CHECK report for BiocGenerics on malbec2
This page was generated on 2019-04-09 11:31:45 -0400 (Tue, 09 Apr 2019).
BiocGenerics 0.29.2 Bioconductor Package Maintainer
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
URL: https://git.bioconductor.org/packages/BiocGenerics |
Branch: master |
Last Commit: 6487557 |
Last Changed Date: 2019-03-04 21:14:56 -0400 (Mon, 04 Mar 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
Summary
Command output
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BiocGenerics.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BiocGenerics_0.29.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/BiocGenerics.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocGenerics/DESCRIPTION’ ... OK
* this is package ‘BiocGenerics’ version ‘0.29.2’
* 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 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’ ‘parallel’
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 'clusterApply':
parLapply
Code: function(cl = NULL, X, fun, ..., chunk.size = NULL)
Docs: function(cl = NULL, X, fun, ...)
Argument names in code not in docs:
chunk.size
parSapply
Code: function(cl = NULL, X, FUN, ..., simplify = TRUE, USE.NAMES =
TRUE, chunk.size = NULL)
Docs: function(cl = NULL, X, FUN, ..., simplify = TRUE, USE.NAMES =
TRUE)
Argument names in code not in docs:
chunk.size
parApply
Code: function(cl = NULL, X, MARGIN, FUN, ..., chunk.size = NULL)
Docs: function(cl = NULL, X, MARGIN, FUN, ...)
Argument names in code not in docs:
chunk.size
parRapply
Code: function(cl = NULL, x, FUN, ..., chunk.size = NULL)
Docs: function(cl = NULL, x, FUN, ...)
Argument names in code not in docs:
chunk.size
parCapply
Code: function(cl = NULL, x, FUN, ..., chunk.size = NULL)
Docs: function(cl = NULL, x, FUN, ...)
Argument names in code not in docs:
chunk.size
parLapplyLB
Code: function(cl = NULL, X, fun, ..., chunk.size = NULL)
Docs: function(cl = NULL, X, fun, ...)
Argument names in code not in docs:
chunk.size
parSapplyLB
Code: function(cl = NULL, X, FUN, ..., simplify = TRUE, USE.NAMES =
TRUE, chunk.size = NULL)
Docs: function(cl = NULL, X, FUN, ..., simplify = TRUE, USE.NAMES =
TRUE)
Argument names in code not in docs:
chunk.size
* 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 or elapsed time > 5s
user system elapsed
plotMA 9.105 0.34 9.612
* 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
‘/home/biocbuild/bbs-3.9-bioc/meat/BiocGenerics.Rcheck/00check.log’
for details.
Installation output
BiocGenerics.Rcheck/00install.out
Tests output
BiocGenerics.Rcheck/tests/run_unitTests.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, colMeans, colSums, 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, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
[1] TRUE
> BiocGenerics:::.test()
RUNIT TEST PROTOCOL -- Mon Apr 8 23:01:23 2019
***********************************************
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
1.112 0.033 1.218
Example timings
BiocGenerics.Rcheck/BiocGenerics-Ex.timings