Mustafa Erhan Ozer
| Snapshot Date: 2025-10-28 13:45 -0400 (Tue, 28 Oct 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 2025-10-29 12:05 -0400 (Wed, 29 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 2163/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.9.0 (landing page) Mustafa Erhan Ozer
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 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: 1.9.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SVMDO_1.9.0.tar.gz |
| StartedAt: 2025-10-29 04:35:41 -0400 (Wed, 29 Oct 2025) |
| EndedAt: 2025-10-29 04:43:17 -0400 (Wed, 29 Oct 2025) |
| EllapsedTime: 455.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SVMDO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SVMDO_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SVMDO.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* 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 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-3.22-bioc/R/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 Patched (2025-08-23 r88802) -- "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: 4729,4299,4853,51181,1801,43
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133,5617,2590,875,574447,11255
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3636,3630,51083,84889,53345,2834
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51478,4669,387,3440,166785,5329
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3284,1019,8932,1029,5328,5476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56729,374291,55750,2689,10,89874
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7099,27247,8195,10379,7248,7381
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 538,2720,3899,196385,3636,79949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4594,8639,1022,644974,6392,1489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7915,3425,5467,131669,642489,5295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79949,361,388585,30061,5798,3643
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4700,3157,34,3710,1401,116519
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100130015,593,9370,10116,51119,7422
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 389692,5743,4669,5270,50943,2146
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2946,383,8714,1595,51083,54901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8813,9365,6548,4729,11255,407008
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1802,23654,54210,941,3417,6927
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1843,3673,5919,10730,3101,51099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64601,10857,55818,8462,53346,5621
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1802,3949,9968,133396,7167,4118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6198,6392,133,80222,4594,6720
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3717,339,7515,2653,5825,5161
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10466,9927,51555,790955,5264,5241
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26175,6505,7352,7289,6932,364
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1889,840,169792,5507,6898,407045
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 293,1514,5789,122961,999,4668
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4137,3122,3034,5581,3978,463
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 221458,5160,1351,2244,30061,3304
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4695,5584,6890,55970,9095,10352
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2271,10841,28951,23654,149775,824
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5476,2487,6609,406937,10753,7409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9575,8604,7376,2157,5515,6198
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2588,10616,768239,2538,27141,9868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9409,567,4712,275,3948,64087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 112817,2335,2159,2495,116228,4723
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2475,10686,3054,801,685,9759
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2847,7350,1893,91647,125170,55065
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1497,3551,23590,89866,6928,4543
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5507,7225,51649,48,200539,43
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 169026,81689,1509,8660,29880,2875
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1442,1270,6339,54931,5723,4552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5498,23038,4779,8504,51441,537
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 590,84902,7528,10423,1022,5837
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 30061,11096,10457,50674,162417,825
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2113,2247,85569,27232,7275,5970
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5167,3553,7054,1355,2166,3627
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1509,64801,3081,196385,201595,5092
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3558,1636,23556,5595,1352,5257
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10165,4502,80222,867,7347,145264
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5551,5373,5860,5740,3291,2729
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1589,154,3980,2731,8202,131118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1201,2710,55486,54148,5255,6347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9971,128486,1346,5345,6888,3703
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 653509,3978,1339,10466,1859,23054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 694,1185,43,3630,1514,6908
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1906,1557,10891,29880,130120,1244
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91869,54658,4282,1369,51117,6794
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 124454,293,79661,55283,3920,5467
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4976,1807,1672,6748,388743,79133
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1363,26003,5230,216,5194,4967
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3930,5207,7276,1339,54931,57620
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10250,4299,6897,84239,1678,2495
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3033,55818,1393,3988,4878,2055
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9374,3663,929,112817,5971,656
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5328,54575,8675,2118,859,8722
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5617,8517,5291,1559,10643,8660
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6888,2787,1595,1355,56652,55532
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3480,3507,5409,9021,54205,5052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6648,29947,361,2632,10226,181
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6576,29880,8604,23556,491,84061
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4879,6445,5727,2592,8802,3240
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56999,5321,55503,4338,26088,655
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3630,5970,959,7347,10423,10911
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 178,29928,4697,2904,9526,23417
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5241,2712,3032,6548,5730,160428
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1537,5315,10753,2804,32,140803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3077,79133,6584,125988,51021,2581
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6338,549,64900,3119,2643,1678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5781,27249,5428,2170,3557,51082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23417,4790,2875,4306,51103,283120
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 211,5409,10195,2767,2693,406906
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64116,4118,55270,170302,407007,642489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54106,119559,9779,54658,23129,94235
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8202,285848,1376,51181,6890,1029
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5071,2055,6569,7385,6248,7274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4726,5175,158,6342,10891,10644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 52,5214,51024,388585,57128,340024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5080,5590,51608,51478,9414,1489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10020,4684,4988,4247,407040,148738
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29843,2890,4125,2034,361,23409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7389,64801,4803,55532,3117,54549
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 178,6262,5306,51128,1282,388743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1281,23417,1595,53632,231,2572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80201,4338,51116,27249,4899,10724
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4879,7424,283459,540,5967,51176
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1277,80339,54809,85569,3458,54931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6748,338821,1607,60,3779,5473
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79644,10842,1028,7498,821,7056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29926,27125,4069,6721,875,28951
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23409,217,23038,1672,2587,867
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26762,25839,340024,6183,55699,2169
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5370,9663,137994,57192,2786,2629
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1029,3030,60684,5723,5824,10243
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5562,3291,1149,9630,79944,28234
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3606,644096,685,2678,10524,118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27125,22820,4049,5618,4864,7026
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8932,25821,3283,54578,91949,6464
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7421,156,9131,3159,5743,51300
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57085,6616,3627,407040,8462,6535
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3995,1075,7225,51103,79949,4233
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2908,84062,2646,4688,84572,2746
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3034,1890,788,629,84705,285362
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3728,5971,1028,7389,5588,5584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 847,51422,100303755,728294,81689,5213
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1491,23410,1544,999,3339,50674
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
215.361 2.539 218.052
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.656 | 0.094 | 3.646 | |