Bioconductor Package Maintainer
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/Category |
| Branch: RELEASE_3_6 |
| Last Commit: eaba50c |
| Last Changed Date: 2017-10-30 12:39:05 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:07:25 -0400 (Thu, 12 Apr 2018).
| Package 184/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Category 2.44.0 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: Category |
| Version: 2.44.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Category_2.44.0.tar.gz |
| StartedAt: 2018-04-11 22:02:13 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:05:03 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 170.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Category.Rcheck |
| Warnings: 0 |
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###
### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Category_2.44.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/Category.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Category/DESCRIPTION’ ... OK
* this is package ‘Category’ version ‘2.44.0’
* 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 ‘Category’ 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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
ChrBandTree-class 5.08 0.104 5.256
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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: OK
Category.Rcheck/00install.out
* installing *source* package ‘Category’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Category)
Category.Rcheck/tests/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("Category") || stop("unable to load Category")
Loading required package: Category
Loading required package: stats4
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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, 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
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
[1] TRUE
> BiocGenerics:::testPackage("Category", "UnitTests", ".*_test\\.R$")
Loading required package: org.Hs.eg.db
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Loading required package: graph
Attaching package: 'GOstats'
The following object is masked from 'package:AnnotationDbi':
makeGOGraph
RUNIT TEST PROTOCOL -- Wed Apr 11 22:05:00 2018
***********************************************
Number of test functions: 9
Number of errors: 0
Number of failures: 0
1 Test Suite :
Category RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9
Number of errors: 0
Number of failures: 0
Warning messages:
1: In makeValidParams(.Object) : removing duplicate IDs in geneIds
2: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds
3: In makeValidParams(.Object) : removing geneIds not in universeGeneIds
4: In makeValidParams(.Object) :
converting geneIds from list to atomic vector via unlist
5: In makeValidParams(.Object) :
converting univ from list to atomic vector via unlist
6: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds
>
> proc.time()
user system elapsed
41.080 1.008 44.115
Category.Rcheck/Category-Ex.timings
| name | user | system | elapsed | |
| ChrBandTree-class | 5.080 | 0.104 | 5.256 | |
| ChrMapHyperGParams-class | 0.000 | 0.000 | 0.001 | |
| ChrMapHyperGResult-class | 0.000 | 0.000 | 0.001 | |
| ChrMapLinearMParams-class | 0 | 0 | 0 | |
| ChrMapLinearMResult-class | 0.000 | 0.000 | 0.001 | |
| DatPkg-class | 0.052 | 0.000 | 0.051 | |
| HyperGResult-accessors | 1.236 | 0.028 | 1.391 | |
| LinearMResult-class | 0.004 | 0.000 | 0.001 | |
| MAPAmat | 2.672 | 0.008 | 2.682 | |
| applyByCategory | 0.000 | 0.000 | 0.003 | |
| cateGOryMatrix | 0.688 | 0.036 | 1.062 | |
| cb_parse_band_Hs | 0 | 0 | 0 | |
| cb_parse_band_Mm | 0.000 | 0.000 | 0.001 | |
| findAMstats | 0.000 | 0.000 | 0.002 | |
| getPathNames | 0.048 | 0.004 | 0.135 | |
| gseattperm | 1.444 | 0.028 | 1.980 | |
| hyperg | 0.536 | 0.000 | 0.536 | |
| makeChrBandGraph | 2.152 | 0.004 | 2.159 | |
| makeEBcontr | 0.112 | 0.004 | 0.128 | |
| probes2MAP | 0.136 | 0.000 | 0.137 | |
| probes2Path | 0.048 | 0.000 | 0.048 | |
| ttperm | 0.012 | 0.000 | 0.012 | |