| Back to Build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-09-07 15:40 -0400 (Sat, 07 Sep 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4711 |
| 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 2070/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.5.5 (landing page) Mustafa Erhan Ozer
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | 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: 1.5.5 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SVMDO_1.5.5.tar.gz |
| StartedAt: 2024-09-07 01:41:17 -0400 (Sat, 07 Sep 2024) |
| EndedAt: 2024-09-07 01:46:14 -0400 (Sat, 07 Sep 2024) |
| EllapsedTime: 297.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SVMDO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SVMDO_1.5.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SVMDO.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 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘1.5.5’
* 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-3.20-bioc/R/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘SVMDO’ ... ** using staged installation ** 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 ** 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 4.4.1 (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(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: 3159,3558,54344,3645,3485,1149
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56302,4828,5096,2597,1493,23590
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 335,51660,23062,64689,56052,6648
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3600,55343,10842,842,5105,51144
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6720,5428,5499,5727,5330,3073
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1277,100,2517,2593,2314,3440
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55902,3767,80347,509,24147,6445
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5372,253943,4697,3489,4069,79644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5071,53905,203859,2990,3122,1490
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2593,123099,406934,10874,2099,22901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1543,391051,1080,5291,51300,57761
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 410,51316,9560,406982,32,3709
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5468,6925,5551,9779,3357,6347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 92609,51300,150379,2517,7325,1374
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3329,4722,219,6521,5330,4544
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3600,2695,1588,10841,4040,149461
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29881,60528,6347,6901,8195,1968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10008,498,10135,2305,2864,5274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3813,3034,514,116150,5967,5971
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2582,2101,210,2694,4125,4925
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6383,24147,4126,55750,4728,3250
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9927,1629,5329,2936,2888,26088
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91869,2152,26762,340024,8802,3157
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 275,3773,353500,23129,147007,7412
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54805,4288,23304,83854,326625,9380
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 186,445,54798,4852,23590,54902
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 477,10157,4780,104,51206,10616
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 161247,54809,10019,10226,3099,8309
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6584,5950,7352,339,253559,54552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2118,10875,654,8842,537,162417
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2950,2952,1401,132158,54476,29078
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5925,1340,1717,8862,56938,91452
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5373,7057,652,6515,1509,7407
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1738,5799,5919,2984,1347,6789
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7494,10682,293,1489,1356,55753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64805,79602,6522,35,199,201305
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55486,4889,79133,5295,407004,5618
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5346,266,1910,10269,665,6390
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3486,6351,6696,29929,84275,1601
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3425,572,4886,5971,2597,3418
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25974,83693,54931,9414,54600,6788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22852,10874,3948,999,7466,2053
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8202,549,1813,212,6582,3978
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 255738,824,119559,5019,7412,10295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 37,7100,1950,51099,3485,51128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5286,10965,2593,3308,55283,4704
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6908,407024,23474,1641,27329,1582
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3382,585,51144,53905,339,91942
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1327,388753,10008,7040,427,846
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3172,1593,2260,6514,84274,4695
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 130120,4232,5499,119559,7450,7515
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3685,5350,1345,7076,91452,718
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1019,23654,7276,8802,27089,25813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8471,4299,4886,132158,10135,51422
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8195,4609,2348,283459,54982,388585
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55858,2542,1369,7026,4705,5730
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 152926,266,6462,8665,57215,3141
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5190,4803,1392,4023,107075310,170302
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25821,79661,6834,1072,6647,2984
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55065,28976,203068,100303755,283120,3948
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1022,1182,210,401,7157,8604
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51021,196385,7389,336,10682,5629
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51649,148979,56923,57761,85446,477
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57107,3991,1056,65985,5562,4552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10577,54902,842,7355,3636,178
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2834,3673,10,3375,7494,9969
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11019,208,123263,6648,5468,10000
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4288,216,3483,7381,5346,104
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3627,8651,948,1716,9969,5599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5745,23462,1071,2799,1019,665
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9559,4729,241,55768,10094,5631
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8651,22797,383,1893,1436,200205
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10165,2792,1734,5214,1716,9451
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6789,6748,1813,1557,2790,2475
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2194,133522,29947,5744,6928,6891
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1203,2243,8694,6648,1859,91869
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3065,10686,91942,5787,283459,9241
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54805,652,793,7274,5370,10466
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3658,5447,1019,2115,353,5621
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51081,6716,9180,26088,5972,84947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2034,3953,3552,1468,5770,3356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3945,509,347,1675,2495,10875
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7084,1594,3481,3728,130120,4023
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6891,7124,1080,330,3480,197
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6602,131669,1890,1798,3482,858
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55005,4973,728,4502,79585,81034
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5250,10935,4524,54148,5069,6891
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4846,6476,345,406913,5193,2348
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7099,2334,4700,406938,28976,7076
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26060,9968,427,867,3630,4118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1807,51604,9388,54896,4803,1621
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 48,4144,7124,5740,79001,5443
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 153,1601,406991,2778,160428,517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56919,213,389,51085,53905,788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8945,6198,10020,6514,9370,7412
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5925,8309,84447,2571,7167,54915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 131118,149461,8877,148738,2334,540
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3123,4668,4232,4887,57215,2776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 538,2099,9180,1376,3373,80347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1508,5588,11095,10382,116085,4089
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6521,57048,53335,2194,55967,137682
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2950,197,11096,9560,9479,5095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4780,64131,5161,11232,83548,112817
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9451,4153,3952,100131801,5644,2792
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51293,84706,54575,5373,81689,55572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6347,3170,85569,79158,4313,10753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4684,5265,2266,4654,56923,3795
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2696,1559,85446,155,8665,3651
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 142,7385,5126,3293,81704,3565
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22933,5286,160428,1956,3651,7919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 496,213,203859,7284,3645,2934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83985,3552,3458,3952,23389,56848
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6554,9056,617,858,51316,4704
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 48,10226,8799,3242,4049,1601
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 181,406922,54575,3945,2847,5160
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
66.366 2.160 68.634
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.708 | 0.016 | 4.016 | |