| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:37:58 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 | ||||
| Package 67/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| annotate 1.78.0 (landing page) Bioconductor Package Maintainer
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the annotate package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: annotate |
| Version: 1.78.0 |
| 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_1.78.0.tar.gz |
| StartedAt: 2023-10-17 02:19:36 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 02:37:50 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 1094.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: annotate.Rcheck |
| Warnings: 0 |
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### Running 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_1.78.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/annotate.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.78.0’
* 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 startup messages can be suppressed ... 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
blastSequences 457.195 5.605 708.335
chrCats 10.555 0.106 15.866
accessionToUID 0.378 0.050 9.635
buildPubMedAbst 0.045 0.004 6.632
* 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
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/annotate.Rcheck/00check.log’
for details.
annotate.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL annotate ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 object is masked from 'package:utils':
findMatches
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 Oct 17 02:37:35 2023
***********************************************
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
9.113 0.654 14.133
annotate.Rcheck/annotate-Ex.timings
| name | user | system | elapsed | |
| ACCNUMStats | 1.716 | 0.044 | 2.678 | |
| GO2heatmap | 0.162 | 0.010 | 0.255 | |
| GOmnplot | 0.064 | 0.008 | 0.110 | |
| HTMLPage-class | 0.000 | 0.000 | 0.001 | |
| LL2homology | 0 | 0 | 0 | |
| PMIDAmat | 0.104 | 0.004 | 0.166 | |
| PWAmat | 2.050 | 0.052 | 3.118 | |
| UniGeneQuery | 0.001 | 0.000 | 0.003 | |
| accessionToUID | 0.378 | 0.050 | 9.635 | |
| annPkgName | 0.001 | 0.000 | 0.001 | |
| aqListGOIDs | 0.152 | 0.012 | 0.218 | |
| blastSequences | 457.195 | 5.605 | 708.335 | |
| buildChromLocation | 1.152 | 0.020 | 1.642 | |
| buildPubMedAbst | 0.045 | 0.004 | 6.632 | |
| chrCats | 10.555 | 0.106 | 15.866 | |
| chromLocation-class | 0.808 | 0.043 | 1.342 | |
| compatibleVersions | 0.058 | 0.003 | 0.091 | |
| dropECode | 0.057 | 0.003 | 0.091 | |
| entrezGeneByID | 0.001 | 0.001 | 0.001 | |
| entrezGeneQuery | 0.000 | 0.001 | 0.001 | |
| filterGOByOntology | 0.064 | 0.003 | 0.102 | |
| findNeighbors | 0.029 | 0.004 | 0.055 | |
| genbank | 0.219 | 0.011 | 1.387 | |
| getAnnMap | 0.062 | 0.009 | 0.111 | |
| getEvidence | 0.066 | 0.004 | 0.103 | |
| getGOTerm | 0.225 | 0.011 | 0.350 | |
| getOntology | 0.054 | 0.004 | 0.083 | |
| getPMInfo | 0.365 | 0.008 | 1.509 | |
| getSYMBOL | 0.138 | 0.028 | 0.250 | |
| getSeq4Acc | 0.019 | 0.003 | 0.905 | |
| hasGOannote | 0.029 | 0.002 | 0.045 | |
| hgByChroms | 0.014 | 0.007 | 0.029 | |
| hgCLengths | 0.001 | 0.002 | 0.003 | |
| hgu95Achroloc | 0.072 | 0.013 | 0.128 | |
| hgu95Achrom | 0.058 | 0.012 | 0.104 | |
| hgu95All | 0.068 | 0.013 | 0.118 | |
| hgu95Asym | 0.069 | 0.013 | 0.116 | |
| homoData-class | 0.003 | 0.001 | 0.003 | |
| htmlpage | 0.022 | 0.003 | 0.036 | |
| isValidkey | 0 | 0 | 0 | |
| makeAnchor | 0.001 | 0.000 | 0.004 | |
| organism | 0.854 | 0.018 | 1.334 | |
| p2LL | 0 | 0 | 0 | |
| pm.abstGrep | 1.029 | 0.027 | 2.721 | |
| pm.getabst | 1.389 | 0.028 | 3.481 | |
| pm.titles | 0.986 | 0.025 | 2.970 | |
| pmAbst2HTML | 0.050 | 0.006 | 1.070 | |
| pmid2MIAME | 0.000 | 0.001 | 0.001 | |
| pmidQuery | 0.001 | 0.000 | 0.001 | |
| pubMedAbst-class | 0.040 | 0.003 | 0.853 | |
| pubmed | 0.029 | 0.003 | 0.765 | |
| readGEOAnn | 0 | 0 | 0 | |
| serializeEnv | 0.001 | 0.001 | 0.004 | |
| setRepository | 0.001 | 0.001 | 0.004 | |
| updateSymbolsToValidKeys | 0.000 | 0.000 | 0.001 | |
| usedChromGenes | 0.084 | 0.015 | 0.145 | |