Mustafa Erhan Ozer
| Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 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 2025-04-22 13:17 -0400 (Tue, 22 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | 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 | | ||||||||
| kunpeng2 | 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: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2025-04-21 23:57:51 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-22 00:04:07 -0400 (Tue, 22 Apr 2025) |
| EllapsedTime: 376.3 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SVMDO.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* 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 ‘1.8.0’
* 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 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 0.879 0.048 7.447
* 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 ‘1.8.0’ ** 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 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
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: 5190,1869,5373,54675,3172,3117
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5826,407021,5745,54576,1589,2835
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57085,112817,5770,729238,7528,5291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5713,283459,3062,2788,6564,85479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 199,9445,9572,5176,3113,10000
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2591,60,28234,5473,4705,7274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 325,3795,55768,4035,4256,5571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51604,3479,6932,7385,1675,6925
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2260,3645,5428,30061,406937,5799
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3875,9382,6319,5364,3062,64788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2760,7132,65080,2152,249,5241
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1893,3101,6938,4313,7494,6794
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84706,27344,10999,2786,1312,23236
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3284,7466,6906,2335,11213,5743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1636,51181,885,7325,50506,84274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10020,10724,6351,1813,5660,54805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2584,22797,54575,22845,5019,84706
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3485,6868,3978,63874,60386,2395
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 196385,10644,10991,2713,388585,345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27247,5617,9498,23410,10116,6513
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5950,6714,60684,29947,10644,2752
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3728,7372,51608,25828,51611,9607
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 200539,255231,26235,9374,5644,6476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8642,1075,7376,2949,2335,476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10466,100506742,51206,3119,326625,857
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5444,51052,3553,3554,2998,43
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3712,2244,2936,941,9021,56729
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 147007,3663,640,29843,283120,388753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7124,55818,51085,26003,125170,265
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406906,9630,3948,23389,2944,7840
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4143,7252,6550,6579,11035,5798
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5329,5792,2110,1581,7248,3709
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9526,2835,23516,10,10221,104
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 28951,231,6519,1072,5373,170302
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5191,161247,5601,401,5962,8803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 617,2948,2896,2785,959,80201
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8877,211,5972,3703,596,3643
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2937,4247,6263,3651,407040,100131801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6236,2791,4988,27010,2875,6198
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 384,1544,160287,131118,53335,84947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6342,5599,23516,2030,2115,6811
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 120227,5836,255231,9131,3158,6382
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7916,6383,6198,5629,2184,1277
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6183,1348,3483,4694,10577,100131801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 217,6236,120227,23304,56919,51738
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6261,51085,56606,4247,55486,1347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2548,7422,23395,87178,5350,5588
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7098,9559,2628,1738,2581,406934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55572,1361,2689,23543,3717,8722
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406947,7319,6609,89866,9429,1409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 476,51478,5745,104,3383,5792
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 563,4700,7879,6374,57570,56729
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79934,8714,3954,4779,5770,2235
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4915,38,2524,54658,51604,411
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6341,10250,6389,4899,5799,1645
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6401,2729,23409,7026,5967,2309
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1843,23590,694,9380,1806,10269
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6513,8517,3308,6788,51144,10841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27141,952,7056,284184,265,84572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51548,6716,4887,166785,10935,89874
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 114814,540,57215,6401,3931,4358
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4887,111,116228,4899,285126,50507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11093,51548,7409,7412,4843,181
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60,596,83693,2588,51128,1582
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 212,9370,23654,92483,2908,29929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9104,6513,54805,4049,407040,7376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9630,3416,728,1606,358,100529063
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5364,1571,7386,3562,3174,7284
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10999,1027,653509,7025,54802,6770
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3291,4337,2587,23417,5190,5329
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3293,1442,3554,3480,5727,29926
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54539,2158,4968,4726,411,3685
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4899,64432,6514,406937,50484,7515
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 642489,5744,6462,496,6514,285362
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1509,5473,7422,9131,3356,6898
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80347,26119,5444,7941,152078,2792
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3030,10686,51422,149461,55858,3356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7421,241,2950,56606,3978,8813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5080,5728,283120,9388,51478,3062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6342,5306,7428,56302,219,51293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100128525,181,203859,7248,130120,84317
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5594,3479,51081,655,5406,79572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6199,153642,4878,11222,384,151
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3945,79068,23062,6439,10000,498
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8678,5078,10616,31,48,22797
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3250,7026,6392,55034,5825,7284
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5321,3553,8803,84902,1636,8309
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406938,54901,81689,339,1200,3479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1281,55670,2243,9630,2639,5967
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23530,38,1268,4803,55034,4790
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 201595,4149,1203,10580,4724,6716
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9104,64432,325,2739,9971,100131801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9054,3159,10466,5193,5176,54658
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2517,2712,1608,2990,51024,7376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1337,4722,6262,160287,3417,5193
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9409,1806,3091,6505,115286,83548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 405,158,23062,9969,940,3920
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3157,4758,5727,6351,9968,1812
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2235,54331,1490,23409,655,509
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 153,3638,729238,7351,3030,4968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 867,221458,1352,10999,134,490
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55788,407004,2746,440138,81034,91452
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2786,1956,1371,4299,11231,87178
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1369,3710,2305,84334,406938,1893
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6898,2834,2752,54968,2952,886
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79585,2946,653,3483,5498,929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7388,2305,406937,55967,4547,10008
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54552,10599,858,653509,5313,210
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29929,3703,1244,90865,8560,4285
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2571,7275,51081,8694,64801,5445
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6696,3630,9415,8818,51241,1509
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10195,2919,2786,10135,5925,2115
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3486,793,7431,120227,376497,345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1890,316,7388,2740,4286,79949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 154,574447,2647,2266,7252,6898
--> return NULL...
2025-04-22 00:03:58.090 R[92886:730397630] XType: com.apple.fonts is not accessible.
2025-04-22 00:03:58.090 R[92886:730397630] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
108.211 1.583 110.630
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.879 | 0.048 | 7.447 | |