| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:27 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 | ||||
|
To the developers/maintainers of the DominoEffect package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 552/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DominoEffect 1.19.0 (landing page) Marija Buljan
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: DominoEffect |
| Version: 1.19.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DominoEffect.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings DominoEffect_1.19.0.tar.gz |
| StartedAt: 2022-12-28 23:23:10 -0500 (Wed, 28 Dec 2022) |
| EndedAt: 2022-12-28 23:27:59 -0500 (Wed, 28 Dec 2022) |
| EllapsedTime: 288.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DominoEffect.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DominoEffect.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings DominoEffect_1.19.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/DominoEffect.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DominoEffect/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DominoEffect' version '1.19.0'
* 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 whether package 'DominoEffect' 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 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 ... NOTE
import_txdb: no visible binding for global variable 'TXTYPE'
Undefined global functions or variables:
TXTYPE
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DominoEffect 1.86 0.11 14.75
GPo_of_hotspots 0.86 0.06 12.99
map_to_func_elem 0.69 0.05 12.29
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'test-all.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/DominoEffect.Rcheck/00check.log'
for details.
DominoEffect.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL DominoEffect ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'DominoEffect' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (DominoEffect)
DominoEffect.Rcheck/tests/test-all.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
> library(testthat)
> test_check("DominoEffect")
Loading required package: DominoEffect
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain; format=fasta' length 483 bytes
==================================================
downloaded 483 bytes
trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain; format=fasta' length 483 bytes
==================================================
downloaded 483 bytes
trying URL 'http://www.uniprot.org/uniprot/O75533.fasta'
Content type 'text/plain; format=fasta' length 1421 bytes
==================================================
downloaded 1421 bytes
trying URL 'http://www.uniprot.org/uniprot/Q9NR22.fasta'
Content type 'text/plain; format=fasta' length 505 bytes
==================================================
downloaded 505 bytes
trying URL 'http://www.uniprot.org/uniprot/O96017.fasta'
Content type 'text/plain; format=fasta' length 655 bytes
==================================================
downloaded 655 bytes
================================================================================
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain; format=fasta' length 483 bytes
==================================================
downloaded 483 bytes
trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain; format=fasta' length 483 bytes
==================================================
downloaded 483 bytes
trying URL 'http://www.uniprot.org/uniprot/Q9NR22.fasta'
Content type 'text/plain; format=fasta' length 505 bytes
==================================================
downloaded 505 bytes
================================================================================
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain; format=fasta' length 483 bytes
==================================================
downloaded 483 bytes
trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain; format=fasta' length 483 bytes
==================================================
downloaded 483 bytes
================================================================================
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain; format=fasta' length 483 bytes
==================================================
downloaded 483 bytes
trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain; format=fasta' length 483 bytes
==================================================
downloaded 483 bytes
trying URL 'http://www.uniprot.org/uniprot/O75533.fasta'
Content type 'text/plain; format=fasta' length 1421 bytes
==================================================
downloaded 1421 bytes
trying URL 'http://www.uniprot.org/uniprot/Q9NR22.fasta'
Content type 'text/plain; format=fasta' length 505 bytes
==================================================
downloaded 505 bytes
trying URL 'http://www.uniprot.org/uniprot/O96017.fasta'
Content type 'text/plain; format=fasta' length 655 bytes
==================================================
downloaded 655 bytes
================================================================================
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 15 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 15 ]
>
> proc.time()
user system elapsed
13.29 1.00 52.04
DominoEffect.Rcheck/DominoEffect-Ex.timings
| name | user | system | elapsed | |
| DominoEffect | 1.86 | 0.11 | 14.75 | |
| GPo_of_hotspots | 0.86 | 0.06 | 12.99 | |
| align_to_unip | 0.12 | 0.03 | 0.16 | |
| calculate_boundary | 0 | 0 | 0 | |
| identify_hotspots | 0.17 | 0.00 | 0.17 | |
| import_txdb | 0 | 0 | 0 | |
| map_to_func_elem | 0.69 | 0.05 | 12.29 | |