| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:38 -0000 (Wed, 01 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
| 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 coMET package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 384/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| coMET 1.31.0 (landing page) Tiphaine Martin
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: coMET |
| Version: 1.31.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:coMET.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings coMET_1.31.0.tar.gz |
| StartedAt: 2023-02-28 00:09:39 -0000 (Tue, 28 Feb 2023) |
| EndedAt: 2023-02-28 00:21:17 -0000 (Tue, 28 Feb 2023) |
| EllapsedTime: 698.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: coMET.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:coMET.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings coMET_1.31.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/coMET.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘coMET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coMET’ version ‘1.31.0’
* 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 ... OK
* checking installed package size ... NOTE
installed size is 19.0Mb
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
comet.web 8.153 0.341 30.488
coMET-package 7.578 0.540 17.618
chromatinHMMAll_UCSC 6.374 0.288 6.662
HistoneAll_UCSC 5.998 0.116 6.115
imprintedGenes_GTEx 5.142 0.100 5.243
* 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’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/coMET.Rcheck/00check.log’
for details.
coMET.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL coMET ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘coMET’ ... ** 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 (coMET)
coMET.Rcheck/tests/runTests.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 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
> BiocGenerics:::testPackage("coMET")
RUNIT TEST PROTOCOL -- Tue Feb 28 00:19:08 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
19.949 0.663 20.596
coMET.Rcheck/coMET-Ex.timings
| name | user | system | elapsed | |
| COSMIC_UCSC | 2.251 | 0.068 | 2.319 | |
| ChIPTF_ENCODE | 1.015 | 0.036 | 1.051 | |
| ClinVarCnv_UCSC | 0.567 | 0.020 | 0.588 | |
| ClinVarMain_UCSC | 0.594 | 0.004 | 0.598 | |
| CoreillCNV_UCSC | 0.608 | 0.004 | 0.612 | |
| DNAse_UCSC | 0 | 0 | 0 | |
| DNaseI_FANTOM | 0.846 | 0.008 | 0.854 | |
| DNaseI_RoadMap | 0.234 | 0.016 | 0.251 | |
| GAD_UCSC | 0.622 | 0.004 | 0.626 | |
| GWAScatalog_UCSC | 0.471 | 0.004 | 0.475 | |
| GeneReviews_UCSC | 0.755 | 0.000 | 0.755 | |
| HiCdata2matrix | 0.032 | 0.000 | 0.033 | |
| HistoneAll_UCSC | 5.998 | 0.116 | 6.115 | |
| HistoneOne_UCSC | 0.513 | 0.044 | 0.557 | |
| ISCA_UCSC | 0.600 | 0.048 | 0.649 | |
| TFBS_FANTOM | 0.606 | 0.024 | 0.630 | |
| bindingMotifsBiomart_ENSEMBL | 0.211 | 0.032 | 0.243 | |
| chrUCSC2ENSEMBL | 0.001 | 0.000 | 0.000 | |
| chromHMM_RoadMap | 0.936 | 0.032 | 0.967 | |
| chromatinHMMAll_UCSC | 6.374 | 0.288 | 6.662 | |
| chromatinHMMOne_UCSC | 0.699 | 0.052 | 0.751 | |
| coMET-package | 7.578 | 0.540 | 17.618 | |
| col2HSV | 0 | 0 | 0 | |
| comet | 4.226 | 0.220 | 4.446 | |
| comet.list | 1.10 | 0.04 | 1.14 | |
| comet.web | 8.153 | 0.341 | 30.488 | |
| complementary | 0.032 | 0.000 | 0.031 | |
| cpgIslands_UCSC | 0.197 | 0.000 | 0.198 | |
| dgfootprints_RoadMap | 1.113 | 0.020 | 1.133 | |
| eQTL | 3.275 | 0.148 | 3.423 | |
| eQTL_GTEx | 1.752 | 0.060 | 1.812 | |
| gcContent_UCSC | 1.448 | 0.020 | 1.467 | |
| genesName_ENSEMBL | 0.003 | 0.000 | 0.003 | |
| genes_ENSEMBL | 1.144 | 0.008 | 1.152 | |
| imprintedGenes_GTEx | 5.142 | 0.100 | 5.243 | |
| interestGenes_ENSEMBL | 1.055 | 0.016 | 1.070 | |
| interestTranscript_ENSEMBL | 1.127 | 0.016 | 1.142 | |
| knownGenes_UCSC | 1.367 | 0.016 | 1.383 | |
| metQTL | 1.773 | 0.012 | 1.785 | |
| miRNATargetRegionsBiomart_ENSEMBL | 0.063 | 0.004 | 0.067 | |
| otherRegulatoryRegionsBiomart_ENSEMBL | 0.136 | 0.000 | 0.136 | |
| pizza | 0.009 | 0.000 | 0.009 | |
| psiQTL_GTEx | 1.551 | 0.008 | 1.559 | |
| refGenes_UCSC | 1.257 | 0.000 | 1.257 | |
| regulationBiomart_ENSEMBL | 0.491 | 0.000 | 0.491 | |
| regulatoryEvidenceBiomart_ENSEMBL | 0.193 | 0.004 | 0.196 | |
| regulatoryFeaturesBiomart_ENSEMBL | 0.189 | 0.008 | 0.197 | |
| regulatorySegmentsBiomart_ENSEMBL | 0.187 | 0.012 | 0.199 | |
| repeatMasker_UCSC | 0.727 | 0.020 | 0.747 | |
| segmentalDups_UCSC | 0.569 | 0.000 | 0.569 | |
| setColors | 0.001 | 0.000 | 0.001 | |
| snpBiomart_ENSEMBL | 0.639 | 0.008 | 0.647 | |
| snpLocations_UCSC | 1.662 | 0.044 | 1.706 | |
| structureBiomart_ENSEMBL | 0.588 | 0.012 | 0.599 | |
| transcript_ENSEMBL | 1.844 | 0.020 | 1.864 | |
| xenorefGenes_UCSC | 0.899 | 0.004 | 0.904 | |