| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:26 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 BiocGenerics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocGenerics.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 172/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocGenerics 0.47.0 (landing page) Hervé Pagès
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: BiocGenerics |
| Version: 0.47.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BiocGenerics.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BiocGenerics_0.47.0.tar.gz |
| StartedAt: 2023-05-09 09:46:33 -0000 (Tue, 09 May 2023) |
| EndedAt: 2023-05-09 09:47:26 -0000 (Tue, 09 May 2023) |
| EllapsedTime: 53.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BiocGenerics.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BiocGenerics.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BiocGenerics_0.47.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BiocGenerics.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* 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 ‘BiocGenerics/DESCRIPTION’ ... OK
* this is package ‘BiocGenerics’ version ‘0.47.0’
* 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 ‘BiocGenerics’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’ ‘utils’ ‘graphics’ ‘stats’
A package should be listed in only one of these fields.
* 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 ... NOTE
'library' or 'require' call to ‘RUnit’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 ... WARNING
Missing link or links in documentation object 'as.data.frame.Rd':
‘[IRanges]{as.data.frame,IntegerRanges-method}’
Missing link or links in documentation object 'order.Rd':
‘[IRanges]{order,IntegerRanges-method}’
Missing link or links in documentation object 'type.Rd':
‘[DelayedArray]{type,ANY-method}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'rep':
‘rep.int’
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 examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotMA 9.308 0.459 9.771
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘run_unitTests.R’
OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/BiocGenerics.Rcheck/00check.log’
for details.
BiocGenerics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BiocGenerics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘BiocGenerics’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘aperm’ in package ‘BiocGenerics’ Creating a new generic function for ‘append’ in package ‘BiocGenerics’ Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’ Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’ Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’ Creating a new generic function for ‘do.call’ in package ‘BiocGenerics’ Creating a new generic function for ‘duplicated’ in package ‘BiocGenerics’ Creating a new generic function for ‘anyDuplicated’ in package ‘BiocGenerics’ Creating a new generic function for ‘eval’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmax’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmin’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’ Creating a new generic function for ‘Reduce’ in package ‘BiocGenerics’ Creating a new generic function for ‘Filter’ in package ‘BiocGenerics’ Creating a new generic function for ‘Find’ in package ‘BiocGenerics’ Creating a new generic function for ‘Map’ in package ‘BiocGenerics’ Creating a new generic function for ‘Position’ in package ‘BiocGenerics’ Creating a new generic function for ‘get’ in package ‘BiocGenerics’ Creating a new generic function for ‘mget’ in package ‘BiocGenerics’ Creating a new generic function for ‘grep’ in package ‘BiocGenerics’ Creating a new generic function for ‘grepl’ in package ‘BiocGenerics’ Creating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’ Creating a new generic function for ‘lapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘sapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘mapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘match’ in package ‘BiocGenerics’ Creating a new generic function for ‘order’ in package ‘BiocGenerics’ Creating a new generic function for ‘paste’ in package ‘BiocGenerics’ Creating a new generic function for ‘rank’ in package ‘BiocGenerics’ Creating a new generic function for ‘rownames’ in package ‘BiocGenerics’ Creating a new generic function for ‘colnames’ in package ‘BiocGenerics’ Creating a new generic function for ‘union’ in package ‘BiocGenerics’ Creating a new generic function for ‘intersect’ in package ‘BiocGenerics’ Creating a new generic function for ‘setdiff’ in package ‘BiocGenerics’ Creating a new generic function for ‘sort’ in package ‘BiocGenerics’ Creating a new generic function for ‘table’ in package ‘BiocGenerics’ Creating a new generic function for ‘tapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘unique’ in package ‘BiocGenerics’ Creating a new generic function for ‘unsplit’ in package ‘BiocGenerics’ Creating a new generic function for ‘var’ in package ‘BiocGenerics’ Creating a new generic function for ‘sd’ in package ‘BiocGenerics’ Creating a new generic function for ‘which.min’ in package ‘BiocGenerics’ Creating a new generic function for ‘which.max’ in package ‘BiocGenerics’ Creating a new generic function for ‘IQR’ in package ‘BiocGenerics’ Creating a new generic function for ‘mad’ in package ‘BiocGenerics’ Creating a new generic function for ‘xtabs’ in package ‘BiocGenerics’ Creating a new generic function for ‘basename’ in package ‘BiocGenerics’ Creating a new generic function for ‘dirname’ in package ‘BiocGenerics’ ** help *** installing help indices ** building package indices ** 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 (BiocGenerics)
BiocGenerics.Rcheck/tests/run_unitTests.Rout
R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
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.
> require("BiocGenerics") || stop("unable to load BiocGenerics package")
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
[1] TRUE
> BiocGenerics:::.test()
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
RUNIT TEST PROTOCOL -- Tue May 9 09:47:18 2023
***********************************************
Number of test functions: 25
Number of errors: 0
Number of failures: 0
1 Test Suite :
BiocGenerics RUnit Tests - 25 test functions, 0 errors, 0 failures
Number of test functions: 25
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
2.635 0.191 2.807
BiocGenerics.Rcheck/BiocGenerics-Ex.timings
| name | user | system | elapsed | |
| BiocGenerics-package | 0.001 | 0.000 | 0.001 | |
| Extremes | 0.005 | 0.004 | 0.009 | |
| IQR | 0.002 | 0.000 | 0.002 | |
| Ontology | 4.299 | 0.196 | 4.496 | |
| annotation | 0.013 | 0.000 | 0.014 | |
| aperm | 0.002 | 0.000 | 0.003 | |
| append | 0.002 | 0.000 | 0.002 | |
| as.data.frame | 0.000 | 0.003 | 0.003 | |
| as.list | 0.026 | 0.001 | 0.027 | |
| as.vector | 0.003 | 0.000 | 0.003 | |
| boxplot | 0.132 | 0.000 | 0.132 | |
| cbind | 0.023 | 0.004 | 0.028 | |
| combine | 0.059 | 0.000 | 0.059 | |
| dbconn | 0.065 | 0.000 | 0.065 | |
| density | 0.000 | 0.001 | 0.002 | |
| dims | 0.033 | 0.004 | 0.037 | |
| do.call | 0.002 | 0.000 | 0.002 | |
| duplicated | 0.005 | 0.000 | 0.005 | |
| eval | 0.003 | 0.000 | 0.003 | |
| evalq | 0.000 | 0.000 | 0.001 | |
| fileName | 3.536 | 0.104 | 3.640 | |
| format | 0.002 | 0.000 | 0.002 | |
| funprog | 0.004 | 0.004 | 0.008 | |
| get | 0.001 | 0.003 | 0.004 | |
| grep | 0.002 | 0.000 | 0.002 | |
| image | 0.03 | 0.00 | 0.03 | |
| is.unsorted | 0.002 | 0.000 | 0.002 | |
| lapply | 0.001 | 0.004 | 0.005 | |
| mad | 0.002 | 0.000 | 0.002 | |
| mapply | 0.000 | 0.001 | 0.002 | |
| match | 0.005 | 0.002 | 0.006 | |
| mean | 0.002 | 0.000 | 0.002 | |
| normalize | 0.027 | 0.004 | 0.031 | |
| nrow | 0.009 | 0.000 | 0.009 | |
| order | 0.003 | 0.000 | 0.003 | |
| organism_species | 0.194 | 0.016 | 0.210 | |
| paste | 0.003 | 0.000 | 0.003 | |
| path | 0.028 | 0.008 | 0.036 | |
| plotMA | 9.308 | 0.459 | 9.771 | |
| plotPCA | 2.652 | 0.048 | 2.700 | |
| rank | 0.017 | 0.000 | 0.017 | |
| relist | 0.003 | 0.001 | 0.003 | |
| rep | 0.003 | 0.000 | 0.003 | |
| residuals | 0.002 | 0.000 | 0.002 | |
| row_colnames | 0.007 | 0.007 | 0.013 | |
| score | 0.093 | 0.005 | 0.098 | |
| sets | 0.010 | 0.000 | 0.011 | |
| sort | 0.003 | 0.000 | 0.003 | |
| start | 0.075 | 0.000 | 0.075 | |
| strand | 0.098 | 0.004 | 0.103 | |
| subset | 0.035 | 0.000 | 0.036 | |
| t | 0.004 | 0.000 | 0.004 | |
| table | 0.003 | 0.000 | 0.003 | |
| tapply | 0.003 | 0.000 | 0.002 | |
| testPackage | 0.414 | 0.000 | 0.418 | |
| toTable | 0.085 | 0.000 | 0.085 | |
| type | 0.214 | 0.012 | 0.226 | |
| unique | 0.002 | 0.000 | 0.003 | |
| unlist | 0.004 | 0.000 | 0.004 | |
| unsplit | 0.002 | 0.000 | 0.002 | |
| updateObject | 0.229 | 0.004 | 0.233 | |
| var | 0.003 | 0.000 | 0.003 | |
| weights | 0.002 | 0.000 | 0.002 | |
| which | 0.158 | 0.004 | 0.162 | |
| which.min | 0.050 | 0.004 | 0.054 | |
| xtabs | 0.032 | 0.000 | 0.033 | |