,5631,9388,55937,2582 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2785,846,4744,7391,3990,84300 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4544,2885,1644,3081,51204,1555 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 33,627,2222,1737,8202,5515 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4729,6571,5190,81788,8228,4143 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1807,5078,1436,175,4716,32 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5443,1499,2717,5162,116519,590 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8560,55034,151,2147,79644,3764 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1186,66036,28958,7167,5443,4795 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 23236,51,2628,2555,118,2194 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9241,4312,9997,7442,5727,55805 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2266,11222,6582,2876,7442,5261 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 54658,4314,3066,6348,4982,51119 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 64116,4162,497231,3077,624,5330 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7084,866,7276,1621,114548,2746 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 56729,4547,3710,51024,1675,1757 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3593,10686,3562,291,3992,5473 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4040,4017,255738,56923,496,6492 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 23054,1364,836,4556,4726,27097 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 387787,1889,2731,3658,595,5133 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5096,797,2495,55630,8455,10094 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 91574,51141,9572,3764,5052,1339 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3700,51106,1490,7292,1435,2309 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 80331,2786,246,123,124454,3099 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4709,407021,217,10874,134,5245 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8074,10730,5270,65018,5330,2006 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6934,388753,5644,6288,6392,51167 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 23474,148713,10497,10935,8942,4069 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2875,410,3054,23600,10020,3552 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7084,3673,1135,149461,57192,84842 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5580,790,1281,3315,54896,116519 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7021,6583,1584,4887,2805,1634 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1601,5071,56052,6928,2539,50507 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6357,773,80224,6615,3458,6342 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9807,3156,54106,596,55970,2903 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2053,3784,5571,1208,5771,2034 --> return NULL... No gene sets have size between 10 and 500 ... --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 29928,100,5077,1634,1232,590 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2647,6678,2167,51181,9255,55532 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5920,64788,427,4338,462,51478 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3784,10559,3077,3689,81570,5950 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10243,4256,1491,6609,4879,6339 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 80201,8202,4129,50615,2731,54578 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8398,6232,5551,7852,4846,10616 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3373,5451,7430,10279,4868,3502 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3569,6657,3570,1586,7390,10295 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8829,3174,5162,7177,9374,2776 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2194,1798,5236,6915,9451,3293 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3484,284184,3651,406938,5476,10008 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6510,3643,28234,28951,2159,4023 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2739,10352,6647,406991,6510,23178 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2948,6804,4760,55283,10,6609 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6648,56999,255738,3673,1147,8050 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 200205,5467,3598,2271,2548,55630 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 23389,5286,2997,3075,10938,5443 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 84557,654,27429,3691,5820,79689 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1672,64801,55034,5449,479,3596 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 57818,4982,3577,7422,10166,1605 --> return NULL... No gene sets have size between 10 and 500 ... --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 26517,2948,4722,50639,155,790 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 51555,55867,10886,6324,5728,56938 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6531,5255,942,959,5329,4828 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3172,211,56938,3949,759,6340 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4852,487,84557,388962,406,5321 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 316,2852,6469,2068,2752,3802 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2119,3995,1508,130120,6554,64131 --> return NULL... No gene sets have size between 10 and 500 ... --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10316,2539,2591,22901,3440,7430 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5428,10195,7528,397491,3980,8722 --> return NULL... No gene sets have size between 10 and 500 ... --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 55750,51004,123099,857,4508,81689 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2588,54658,476,2702,1678,84277 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3708,1352,5288,10000,25839,116519 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 340024,3691,3479,846,7128,57570 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5621,5579,11232,3956,23436,116150 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6915,5837,338,686,7350,7274 --> return NULL... [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ] > > proc.time() user system elapsed 53.933 0.924 54.837
SVMDO.Rcheck/SVMDO-Ex.timings
name | user | system | elapsed | |
runGUI | 0.665 | 0.031 | 0.700 | |