| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:18 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 54/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| annotate 1.77.0 (landing page) Bioconductor Package Maintainer
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: annotate |
| Version: 1.77.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:annotate.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings annotate_1.77.0.tar.gz |
| StartedAt: 2022-12-28 21:32:13 -0500 (Wed, 28 Dec 2022) |
| EndedAt: 2022-12-28 21:34:49 -0500 (Wed, 28 Dec 2022) |
| EllapsedTime: 155.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: annotate.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:annotate.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings annotate_1.77.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/annotate.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'annotate/DESCRIPTION' ... OK
* this is package 'annotate' version '1.77.0'
* 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 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 ... NOTE
Unexported object imported by a ':::' call: 'BiocGenerics:::testPackage'
See the note in ?`:::` about the use of this operator.
* 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 ... NOTE
checkRd: (-1) chrCats.Rd:13: Escaped LaTeX specials: \_
checkRd: (-1) chrCats.Rd:14: Escaped LaTeX specials: \_
checkRd: (-1) chrCats.Rd:47: Escaped LaTeX specials: \_
checkRd: (-1) chrCats.Rd:53: Escaped LaTeX specials: \_
checkRd: (-1) chrCats.Rd:60: Escaped LaTeX specials: \_
checkRd: (-1) chrCats.Rd:69: Escaped LaTeX specials: \_ \_
checkRd: (-1) chrCats.Rd:77: Escaped LaTeX specials: \_
checkRd: (-1) htmlpage.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) htmlpage.Rd:57: Escaped LaTeX specials: \_
* 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 6.57 0.14 6.74
blastSequences 0.12 0.03 29.53
* 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: 2 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/annotate.Rcheck/00check.log'
for details.
annotate.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL annotate ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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.
> 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, aperm, 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: org.Hs.eg.db
'select()' returned 1:many mapping between keys and columns
RUNIT TEST PROTOCOL -- Wed Dec 28 21:34:38 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
5.62 0.51 6.12
annotate.Rcheck/annotate-Ex.timings
| name | user | system | elapsed | |
| ACCNUMStats | 0.90 | 0.03 | 0.94 | |
| GO2heatmap | 0.11 | 0.00 | 0.11 | |
| GOmnplot | 0.03 | 0.00 | 0.03 | |
| HTMLPage-class | 0 | 0 | 0 | |
| LL2homology | 0 | 0 | 0 | |
| PMIDAmat | 0.07 | 0.00 | 0.06 | |
| PWAmat | 1.39 | 0.02 | 1.41 | |
| UniGeneQuery | 0 | 0 | 0 | |
| accessionToUID | 0.22 | 0.01 | 2.08 | |
| annPkgName | 0 | 0 | 0 | |
| aqListGOIDs | 0.13 | 0.00 | 0.13 | |
| blastSequences | 0.12 | 0.03 | 29.53 | |
| buildChromLocation | 0.44 | 0.02 | 0.45 | |
| buildPubMedAbst | 0.02 | 0.00 | 0.36 | |
| chrCats | 6.57 | 0.14 | 6.74 | |
| chromLocation-class | 0.46 | 0.00 | 0.45 | |
| compatibleVersions | 0.03 | 0.00 | 0.04 | |
| dropECode | 0.03 | 0.00 | 0.03 | |
| entrezGeneByID | 0 | 0 | 0 | |
| entrezGeneQuery | 0 | 0 | 0 | |
| filterGOByOntology | 0.05 | 0.00 | 0.04 | |
| findNeighbors | 0.00 | 0.01 | 0.05 | |
| genbank | 0.12 | 0.02 | 0.49 | |
| getAnnMap | 0.05 | 0.00 | 0.07 | |
| getEvidence | 0.03 | 0.01 | 0.05 | |
| getGOTerm | 0.11 | 0.03 | 0.14 | |
| getOntology | 0.03 | 0.00 | 0.03 | |
| getPMInfo | 0.30 | 0.00 | 0.64 | |
| getSYMBOL | 0.09 | 0.00 | 0.10 | |
| getSeq4Acc | 0.00 | 0.00 | 0.43 | |
| hasGOannote | 0.00 | 0.02 | 0.02 | |
| hgByChroms | 0.02 | 0.00 | 0.02 | |
| hgCLengths | 0 | 0 | 0 | |
| hgu95Achroloc | 0.03 | 0.03 | 0.06 | |
| hgu95Achrom | 0.03 | 0.02 | 0.04 | |
| hgu95All | 0.05 | 0.01 | 0.07 | |
| hgu95Asym | 0.03 | 0.02 | 0.04 | |
| homoData-class | 0 | 0 | 0 | |
| htmlpage | 0.01 | 0.00 | 0.02 | |
| isValidkey | 0.00 | 0.00 | 0.02 | |
| makeAnchor | 0 | 0 | 0 | |
| organism | 0.76 | 0.00 | 0.76 | |
| p2LL | 0 | 0 | 0 | |
| pm.abstGrep | 0.55 | 0.01 | 1.27 | |
| pm.getabst | 0.58 | 0.00 | 1.33 | |
| pm.titles | 0.55 | 0.00 | 1.33 | |
| pmAbst2HTML | 0.03 | 0.00 | 0.36 | |
| pmid2MIAME | 0 | 0 | 0 | |
| pmidQuery | 0 | 0 | 0 | |
| pubMedAbst-class | 0.03 | 0.00 | 0.37 | |
| pubmed | 0.00 | 0.01 | 0.33 | |
| readGEOAnn | 0 | 0 | 0 | |
| serializeEnv | 0 | 0 | 0 | |
| setRepository | 0 | 0 | 0 | |
| updateSymbolsToValidKeys | 0 | 0 | 0 | |
| usedChromGenes | 0.04 | 0.02 | 0.06 | |