Tiphaine Martin
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/coMET |
| git_branch: RELEASE_3_17 |
| git_last_commit: 208d035 |
| git_last_commit_date: 2023-04-25 11:41:26 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:00 -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 404/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| coMET 1.32.0 (landing page) Tiphaine Martin
| kjohnson2 | macOS 12.6.1 Monterey / 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: 1.32.0 |
| 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_1.32.0.tar.gz |
| StartedAt: 2023-10-17 11:05:48 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 11:19:40 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 832.5 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_1.32.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/coMET.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 ‘coMET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coMET’ version ‘1.32.0’
* 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-3.17-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 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 ... 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 ... 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
comet.web 9.197 0.335 32.410
coMET-package 7.466 0.219 23.501
HistoneAll_UCSC 5.842 0.062 7.986
chromatinHMMAll_UCSC 5.806 0.060 8.940
imprintedGenes_GTEx 5.011 0.087 7.464
comet 3.775 0.078 5.911
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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: 1 WARNING, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.17-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/4.3-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 4.3.1 (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.
> 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, sort, 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 -- Tue Oct 17 11:19:20 2023
***********************************************
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
17.565 0.750 27.134
coMET.Rcheck/coMET-Ex.timings
| name | user | system | elapsed | |
| COSMIC_UCSC | 2.136 | 0.103 | 3.395 | |
| ChIPTF_ENCODE | 0.948 | 0.019 | 1.436 | |
| ClinVarCnv_UCSC | 0.575 | 0.019 | 0.857 | |
| ClinVarMain_UCSC | 0.575 | 0.008 | 0.855 | |
| CoreillCNV_UCSC | 0.577 | 0.012 | 0.899 | |
| DNAse_UCSC | 0.000 | 0.001 | 0.001 | |
| DNaseI_FANTOM | 0.852 | 0.019 | 1.345 | |
| DNaseI_RoadMap | 0.242 | 0.010 | 0.384 | |
| GAD_UCSC | 0.602 | 0.011 | 0.929 | |
| GWAScatalog_UCSC | 0.459 | 0.010 | 0.725 | |
| GeneReviews_UCSC | 0.718 | 0.012 | 1.119 | |
| HiCdata2matrix | 0.038 | 0.006 | 0.060 | |
| HistoneAll_UCSC | 5.842 | 0.062 | 7.986 | |
| HistoneOne_UCSC | 0.499 | 0.009 | 0.654 | |
| ISCA_UCSC | 0.578 | 0.012 | 0.764 | |
| TFBS_FANTOM | 0.587 | 0.012 | 0.884 | |
| bindingMotifsBiomart_ENSEMBL | 0.170 | 0.014 | 0.276 | |
| chrUCSC2ENSEMBL | 0.000 | 0.000 | 0.001 | |
| chromHMM_RoadMap | 0.891 | 0.023 | 1.410 | |
| chromatinHMMAll_UCSC | 5.806 | 0.060 | 8.940 | |
| chromatinHMMOne_UCSC | 0.628 | 0.010 | 0.976 | |
| coMET-package | 7.466 | 0.219 | 23.501 | |
| col2HSV | 0 | 0 | 0 | |
| comet | 3.775 | 0.078 | 5.911 | |
| comet.list | 0.913 | 0.014 | 1.426 | |
| comet.web | 9.197 | 0.335 | 32.410 | |
| complementary | 0.026 | 0.002 | 0.043 | |
| cpgIslands_UCSC | 0.170 | 0.006 | 0.268 | |
| dgfootprints_RoadMap | 0.996 | 0.018 | 1.529 | |
| eQTL | 1.971 | 0.034 | 2.962 | |
| eQTL_GTEx | 1.707 | 0.025 | 2.653 | |
| gcContent_UCSC | 1.197 | 0.015 | 1.827 | |
| genesName_ENSEMBL | 0.003 | 0.003 | 0.006 | |
| genes_ENSEMBL | 1.108 | 0.016 | 1.673 | |
| imprintedGenes_GTEx | 5.011 | 0.087 | 7.464 | |
| interestGenes_ENSEMBL | 0.974 | 0.012 | 1.503 | |
| interestTranscript_ENSEMBL | 1.033 | 0.012 | 1.599 | |
| knownGenes_UCSC | 1.271 | 0.017 | 1.926 | |
| metQTL | 1.776 | 0.030 | 2.747 | |
| miRNATargetRegionsBiomart_ENSEMBL | 0.061 | 0.005 | 0.086 | |
| otherRegulatoryRegionsBiomart_ENSEMBL | 0.124 | 0.009 | 0.164 | |
| pizza | 0.007 | 0.002 | 0.011 | |
| psiQTL_GTEx | 1.538 | 0.023 | 2.227 | |
| refGenes_UCSC | 1.222 | 0.015 | 1.552 | |
| regulationBiomart_ENSEMBL | 0.442 | 0.009 | 0.537 | |
| regulatoryEvidenceBiomart_ENSEMBL | 0.190 | 0.016 | 0.262 | |
| regulatoryFeaturesBiomart_ENSEMBL | 0.198 | 0.016 | 0.273 | |
| regulatorySegmentsBiomart_ENSEMBL | 0.200 | 0.016 | 0.271 | |
| repeatMasker_UCSC | 0.737 | 0.011 | 0.851 | |
| segmentalDups_UCSC | 0.544 | 0.007 | 0.571 | |
| setColors | 0.001 | 0.000 | 0.002 | |
| snpBiomart_ENSEMBL | 0.630 | 0.010 | 0.663 | |
| snpLocations_UCSC | 1.483 | 0.022 | 2.068 | |
| structureBiomart_ENSEMBL | 0.595 | 0.010 | 0.931 | |
| transcript_ENSEMBL | 1.737 | 0.021 | 2.523 | |
| xenorefGenes_UCSC | 0.849 | 0.013 | 1.216 | |