Mustafa Erhan Ozer
| Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/SVMDO |
| git_branch: RELEASE_3_19 |
| git_last_commit: 8015edf |
| git_last_commit_date: 2024-04-30 11:49:19 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| 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 2112/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.4.0 (landing page) Mustafa Erhan Ozer
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | 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: 1.4.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SVMDO_1.4.0.tar.gz |
| StartedAt: 2024-06-13 04:12:26 -0400 (Thu, 13 Jun 2024) |
| EndedAt: 2024-06-13 04:17:11 -0400 (Thu, 13 Jun 2024) |
| EllapsedTime: 284.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SVMDO.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SVMDO_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SVMDO.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 ‘1.4.0’
* 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-3.19-bioc/R/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘SVMDO’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading `shiny::dataTableOutput()` is deprecated as of shiny 1.8.1. Please use `DT::DTOutput()` instead. Since you have a suitable version of DT (>= v0.32.1), shiny::dataTableOutput() will automatically use DT::DTOutput() under-the-hood. If this happens to break your app, set `options(shiny.legacy.datatable = TRUE)` to get the legacy datatable implementation (or `FALSE` to squelch this message). See <https://rstudio.github.io/DT/shiny.html> for more information. ** 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 4.4.0 (2024-04-24) -- "Puppy Cup"
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: 2864,4724,2170,8639,5598,100
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 316,5901,1339,64772,4323,84833
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10522,10682,2904,130589,2180,256764
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25915,5213,1050,55967,2745,23101
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7253,9526,8455,10874,6427,3768
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1789,7139,7525,84868,929,26191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6932,6714,3600,3980,325,9868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2335,5160,617,3105,2746,285126
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9588,100506742,1361,2169,3559,3586
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6526,9630,5589,59340,8473,10166
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3700,79144,5096,4654,2170,665
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3098,2834,2852,133522,80270,5445
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55768,57048,84706,10524,9377,23586
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3174,6814,406938,7132,4009,435
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2713,4524,5211,4656,2729,6342
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53345,2729,4656,4337,5744,4594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6311,2804,51181,2006,79071,3688
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 642489,197,3174,253827,2260,3406
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 361,643394,6868,2641,5367,5515
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4318,54796,10643,124976,90070,84317
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7019,8764,8877,2135,6579,728294
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64900,104,1803,91942,3596,2115
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2908,6530,1807,538,1950,387787
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7026,6678,4715,7133,1200,3930
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5499,7124,1910,3759,8691,2820
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4012,26762,361,1052,51422,406
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3606,83440,241,9759,50674,105372280
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2110,83884,26873,7291,4704,4803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8842,2717,8074,116228,4889,54600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 35,55937,7100,4846,3507,1514
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5445,27344,9518,3572,90624,4338
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10911,1608,55343,284184,7284,84274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2593,563,4128,101180976,23389,55340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3779,210,409,10020,351,84902
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2683,920,23178,4277,54600,8773
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1436,50639,187,9971,10279,8877
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2683,2643,3486,599,1893,56923
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3054,6915,6272,3600,1889,23389
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1595,475,4210,3373,114548,29928
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60684,540,3170,55818,1595,1604
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9968,3717,4938,1435,811,5168
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100156321,1352,4144,5443,50507,2688
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10549,5660,5188,255308,4704,10159
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 410,6389,2597,3292,9409,84340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10221,293,6464,364,7057,2697
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 107075310,773,79144,4860,100133941,387787
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2184,55278,1889,3105,6716,2876
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 151,90480,3489,23753,642489,6794
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1149,348,100128525,9437,4277,5023
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 120227,3600,4716,51601,2052,875
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 152926,29843,1075,1489,5139,4162
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5925,4886,8431,6941,7525,479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6556,129787,5009,3811,5741,8841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6351,537,30061,5190,57104,102
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57678,1468,2889,3690,686,643181
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2805,4729,55818,53345,2520,5054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10316,64805,7040,10272,6515,200186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5588,6097,518,56922,6941,7408
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 940,2180,4489,54539,3624,1950
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7021,119559,776,4688,80207,10841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1649,7839,8195,239,57678,125988
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 28976,364,4976,175,8856,728441
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10457,1030,60,1629,1029,5315
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2006,5191,3383,80724,8813,5372
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4702,5594,366,3815,3816,8835
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56458,10549,3938,4779,2641,4247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7010,886,54210,3598,8743,4988
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 811,1593,8942,10279,83440,5588
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23436,6374,3484,55486,125988,9575
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3995,1329,2235,6019,359,22877
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2932,1232,4282,4891,51141,1270
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4041,5950,51478,5447,123,3674
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2548,5265,6337,3845,3145,6649
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7839,796,2792,27247,84300,94235
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11232,10845,4826,4149,5370,2113
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2628,7292,6258,406906,656,2642
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 650,9560,3953,7369,51,1186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5106,3636,7352,5184,779,1056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116150,5467,53335,411,6772,4773
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
52.267 1.824 54.069
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.616 | 0.044 | 0.663 | |