Marija Buljan
| Snapshot Date: 2025-01-10 13:40 -0500 (Fri, 10 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/DominoEffect |
| git_branch: devel |
| git_last_commit: deeeeac |
| git_last_commit_date: 2024-10-29 10:25:49 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-11 11:46 -0500 (Sat, 11 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4760 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4479 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4443 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4391 |
| 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 592/2277 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DominoEffect 1.27.0 (landing page) Marija Buljan
| 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 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the DominoEffect package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DominoEffect.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: DominoEffect |
| Version: 1.27.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:DominoEffect.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DominoEffect_1.27.0.tar.gz |
| StartedAt: 2025-01-11 06:07:32 -0000 (Sat, 11 Jan 2025) |
| EndedAt: 2025-01-11 06:17:05 -0000 (Sat, 11 Jan 2025) |
| EllapsedTime: 572.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: DominoEffect.Rcheck |
| Warnings: 5 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:DominoEffect.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DominoEffect_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/DominoEffect.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DominoEffect/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DominoEffect’ version ‘1.27.0’
* 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 ‘DominoEffect’ can be installed ... WARNING
Found the following significant warnings:
Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/DominoEffect.Rcheck/00install.out’ for details.
* 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 ... NOTE
Warning: program compiled against libxml 212 using older 211
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
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 ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 3.664 0.346 53.293
map_to_func_elem 2.014 0.433 27.434
GPo_of_hotspots 2.121 0.260 32.497
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.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: 5 WARNINGs, 5 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/DominoEffect.Rcheck/00check.log’
for details.
DominoEffect.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL DominoEffect ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘DominoEffect’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (DominoEffect)
DominoEffect.Rcheck/tests/test-all.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
> library(testthat)
> test_check("DominoEffect")
Loading required package: DominoEffect
Warning: program compiled against libxml 212 using older 211
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 5 | SKIP 0 | PASS 15 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 15 ]
>
> proc.time()
user system elapsed
26.801 2.682 107.344
DominoEffect.Rcheck/DominoEffect-Ex.timings
| name | user | system | elapsed | |
| DominoEffect | 3.664 | 0.346 | 53.293 | |
| GPo_of_hotspots | 2.121 | 0.260 | 32.497 | |
| align_to_unip | 0.233 | 0.040 | 0.274 | |
| calculate_boundary | 0.000 | 0.000 | 0.001 | |
| identify_hotspots | 0.213 | 0.028 | 0.241 | |
| import_txdb | 0 | 0 | 0 | |
| map_to_func_elem | 2.014 | 0.433 | 27.434 | |