| Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:07:01 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 BiocGenerics package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 157/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocGenerics 0.41.2 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: BiocGenerics |
| Version: 0.41.2 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocGenerics.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BiocGenerics_0.41.2.tar.gz |
| StartedAt: 2022-03-17 18:32:04 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:33:01 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 57.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BiocGenerics.Rcheck |
| Warnings: 2 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocGenerics.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BiocGenerics_0.41.2.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/BiocGenerics.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiocGenerics/DESCRIPTION' ... OK
* this is package 'BiocGenerics' version '0.41.2'
* 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 '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}'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'updateObject':
updateObjectFromSlots
Code: function(object, objclass = class(object)[[1L]], ..., verbose =
FALSE)
Docs: function(object, objclass = class(object), ..., verbose =
FALSE)
Mismatches in argument default values:
Name: 'objclass' Code: class(object)[[1L]] Docs: class(object)
* 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 5.53 0.37 5.92
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'run_unitTests.R'
OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 3 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/BiocGenerics.Rcheck/00check.log'
for details.
BiocGenerics.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BiocGenerics
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'BiocGenerics' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
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
converting help for package 'BiocGenerics'
finding HTML links ... done
BiocGenerics-package html
Extremes html
IQR html
Ontology html
S3-classes-as-S4-classes html
annotation html
append html
as.data.frame html
as.list html
as.vector html
boxplot html
cbind html
colSums html
combine html
dbconn html
density html
dge html
dims html
do.call html
duplicated html
eval html
evalq html
fileName html
funprog html
get html
grep html
image html
is.unsorted html
lapply html
mad html
mapply html
match html
mean html
normalize html
nrow html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-BiocGenerics/00new/BiocGenerics/help/NROW.html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-BiocGenerics/00new/BiocGenerics/help/NCOL.html
order html
organism_species html
paste html
path html
plotMA html
plotPCA html
rank html
relist html
rep html
residuals html
row_colnames html
score html
sets html
sort html
start html
strand html
subset html
t html
table html
tapply html
testPackage html
toTable html
type html
unique html
unlist html
unsplit html
updateObject html
var html
weights html
which html
which.min html
xtabs html
** 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)
Making 'packages.html' ... done
BiocGenerics.Rcheck/tests/run_unitTests.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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.
> 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, 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()
RUNIT TEST PROTOCOL -- Thu Mar 17 18:32:45 2022
***********************************************
Number of test functions: 24
Number of errors: 0
Number of failures: 0
1 Test Suite :
BiocGenerics RUnit Tests - 24 test functions, 0 errors, 0 failures
Number of test functions: 24
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
0.85 0.04 0.89
BiocGenerics.Rcheck/BiocGenerics-Ex.timings
| name | user | system | elapsed | |
| BiocGenerics-package | 0 | 0 | 0 | |
| Extremes | 0.01 | 0.00 | 0.02 | |
| IQR | 0 | 0 | 0 | |
| Ontology | 3.47 | 0.25 | 3.72 | |
| annotation | 0.00 | 0.02 | 0.01 | |
| append | 0 | 0 | 0 | |
| as.data.frame | 0 | 0 | 0 | |
| as.list | 0.03 | 0.00 | 0.03 | |
| as.vector | 0 | 0 | 0 | |
| boxplot | 0.15 | 0.00 | 0.14 | |
| cbind | 0.01 | 0.00 | 0.02 | |
| colSums | 0 | 0 | 0 | |
| combine | 0.05 | 0.00 | 0.05 | |
| dbconn | 0.03 | 0.00 | 0.03 | |
| density | 0 | 0 | 0 | |
| dims | 0.02 | 0.00 | 0.01 | |
| do.call | 0 | 0 | 0 | |
| duplicated | 0 | 0 | 0 | |
| eval | 0 | 0 | 0 | |
| evalq | 0 | 0 | 0 | |
| fileName | 2.00 | 0.15 | 2.14 | |
| funprog | 0 | 0 | 0 | |
| get | 0.01 | 0.00 | 0.02 | |
| grep | 0 | 0 | 0 | |
| image | 0.02 | 0.00 | 0.01 | |
| is.unsorted | 0.01 | 0.00 | 0.02 | |
| lapply | 0 | 0 | 0 | |
| mad | 0 | 0 | 0 | |
| mapply | 0 | 0 | 0 | |
| match | 0 | 0 | 0 | |
| mean | 0 | 0 | 0 | |
| normalize | 0.01 | 0.00 | 0.02 | |
| nrow | 0 | 0 | 0 | |
| order | 0 | 0 | 0 | |
| organism_species | 0.16 | 0.00 | 0.16 | |
| paste | 0 | 0 | 0 | |
| path | 0.03 | 0.00 | 0.03 | |
| plotMA | 5.53 | 0.37 | 5.92 | |
| plotPCA | 2.45 | 0.03 | 2.50 | |
| rank | 0.02 | 0.00 | 0.02 | |
| relist | 0 | 0 | 0 | |
| rep | 0 | 0 | 0 | |
| residuals | 0 | 0 | 0 | |
| row_colnames | 0.00 | 0.02 | 0.02 | |
| score | 0.06 | 0.00 | 0.06 | |
| sets | 0.02 | 0.00 | 0.01 | |
| sort | 0 | 0 | 0 | |
| start | 0.04 | 0.00 | 0.05 | |
| strand | 0.05 | 0.03 | 0.08 | |
| subset | 0.03 | 0.00 | 0.03 | |
| t | 0 | 0 | 0 | |
| table | 0 | 0 | 0 | |
| tapply | 0 | 0 | 0 | |
| testPackage | 0.28 | 0.01 | 0.30 | |
| toTable | 0.10 | 0.02 | 0.11 | |
| type | 0.18 | 0.05 | 0.23 | |
| unique | 0.02 | 0.00 | 0.02 | |
| unlist | 0 | 0 | 0 | |
| unsplit | 0 | 0 | 0 | |
| updateObject | 0.26 | 0.00 | 0.26 | |
| var | 0.02 | 0.00 | 0.02 | |
| weights | 0 | 0 | 0 | |
| which | 0.12 | 0.01 | 0.14 | |
| which.min | 0.05 | 0.02 | 0.07 | |
| xtabs | 0.03 | 0.01 | 0.04 | |