Tiphaine Martin
| Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/coMET |
| git_branch: RELEASE_3_18 |
| git_last_commit: 79c0b13 |
| git_last_commit_date: 2023-10-24 11:45:22 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:35:52 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 409/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| coMET 1.34.0 (landing page) Tiphaine Martin
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the coMET package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/coMET.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: 1.34.0 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:coMET.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings coMET_1.34.0.tar.gz |
| StartedAt: 2024-04-15 21:26:49 -0400 (Mon, 15 Apr 2024) |
| EndedAt: 2024-04-15 21:37:59 -0400 (Mon, 15 Apr 2024) |
| EllapsedTime: 669.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: coMET.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:coMET.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings coMET_1.34.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/coMET.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘coMET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coMET’ version ‘1.34.0’
* 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 ‘/home/biocbuild/bbs-3.18-bioc/meat/coMET.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 19.1Mb
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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
comet.web 8.178 0.445 27.160
coMET-package 6.679 0.575 20.582
* 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 ...
‘coMET.Rnw’... failed
ERROR
Errors in running code in vignettes:
when running code in ‘coMET.Rnw’
...
> data(genetrack4RM)
> listRoadMap <- list(genetrack, promRMtrack, dyaRMtrack)
> plotTracks(listRoadMap, chromosome = chr, from = start,
+ to = end)
When sourcing 'coMET.R':
Error: invalid font type
Execution halted
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 4 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/coMET.Rcheck/00check.log’
for details.
coMET.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL coMET ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 -- Mon Apr 15 21:34:49 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
15.220 0.712 15.923
coMET.Rcheck/coMET-Ex.timings
| name | user | system | elapsed | |
| COSMIC_UCSC | 1.800 | 0.064 | 1.865 | |
| ChIPTF_ENCODE | 0.695 | 0.063 | 0.760 | |
| ClinVarCnv_UCSC | 0.417 | 0.008 | 0.425 | |
| ClinVarMain_UCSC | 0.407 | 0.004 | 0.410 | |
| CoreillCNV_UCSC | 0.395 | 0.000 | 0.395 | |
| DNAse_UCSC | 0 | 0 | 0 | |
| DNaseI_FANTOM | 0.616 | 0.000 | 0.615 | |
| DNaseI_RoadMap | 0.186 | 0.001 | 0.186 | |
| GAD_UCSC | 0.411 | 0.032 | 0.444 | |
| GWAScatalog_UCSC | 0.333 | 0.011 | 0.345 | |
| GeneReviews_UCSC | 0.544 | 0.000 | 0.545 | |
| HiCdata2matrix | 0.025 | 0.001 | 0.025 | |
| HistoneAll_UCSC | 4.130 | 0.015 | 4.146 | |
| HistoneOne_UCSC | 0.357 | 0.000 | 0.357 | |
| ISCA_UCSC | 0.443 | 0.007 | 0.451 | |
| TFBS_FANTOM | 0.404 | 0.000 | 0.404 | |
| bindingMotifsBiomart_ENSEMBL | 0.122 | 0.017 | 0.138 | |
| chrUCSC2ENSEMBL | 0.001 | 0.000 | 0.001 | |
| chromHMM_RoadMap | 0.660 | 0.015 | 0.676 | |
| chromatinHMMAll_UCSC | 4.290 | 0.004 | 4.295 | |
| chromatinHMMOne_UCSC | 0.422 | 0.004 | 0.426 | |
| coMET-package | 6.679 | 0.575 | 20.582 | |
| col2HSV | 0.001 | 0.000 | 0.001 | |
| comet | 2.876 | 0.100 | 2.976 | |
| comet.list | 0.685 | 0.012 | 0.698 | |
| comet.web | 8.178 | 0.445 | 27.160 | |
| complementary | 0.025 | 0.000 | 0.025 | |
| cpgIslands_UCSC | 0.131 | 0.000 | 0.131 | |
| dgfootprints_RoadMap | 0.726 | 0.020 | 0.746 | |
| eQTL | 1.370 | 0.044 | 1.415 | |
| eQTL_GTEx | 1.312 | 0.036 | 1.348 | |
| gcContent_UCSC | 1.362 | 0.104 | 1.467 | |
| genesName_ENSEMBL | 0.003 | 0.000 | 0.003 | |
| genes_ENSEMBL | 0.866 | 0.012 | 0.877 | |
| imprintedGenes_GTEx | 3.641 | 0.044 | 3.685 | |
| interestGenes_ENSEMBL | 0.789 | 0.012 | 0.800 | |
| interestTranscript_ENSEMBL | 0.809 | 0.040 | 0.849 | |
| knownGenes_UCSC | 0.870 | 0.008 | 0.877 | |
| metQTL | 1.199 | 0.000 | 1.199 | |
| miRNATargetRegionsBiomart_ENSEMBL | 0.043 | 0.000 | 0.043 | |
| otherRegulatoryRegionsBiomart_ENSEMBL | 0.090 | 0.004 | 0.095 | |
| pizza | 0.006 | 0.000 | 0.006 | |
| psiQTL_GTEx | 1.048 | 0.012 | 1.060 | |
| refGenes_UCSC | 0.97 | 0.00 | 0.97 | |
| regulationBiomart_ENSEMBL | 0.371 | 0.000 | 0.371 | |
| regulatoryEvidenceBiomart_ENSEMBL | 0.142 | 0.000 | 0.141 | |
| regulatoryFeaturesBiomart_ENSEMBL | 0.168 | 0.000 | 0.167 | |
| regulatorySegmentsBiomart_ENSEMBL | 0.154 | 0.004 | 0.159 | |
| repeatMasker_UCSC | 0.530 | 0.008 | 0.539 | |
| segmentalDups_UCSC | 0.425 | 0.000 | 0.426 | |
| setColors | 0.001 | 0.000 | 0.001 | |
| snpBiomart_ENSEMBL | 0.443 | 0.016 | 0.459 | |
| snpLocations_UCSC | 1.09 | 0.02 | 1.11 | |
| structureBiomart_ENSEMBL | 0.424 | 0.012 | 0.436 | |
| transcript_ENSEMBL | 1.296 | 0.028 | 1.324 | |
| xenorefGenes_UCSC | 0.597 | 0.004 | 0.602 | |