Tiphaine Martin
| Snapshot Date: 2024-05-11 09:00:03 -0400 (Sat, 11 May 2024) |
| git_url: https://git.bioconductor.org/packages/coMET |
| git_branch: devel |
| git_last_commit: d78add3 |
| git_last_commit_date: 2024-04-30 11:45:58 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-13 11:32:02 -0400 (Mon, 13 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
| 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 403/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| coMET 1.37.0 (landing page) Tiphaine Martin
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the coMET 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: coMET |
| Version: 1.37.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:coMET.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings coMET_1.37.0.tar.gz |
| StartedAt: 2024-05-12 09:23:43 -0400 (Sun, 12 May 2024) |
| EndedAt: 2024-05-12 09:33:35 -0400 (Sun, 12 May 2024) |
| EllapsedTime: 591.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: coMET.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:coMET.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings coMET_1.37.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/coMET.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘coMET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coMET’ version ‘1.37.0’
* 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 ‘coMET’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET'
See ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/coMET.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 18.9Mb
sub-directories of 1Mb or more:
data 7.6Mb
extdata 10.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 ... NOTE
draw.plot.annotation : <anonymous>: no visible global function
definition for 'ggplotGrob'
draw.plot.annotation: no visible global function definition for
'viewTracks'
draw.plot.annotation: no visible global function definition for
'trackList'
eQTL: no visible binding for global variable 'chromosome_stop'
eQTL: no visible binding for global variable 'chromosome_start'
eQTL: no visible binding for global variable 'chromosome_name'
eQTL_GTEx: no visible binding for global variable 'snp_pos'
eQTL_GTEx: no visible binding for global variable 'snp_chrom'
eQTL_GTEx: no visible binding for global variable 'gene_start'
eQTL_GTEx: no visible binding for global variable 'gene_stop'
eQTL_GTEx: no visible binding for global variable 'gene_chr'
geneExpression_GTEx: no visible global function definition for 'as'
metQTL: no visible binding for global variable 'chromosome_stop'
metQTL: no visible binding for global variable 'chromosome_start'
metQTL: no visible binding for global variable 'chromosome_name'
pizza: no visible global function definition for 'par'
pizza: no visible global function definition for 'plot.new'
pizza: no visible global function definition for 'plot.window'
pizza: no visible global function definition for 'polygon'
pizza: no visible global function definition for 'lines'
pizza: no visible global function definition for 'text'
psiQTL_GTEx: no visible binding for global variable 'pos_snp'
psiQTL_GTEx: no visible binding for global variable 'chr_snp'
psiQTL_GTEx: no visible binding for global variable 'pos_middle_exon'
psiQTL_GTEx: no visible binding for global variable 'chr_exon'
Undefined global functions or variables:
as chr_exon chr_snp chromosome_name chromosome_start chromosome_stop
gene_chr gene_start gene_stop ggplotGrob lines par plot.new
plot.window polygon pos_middle_exon pos_snp snp_chrom snp_pos text
trackList viewTracks
Consider adding
importFrom("graphics", "lines", "par", "plot.new", "plot.window",
"polygon", "text")
importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) ChIPTF_ENCODE.Rd:36: 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 ... NOTE
Objects in \usage without \alias in Rd file 'check.configVar.cometlist.Rd':
‘check.configVar.cometlist’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
comet.web 8.137 0.233 16.683
coMET-package 7.465 0.188 14.305
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/coMET.Rcheck/00check.log’
for details.
coMET.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL coMET ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘coMET’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET' ** testing if installed package can be loaded from final location Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET' ** testing if installed package keeps a record of temporary installation path * DONE (coMET)
coMET.Rcheck/tests/runTests.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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("coMET") || stop("unable to load Package:coMET")
Loading required package: coMET
Loading required package: grid
Loading required package: biomaRt
Loading required package: Gviz
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
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, table, tapply,
union, unique, unsplit, which.max, which.min
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: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: psych
Attaching package: 'psych'
The following object is masked from 'package:GenomicRanges':
distance
The following objects are masked from 'package:IRanges':
distance, reflect
[1] TRUE
Warning message:
replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET'
> BiocGenerics:::testPackage("coMET")
RUNIT TEST PROTOCOL -- Sun May 12 09:33:20 2024
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
coMET 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
19.989 0.782 20.888
coMET.Rcheck/coMET-Ex.timings
| name | user | system | elapsed | |
| COSMIC_UCSC | 2.587 | 0.076 | 2.671 | |
| ChIPTF_ENCODE | 0.803 | 0.027 | 0.832 | |
| ClinVarCnv_UCSC | 1.946 | 0.023 | 1.974 | |
| ClinVarMain_UCSC | 0.434 | 0.005 | 0.440 | |
| CoreillCNV_UCSC | 0.467 | 0.006 | 0.475 | |
| DNAse_UCSC | 0.001 | 0.000 | 0.001 | |
| DNaseI_FANTOM | 0.768 | 0.009 | 0.781 | |
| DNaseI_RoadMap | 0.237 | 0.007 | 0.247 | |
| GAD_UCSC | 0.503 | 0.008 | 0.511 | |
| GWAScatalog_UCSC | 0.361 | 0.005 | 0.368 | |
| GeneReviews_UCSC | 0.570 | 0.006 | 0.578 | |
| HiCdata2matrix | 0.034 | 0.006 | 0.041 | |
| HistoneAll_UCSC | 4.576 | 0.022 | 4.615 | |
| HistoneOne_UCSC | 0.420 | 0.007 | 0.427 | |
| ISCA_UCSC | 0.488 | 0.007 | 0.497 | |
| TFBS_FANTOM | 0.465 | 0.006 | 0.472 | |
| bindingMotifsBiomart_ENSEMBL | 0.148 | 0.012 | 0.162 | |
| chrUCSC2ENSEMBL | 0.000 | 0.000 | 0.001 | |
| chromHMM_RoadMap | 0.725 | 0.015 | 0.743 | |
| chromatinHMMAll_UCSC | 4.578 | 0.024 | 4.618 | |
| chromatinHMMOne_UCSC | 0.499 | 0.006 | 0.510 | |
| coMET-package | 7.465 | 0.188 | 14.305 | |
| col2HSV | 0 | 0 | 0 | |
| comet | 3.093 | 0.042 | 3.145 | |
| comet.list | 0.680 | 0.005 | 0.690 | |
| comet.web | 8.137 | 0.233 | 16.683 | |
| complementary | 0.027 | 0.001 | 0.030 | |
| cpgIslands_UCSC | 0.157 | 0.004 | 0.162 | |
| dgfootprints_RoadMap | 0.831 | 0.011 | 0.845 | |
| eQTL | 1.852 | 0.018 | 1.874 | |
| eQTL_GTEx | 1.374 | 0.017 | 1.400 | |
| gcContent_UCSC | 1.917 | 0.017 | 1.947 | |
| genesName_ENSEMBL | 0.004 | 0.003 | 0.007 | |
| genes_ENSEMBL | 0.902 | 0.008 | 0.914 | |
| imprintedGenes_GTEx | 3.991 | 0.051 | 4.057 | |
| interestGenes_ENSEMBL | 0.743 | 0.006 | 0.750 | |
| interestTranscript_ENSEMBL | 0.913 | 0.009 | 0.924 | |
| knownGenes_UCSC | 0.963 | 0.007 | 0.971 | |
| metQTL | 1.387 | 0.018 | 1.415 | |
| miRNATargetRegionsBiomart_ENSEMBL | 0.050 | 0.004 | 0.054 | |
| otherRegulatoryRegionsBiomart_ENSEMBL | 0.132 | 0.008 | 0.139 | |
| pizza | 0.006 | 0.002 | 0.008 | |
| psiQTL_GTEx | 1.161 | 0.012 | 1.180 | |
| refGenes_UCSC | 0.954 | 0.007 | 0.964 | |
| regulationBiomart_ENSEMBL | 0.359 | 0.004 | 0.364 | |
| regulatoryEvidenceBiomart_ENSEMBL | 0.154 | 0.012 | 0.168 | |
| regulatoryFeaturesBiomart_ENSEMBL | 0.150 | 0.013 | 0.164 | |
| regulatorySegmentsBiomart_ENSEMBL | 0.151 | 0.012 | 0.164 | |
| repeatMasker_UCSC | 0.568 | 0.006 | 0.575 | |
| segmentalDups_UCSC | 0.448 | 0.005 | 0.455 | |
| setColors | 0.000 | 0.000 | 0.001 | |
| snpBiomart_ENSEMBL | 0.506 | 0.005 | 0.514 | |
| snpLocations_UCSC | 1.102 | 0.007 | 1.113 | |
| structureBiomart_ENSEMBL | 0.450 | 0.005 | 0.457 | |
| transcript_ENSEMBL | 1.423 | 0.010 | 1.446 | |
| xenorefGenes_UCSC | 0.670 | 0.007 | 0.678 | |