Mustafa Erhan Ozer
| Snapshot Date: 2025-08-07 13:40 -0400 (Thu, 07 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/SVMDO |
| git_branch: RELEASE_3_21 |
| git_last_commit: 8259124 |
| git_last_commit_date: 2025-04-15 13:15:07 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-08-11 11:41 -0400 (Mon, 11 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 2139/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.8.0 (landing page) Mustafa Erhan Ozer
| nebbiolo1 | Linux (Ubuntu 24.04.2 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 | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
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: 1.8.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SVMDO_1.8.0.tar.gz |
| StartedAt: 2025-08-11 03:20:34 -0400 (Mon, 11 Aug 2025) |
| EndedAt: 2025-08-11 03:25:32 -0400 (Mon, 11 Aug 2025) |
| EllapsedTime: 297.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SVMDO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SVMDO_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SVMDO.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘1.8.0’
* 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-3.21-bioc/R/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘SVMDO’ ... ** this is package ‘SVMDO’ version ‘1.8.0’ ** 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 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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: 26291,2170,3373,940,6772,51422
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55486,6183,1029,145264,3557,7919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51103,22933,6696,3440,796,2632
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91574,130120,4726,23236,7471,5189
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4860,4889,6566,8665,491,30061
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2653,6932,100128525,2878,9572,8651
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57085,1491,5255,55753,55788,5660
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4314,11095,5080,85479,7350,1889
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2673,22820,57107,5167,6821,57678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5442,801,266,2056,284958,3673
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53632,5276,2947,653,5286,4724
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 285126,4688,10382,477,11254,2592
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 858,55034,51608,3291,3357,3991
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9507,6382,5828,53632,54106,3692
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5798,5473,2524,1376,2064,83439
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2820,147007,8431,4702,5919,867
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9420,81570,4609,5443,2542,10753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10229,54802,51079,51241,9997,27141
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5967,3060,140803,2030,5315,632
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7351,51085,6402,3783,407011,55186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5551,10059,2639,6890,3417,2903
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 653,6183,1149,594,2791,885
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1910,6341,9607,345,29880,1992
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5506,6566,5588,56302,4760,7099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 359,7372,54205,4153,574447,26521
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 219,55902,2791,7515,4015,92483
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5770,388585,572,2720,10935,2896
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5176,6536,11213,5468,7292,599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3351,57761,8660,25839,2639,4864
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83854,4286,5563,90865,5053,25974
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 213,79949,551,1537,3559,6789
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2548,5069,64900,3418,4729,4976
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79934,10,4049,6948,5781,3486
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5798,7528,7407,3795,2638,790955
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55630,57104,23590,4232,2713,5836
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3717,105372280,10991,6714,196385,50943
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 197,5592,51204,3081,283459,3117
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 15,10466,22796,51117,23411,5515
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 643181,10094,23411,51167,84701,10128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7407,2834,10730,5465,7350,5443
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4552,63931,407004,7098,1605,581
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1234,5092,7098,4723,1992,7422
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3062,6584,4552,54901,3485,5373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55486,2787,10128,51604,1019,2524
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6934,1734,842,2581,4313,7132
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5584,54205,10753,7057,131669,493753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25974,10423,2152,57192,56052,2645
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79633,4153,140803,116228,56848,80347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6347,3570,463,54931,627,197131
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1468,183,6718,8842,1346,629
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1909,5825,948,5442,11035,26175
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7421,186,53345,6786,51094,210
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8678,9672,479,26517,5506,51608
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84239,5274,79587,664,5295,2694
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54567,6550,7381,491,6928,4159
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1373,3554,6891,5211,79585,5745
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11131,4669,10580,570,111,83439
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 958,11232,10159,26354,28976,344
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55970,84239,7167,6938,55283,217
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64788,29078,7942,5447,6833,959
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1508,2314,53905,1906,1149,54806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80270,6521,142,407011,7275,2006
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3481,7026,4915,1352,4684,3162
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116228,53345,10243,1497,64116,5507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388372,5506,5562,351,84300,627
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9919,4688,10250,4790,208,1893
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3606,10159,1352,1490,6584,3667
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 538,6183,355,1806,84572,6401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1594,1281,253943,5139,7077,4656
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 137682,55937,1757,7915,4709,6356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29960,7515,3636,11136,4357,116519
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407009,7471,5660,213,6263,4668
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23175,7480,5799,5805,1442,63874
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1149,9560,23038,4790,2919,54968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56052,2587,8651,54675,1376,56623
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6772,3728,130589,3030,57761,65985
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6347,6236,406906,131669,1361,4705
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4502,51004,79572,5052,5740,51204
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1339,2115,3600,3596,6392,1376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2053,10269,4232,518,51117,37
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7057,9021,1436,11231,2147,160287
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1581,55970,8639,81704,1606,57678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55034,387787,3351,91452,51167,3490
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51103,6929,9575,488,249,125170
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11019,104909134,8932,23474,28234,8639
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64116,8862,22797,189,7422,325
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54805,4846,4982,2890,116228,5193
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57048,8802,5327,706,347,1798
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4543,868,3158,2947,2984,376497
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2639,1347,440503,10195,6891,2683
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 653,51,9692,10724,6927,9415
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6387,51181,51604,148979,79736,55343
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81033,5288,4697,3482,2804,2888
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10102,5787,1806,406991,229,6789
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5409,9971,407008,2731,55532,5190
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53335,1621,3875,26088,5091,1557
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84062,4700,1582,4828,462,19
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3172,2645,4722,9332,15,7276
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5365,79572,1203,9498,653,7347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51004,1645,2919,55526,10383,84572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6183,9241,5860,5126,9759,3358
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2305,6925,3440,100529063,4715,153
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3482,9104,7132,540,4713,10221
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5160,513,4942,83854,6513,3032
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 130120,440138,6908,200810,3562,1734
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50814,55630,89866,3636,51144,538
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2788,2903,56729,5445,2629,285126
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54915,155,3283,6374,114814,6888
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6374,80207,6927,51081,203068,151
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5506,361,169792,728,54577,3570
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51204,23389,4282,2710,6262,5594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 434,51099,2538,10316,5789,6925
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5830,2694,5445,2712,56606,94235
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8678,2200,1649,6476,836,26175
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 156,339,32,8803,5350,30061
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
65.718 0.997 66.836
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.717 | 0.072 | 3.822 | |