Mustafa Erhan Ozer
| Snapshot Date: 2025-06-26 13:25 -0400 (Thu, 26 Jun 2025) |
| git_url: https://git.bioconductor.org/packages/SVMDO |
| git_branch: devel |
| git_last_commit: 7851a60 |
| git_last_commit_date: 2025-04-15 13:15:07 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-06-27 12:09 -0400 (Fri, 27 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4772 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4515 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4556 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4500 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4499 |
| 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 2112/2310 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.9.0 (landing page) Mustafa Erhan Ozer
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.9.0 |
| 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_1.9.0.tar.gz |
| StartedAt: 2025-06-26 23:51:28 -0400 (Thu, 26 Jun 2025) |
| EndedAt: 2025-06-26 23:56:59 -0400 (Thu, 26 Jun 2025) |
| EllapsedTime: 330.4 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_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SVMDO.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘1.9.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runGUI 0.698 0.04 7.198
* 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/4.5-x86_64/Resources/library’ * installing *source* package ‘SVMDO’ ... ** this is package ‘SVMDO’ version ‘1.9.0’ ** 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-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: 5367,119559,11213,664,3065,4125
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54896,2581,5590,706,729230,1890
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60528,57215,9498,574447,2516,152078
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50507,1893,3074,406938,6536,35
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2539,51144,84693,6550,81034,5599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50506,3899,4000,8642,4722,52
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2184,160428,7391,284958,407004,858
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2760,3479,796,84693,8879,388753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84701,2310,80270,599,4688,518
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 477,6183,123263,54901,1234,10135
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406938,3489,1345,54552,6439,2328
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 285362,54901,155,3700,407024,6236
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 147007,55005,1022,4915,7292,9607
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 114548,4089,3417,653509,200205,656
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3383,6198,5270,3099,3576,2475
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406922,54575,7319,1509,1329,3291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 708,9054,8050,2628,3712,81704
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51548,91647,3460,9374,23411,5501
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1605,7424,6821,64131,3309,79087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9021,868,5826,79934,5971,10295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5967,941,1352,10616,292,768239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 208,6714,868,64900,2064,7172
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7172,2559,203,128486,3373,4015
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54549,84062,104,1329,6811,427
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10020,3284,2717,7480,3645,51083
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6678,6569,84706,338821,344,3958
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81689,7391,627,1889,9429,339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4232,51128,7078,1029,2805,55532
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5369,3643,29926,5571,4968,7248
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3995,6786,6515,1968,25915,5069
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 160428,7355,51478,10991,211,2688
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2798,5295,1201,79949,1203,3309
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84902,2731,1737,3145,388962,178
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1843,1281,26235,3034,3290,79001
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3920,2243,54578,388585,4137,5126
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1356,6908,6236,1282,5370,54901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51204,93587,6927,1584,3684,2280
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3159,2688,5562,50674,4729,941
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 644096,63892,5444,2820,2200,29960
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54658,2784,3663,4012,51024,29843
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1208,50814,83439,10352,2280,183
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3684,57128,79087,2919,790955,1345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3304,2786,283459,33,51094,8945
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2280,80207,51478,55768,5315,4000
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 340024,407007,6927,5970,4864,54798
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54982,875,3931,338821,51478,1028
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6261,6448,1675,48,10935,6356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1812,137682,5830,5571,4040,268
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10352,8772,6402,57505,10157,83854
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116228,7372,8772,3685,3145,339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9945,114548,9672,81704,406938,3073
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2720,4723,885,191,1374,5601
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5499,29880,6794,1737,6938,10845
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10221,1807,2752,3458,1514,4318
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7019,6521,3703,7372,6564,490
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 114814,344905,407024,55768,83548,644974
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 92609,6403,2099,63892,27141,6341
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10116,79001,2113,1789,5193,3304
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2158,10857,445,6439,596,255231
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10316,4012,859,1738,29960,6198
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407010,6718,1641,6324,3958,158
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27247,2632,4899,162417,1361,4144
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1588,9451,2101,3559,54476,26060
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 338,1585,1175,3991,10116,2896
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 138050,11131,169792,79572,55670,54600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9968,83985,7407,57085,1471,51649
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11093,3293,2643,4988,55818,3638
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3480,10020,5919,51144,1355,10166
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5092,627,90624,92935,2590,694
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1327,34,7381,196385,1361,29968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 170302,345,148738,107075310,4012,4843
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123,316,5579,4548,51117,539
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26088,10644,718,54549,53905,1208
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5644,81033,9370,406982,2587,55278
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3098,8648,91949,54576,6402,1678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1175,83884,2592,2793,7284,79068
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3717,3570,23062,22845,886,2904
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 152078,9382,8504,4780,80339,811
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 92935,7431,2632,2303,2697,6715
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100,28957,1641,5744,26291,4544
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57505,8743,8772,1607,2109,10965
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1717,55270,427,316,3670,255308
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1347,4118,4790,384,2932,3383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11255,6531,7840,153,582,85446
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53905,83854,26762,5723,4702,7409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2099,1801,653509,5257,9560,5069
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6341,6262,27141,54809,361,5080
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5241,2944,51052,5265,51117,1201
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10,8309,1813,335,60684,1277
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5617,4285,11093,4828,6772,7099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5571,23274,55186,1738,2695,5713
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9698,1149,38,5798,4899,8722
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2159,410,2804,6772,10599,387787
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6535,2539,84902,2582,3988,5743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 221458,5501,8803,4886,28976,116519
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2697,2628,1559,3930,1371,55753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1080,54539,10935,7076,3791,5167
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10644,51099,4695,5950,1734,7132
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 58528,6476,10938,5447,4982,131118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3485,1401,5329,7098,51167,23462
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1606,1201,6391,2778,2799,23274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5167,2944,350,123263,203859,54675
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 844,779,5901,1801,5428,1678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55526,6794,1435,1497,100128525,1675
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5467,10295,1337,55186,1185,1636
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10000,432369,83884,4306,26227,376497
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57128,64131,55788,6505,10000,27329
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4543,4358,5702,6329,2697,2903
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 364,54902,2538,3995,55937,10116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2890,2159,84701,9095,10466,2053
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1497,132,8195,2487,570,178
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81570,11096,3295,170302,169792,3576
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 249,3291,6770,440503,8743,3562
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57017,9779,43,316,2056,1392
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9560,84342,388962,477,1490,1582
--> return NULL...
2025-06-26 23:56:49.834 R[93033:60923774] XType: com.apple.fonts is not accessible.
2025-06-26 23:56:49.835 R[93033:60923774] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
62.587 1.290 64.376
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.698 | 0.040 | 7.198 | |