| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:45 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 | ||||
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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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 2019/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.1.0 (landing page) Mustafa Erhan Özer
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: SVMDO |
| Version: 1.1.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings SVMDO_1.1.0.tar.gz |
| StartedAt: 2023-05-30 20:58:23 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 21:03:48 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 325.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SVMDO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings SVMDO_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SVMDO.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘1.1.0’
* 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 R 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘SVMDO_guide.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
SVMDO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘SVMDO’ ... ** 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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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: 4088,52,64116,2739,60,89874
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79158,57678,2539,475,109,79731
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6915,3283,3930,9575,3592,3558
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 493753,3712,1075,3832,339,7225
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6522,1208,4286,407006,2512,5580
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7352,35,100529063,2875,1543,79585
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 729230,80207,9415,5629,4171,11266
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7077,79087,4795,2932,3174,5087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57104,84274,9588,205327,10059,2581
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4594,3157,9619,5473,4233,6786
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 158,79661,868,6532,1051,407024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3033,7364,5443,5662,5193,153642
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3375,6236,1113,33,57620,138050
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1555,10059,5350,3426,23274,8309
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6515,2555,5095,4548,7372,9607
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80201,23082,497231,406903,1843,6522
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54968,5069,842,54915,1444,6357
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1393,5798,2847,7054,182,51604
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5728,407006,166785,6526,55024,5970
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51660,55600,54968,1594,10272,270
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1364,5175,55788,4973,10128,7941
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8462,3159,10229,538,5270,23236
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79158,347,1033,823,2166,9826
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6514,2678,7839,2806,133396,29968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10666,406906,7528,6019,5211,26291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 255738,2696,6720,80339,4722,8609
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5745,471,57580,9969,4855,8722
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 776,84706,6441,8772,55331,7200
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3569,84947,445,475,1893,4091
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5538,1435,1644,5579,23516,5580
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3292,6389,55829,4729,2328,25974
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53346,25915,51004,56652,1573,3482
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 181,3460,5228,6280,84061,1489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 841,1382,3690,5741,1244,10272
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25974,79689,2184,5053,3700,6582
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11095,958,5315,1393,6448,4886
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5662,38,7275,3558,387787,5925
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 391051,5228,1033,3358,7287,59340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4544,11231,7292,1672,7056,3995
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7841,4718,50615,84277,3482,2739
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4671,9382,9826,4214,653,2660
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8309,2310,25839,200205,4828,3920
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6720,5290,6715,842,9414,2222
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55937,1634,1621,134,11035,3708
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10842,7372,793,3351,9868,1869
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1234,1442,4150,56052,2645,407008
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91452,5306,5593,3667,253827,340706
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 943,1636,9507,1191,572,6690
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407021,6718,6927,4671,51316,3141
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9382,7036,585,2222,19,25805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2875,9672,2695,652,3074,266
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5274,55863,6722,1589,7021,9122
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23706,7200,55034,1022,1513,6556
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56999,9437,29968,4976,25805,4508
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8856,5092,153642,8604,2710,23175
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 387082,26191,4891,3623,56848,3956
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9437,9572,30009,6510,5331,5599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7297,7345,8799,104909134,3417,1022
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4276,23556,4914,65993,9882,84706
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4580,2495,344905,10886,55315,6526
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54600,9607,627,3816,1401,3708
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 196385,80201,2517,4018,9663,55858
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1807,337,56718,26291,10320,5594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4214,10295,3948,4654,64432,6288
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7919,3845,1586,7249,2547,29126
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8665,644096,4060,79949,85476,361
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4828,5194,3551,2495,8784,29947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 197322,3099,728642,4891,138050,57061
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6382,7384,7412,2593,3082,6622
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5802,9518,7128,3105,85476,6469
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84062,9526,7430,4125,85569,23753
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 488,1369,90070,2064,63892,51478
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3569,1815,51316,1789,1909,7046
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2582,5345,6774,8842,114899,6296
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2875,8854,10682,406922,79949,2203
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6382,54704,5122,7480,6448,7412
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5617,51079,1352,4521,7364,5687
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 114899,387082,102,55572,6462,2740
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6898,9560,409,6446,2946,1080
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
26.120 1.035 27.126
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.590 | 0.008 | 0.601 | |