| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:07:37 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 annotate package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/annotate.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 59/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| annotate 1.72.0 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: annotate |
| Version: 1.72.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:annotate.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings annotate_1.72.0.tar.gz |
| StartedAt: 2022-04-12 10:16:15 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 10:21:51 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 336.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: annotate.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:annotate.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings annotate_1.72.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/annotate.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.72.0’
* 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 ‘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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
chrCats 19.717 0.099 19.841
pm.getabst 1.346 0.026 5.301
blastSequences 0.696 0.046 102.500
* 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
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL annotate ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘annotate’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** 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 (annotate)
annotate.Rcheck/tests/annotate_unit_tests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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: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
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 objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: org.Hs.eg.db
'select()' returned 1:many mapping between keys and columns
RUNIT TEST PROTOCOL -- Tue Apr 12 10:21:40 2022
***********************************************
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
10.921 0.684 11.595
annotate.Rcheck/annotate-Ex.timings
| name | user | system | elapsed | |
| ACCNUMStats | 3.024 | 0.041 | 3.070 | |
| GO2heatmap | 0.233 | 0.010 | 0.245 | |
| GOmnplot | 0.086 | 0.006 | 0.093 | |
| HTMLPage-class | 0.000 | 0.000 | 0.001 | |
| LL2homology | 0.000 | 0.000 | 0.001 | |
| PMIDAmat | 0.160 | 0.005 | 0.168 | |
| PWAmat | 2.914 | 0.045 | 2.961 | |
| UniGeneQuery | 0.001 | 0.000 | 0.001 | |
| accessionToUID | 0.503 | 0.044 | 3.272 | |
| annPkgName | 0.001 | 0.001 | 0.001 | |
| aqListGOIDs | 0.23 | 0.02 | 0.25 | |
| blastSequences | 0.696 | 0.046 | 102.500 | |
| buildChromLocation | 1.162 | 0.055 | 1.221 | |
| buildPubMedAbst | 0.062 | 0.002 | 0.670 | |
| chrCats | 19.717 | 0.099 | 19.841 | |
| chromLocation-class | 1.074 | 0.053 | 1.127 | |
| compatibleVersions | 0.064 | 0.004 | 0.068 | |
| dropECode | 0.070 | 0.002 | 0.073 | |
| entrezGeneByID | 0.001 | 0.000 | 0.001 | |
| entrezGeneQuery | 0.002 | 0.001 | 0.001 | |
| filterGOByOntology | 0.060 | 0.002 | 0.061 | |
| findNeighbors | 0.030 | 0.003 | 0.036 | |
| genbank | 0.295 | 0.017 | 1.192 | |
| getAnnMap | 0.054 | 0.011 | 0.067 | |
| getEvidence | 0.082 | 0.004 | 0.086 | |
| getGOTerm | 0.354 | 0.008 | 0.365 | |
| getOntology | 0.069 | 0.004 | 0.072 | |
| getPMInfo | 0.584 | 0.004 | 1.299 | |
| getSYMBOL | 0.175 | 0.021 | 0.234 | |
| getSeq4Acc | 0.023 | 0.002 | 0.610 | |
| hasGOannote | 0.039 | 0.001 | 0.040 | |
| hgByChroms | 0.021 | 0.002 | 0.024 | |
| hgCLengths | 0.001 | 0.003 | 0.004 | |
| hgu95Achroloc | 0.072 | 0.004 | 0.075 | |
| hgu95Achrom | 0.084 | 0.005 | 0.089 | |
| hgu95All | 0.082 | 0.005 | 0.089 | |
| hgu95Asym | 0.082 | 0.004 | 0.086 | |
| homoData-class | 0.002 | 0.001 | 0.002 | |
| htmlpage | 0.027 | 0.002 | 0.030 | |
| isValidkey | 0.000 | 0.000 | 0.001 | |
| makeAnchor | 0.001 | 0.000 | 0.001 | |
| organism | 1.242 | 0.082 | 1.325 | |
| p2LL | 0 | 0 | 0 | |
| pm.abstGrep | 1.469 | 0.031 | 2.639 | |
| pm.getabst | 1.346 | 0.026 | 5.301 | |
| pm.titles | 1.506 | 0.042 | 2.573 | |
| pmAbst2HTML | 0.077 | 0.005 | 0.761 | |
| pmid2MIAME | 0 | 0 | 0 | |
| pmidQuery | 0.000 | 0.000 | 0.001 | |
| pubMedAbst-class | 0.055 | 0.002 | 0.672 | |
| pubmed | 0.034 | 0.003 | 0.717 | |
| readGEOAnn | 0 | 0 | 0 | |
| serializeEnv | 0.002 | 0.000 | 0.002 | |
| setRepository | 0.002 | 0.001 | 0.002 | |
| updateSymbolsToValidKeys | 0 | 0 | 0 | |
| usedChromGenes | 0.112 | 0.007 | 0.119 | |