Bioconductor Package Maintainer
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/annotate |
| Branch: RELEASE_3_6 |
| Last Commit: 95ec3b0 |
| Last Changed Date: 2018-03-20 17:08:59 -0400 (Tue, 20 Mar 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:06:50 -0400 (Thu, 12 Apr 2018).
| Package 49/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| annotate 1.56.2 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: annotate |
| Version: 1.56.2 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.56.2.tar.gz |
| StartedAt: 2018-04-11 21:26:06 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 21:28:34 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 148.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: annotate.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 annotate_1.56.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/annotate.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 ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.56.2’
* 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 ‘annotate’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
chrCats 12.248 0.00 12.256
blastSequences 0.456 0.12 27.859
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘annotate_unit_tests.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
annotate.Rcheck/00install.out
* installing *source* package ‘annotate’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (annotate)
annotate.Rcheck/tests/annotate_unit_tests.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.
> BiocGenerics:::testPackage("annotate")
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: org.Hs.eg.db
'select()' returned 1:many mapping between keys and columns
RUNIT TEST PROTOCOL -- Wed Apr 11 21:28:31 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
annotate RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
5.520 0.152 5.671
annotate.Rcheck/annotate-Ex.timings
| name | user | system | elapsed | |
| ACCNUMStats | 1.648 | 0.020 | 1.670 | |
| GO2heatmap | 0.196 | 0.000 | 0.196 | |
| GOmnplot | 0.056 | 0.008 | 0.065 | |
| HTMLPage-class | 0 | 0 | 0 | |
| LL2homology | 0.000 | 0.000 | 0.001 | |
| PMIDAmat | 0.084 | 0.008 | 0.414 | |
| PWAmat | 1.872 | 0.000 | 1.873 | |
| UniGeneQuery | 0.000 | 0.000 | 0.002 | |
| accessionToUID | 1.116 | 0.040 | 2.710 | |
| annPkgName | 0.000 | 0.000 | 0.002 | |
| aqListGOIDs | 0.296 | 0.004 | 0.301 | |
| blastSequences | 0.456 | 0.120 | 27.859 | |
| buildChromLocation | 0.528 | 0.004 | 0.531 | |
| buildPubMedAbst | 0.164 | 0.016 | 0.695 | |
| chrCats | 12.248 | 0.000 | 12.256 | |
| chromLocation-class | 0.460 | 0.004 | 0.464 | |
| compatibleVersions | 0.044 | 0.000 | 0.047 | |
| dropECode | 0.044 | 0.000 | 0.046 | |
| entrezGeneByID | 0.000 | 0.000 | 0.001 | |
| entrezGeneQuery | 0.000 | 0.000 | 0.001 | |
| filterGOByOntology | 0.072 | 0.000 | 0.072 | |
| findNeighbors | 0.028 | 0.000 | 0.271 | |
| genbank | 0.260 | 0.004 | 0.662 | |
| getAnnMap | 0.060 | 0.004 | 0.250 | |
| getEvidence | 0.164 | 0.000 | 0.171 | |
| getGOTerm | 0.468 | 0.000 | 0.503 | |
| getOntology | 0.064 | 0.000 | 0.065 | |
| getPMInfo | 0.784 | 0.004 | 1.219 | |
| getSYMBOL | 0.140 | 0.008 | 0.292 | |
| getSeq4Acc | 0.064 | 0.012 | 0.417 | |
| hasGOannote | 0.028 | 0.000 | 0.028 | |
| hgByChroms | 0.016 | 0.000 | 0.015 | |
| hgCLengths | 0.004 | 0.000 | 0.001 | |
| hgu95Achroloc | 0.064 | 0.004 | 0.068 | |
| hgu95Achrom | 0.052 | 0.004 | 0.055 | |
| hgu95All | 0.06 | 0.00 | 0.06 | |
| hgu95Asym | 0.060 | 0.004 | 0.062 | |
| homoData-class | 0.004 | 0.000 | 0.003 | |
| htmlpage | 0.460 | 0.000 | 0.461 | |
| isValidkey | 0.000 | 0.000 | 0.001 | |
| makeAnchor | 0 | 0 | 0 | |
| organism | 0.588 | 0.000 | 0.587 | |
| p2LL | 0 | 0 | 0 | |
| pm.abstGrep | 0.928 | 0.004 | 1.930 | |
| pm.getabst | 1.108 | 0.000 | 2.124 | |
| pm.titles | 1.020 | 0.008 | 2.049 | |
| pmAbst2HTML | 0.144 | 0.000 | 0.517 | |
| pmid2MIAME | 0 | 0 | 0 | |
| pmidQuery | 0.000 | 0.000 | 0.001 | |
| pubMedAbst-class | 0.132 | 0.000 | 0.661 | |
| pubmed | 0.124 | 0.000 | 0.637 | |
| readGEOAnn | 0.000 | 0.000 | 0.001 | |
| serializeEnv | 0.000 | 0.000 | 0.002 | |
| setRepository | 0.004 | 0.000 | 0.003 | |
| updateSymbolsToValidKeys | 0.000 | 0.000 | 0.001 | |
| usedChromGenes | 0.080 | 0.000 | 0.083 | |