| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:28 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 397/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| coMET 1.33.0 (landing page) Tiphaine Martin
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: coMET |
| Version: 1.33.0 |
| 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/site-library --timings coMET_1.33.0.tar.gz |
| StartedAt: 2023-05-09 12:21:30 -0000 (Tue, 09 May 2023) |
| EndedAt: 2023-05-09 12:34:23 -0000 (Tue, 09 May 2023) |
| EllapsedTime: 773.0 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/site-library --timings coMET_1.33.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/coMET.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* 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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘coMET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coMET’ version ‘1.33.0’
* 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 8.548 0.744 39.875
coMET-package 7.478 1.103 17.471
HistoneAll_UCSC 5.650 0.092 5.742
chromatinHMMAll_UCSC 5.683 0.044 5.727
imprintedGenes_GTEx 5.167 0.072 5.239
* 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-devel_2023-03-12_r83975-bin/site-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) (2023-03-12 r83975) -- "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 May 9 12:31:39 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
20.008 1.188 21.179
coMET.Rcheck/coMET-Ex.timings
| name | user | system | elapsed | |
| COSMIC_UCSC | 2.468 | 0.092 | 2.560 | |
| ChIPTF_ENCODE | 0.984 | 0.020 | 1.004 | |
| ClinVarCnv_UCSC | 0.546 | 0.064 | 0.611 | |
| ClinVarMain_UCSC | 0.575 | 0.048 | 0.624 | |
| CoreillCNV_UCSC | 0.547 | 0.000 | 0.547 | |
| DNAse_UCSC | 0.000 | 0.000 | 0.001 | |
| DNaseI_FANTOM | 0.808 | 0.004 | 0.812 | |
| DNaseI_RoadMap | 0.241 | 0.008 | 0.249 | |
| GAD_UCSC | 0.580 | 0.008 | 0.587 | |
| GWAScatalog_UCSC | 0.447 | 0.000 | 0.447 | |
| GeneReviews_UCSC | 0.701 | 0.008 | 0.709 | |
| HiCdata2matrix | 0.033 | 0.000 | 0.033 | |
| HistoneAll_UCSC | 5.650 | 0.092 | 5.742 | |
| HistoneOne_UCSC | 0.465 | 0.000 | 0.465 | |
| ISCA_UCSC | 0.559 | 0.003 | 0.563 | |
| TFBS_FANTOM | 0.539 | 0.000 | 0.539 | |
| bindingMotifsBiomart_ENSEMBL | 0.199 | 0.004 | 0.202 | |
| chrUCSC2ENSEMBL | 0 | 0 | 0 | |
| chromHMM_RoadMap | 0.858 | 0.004 | 0.862 | |
| chromatinHMMAll_UCSC | 5.683 | 0.044 | 5.727 | |
| chromatinHMMOne_UCSC | 0.579 | 0.012 | 0.591 | |
| coMET-package | 7.478 | 1.103 | 17.471 | |
| col2HSV | 0.001 | 0.000 | 0.000 | |
| comet | 4.060 | 0.280 | 4.339 | |
| comet.list | 1.068 | 0.016 | 1.085 | |
| comet.web | 8.548 | 0.744 | 39.875 | |
| complementary | 0.030 | 0.004 | 0.034 | |
| cpgIslands_UCSC | 0.219 | 0.016 | 0.234 | |
| dgfootprints_RoadMap | 1.020 | 0.116 | 1.137 | |
| eQTL | 2.073 | 0.020 | 2.092 | |
| eQTL_GTEx | 3.288 | 0.172 | 3.460 | |
| gcContent_UCSC | 1.558 | 0.020 | 1.578 | |
| genesName_ENSEMBL | 0.001 | 0.003 | 0.004 | |
| genes_ENSEMBL | 1.168 | 0.000 | 1.168 | |
| imprintedGenes_GTEx | 5.167 | 0.072 | 5.239 | |
| interestGenes_ENSEMBL | 1.033 | 0.016 | 1.049 | |
| interestTranscript_ENSEMBL | 1.098 | 0.004 | 1.102 | |
| knownGenes_UCSC | 1.296 | 0.003 | 1.299 | |
| metQTL | 1.790 | 0.024 | 1.814 | |
| miRNATargetRegionsBiomart_ENSEMBL | 0.066 | 0.000 | 0.066 | |
| otherRegulatoryRegionsBiomart_ENSEMBL | 0.134 | 0.000 | 0.134 | |
| pizza | 0.009 | 0.000 | 0.009 | |
| psiQTL_GTEx | 1.528 | 0.016 | 1.544 | |
| refGenes_UCSC | 1.267 | 0.044 | 1.311 | |
| regulationBiomart_ENSEMBL | 0.485 | 0.004 | 0.490 | |
| regulatoryEvidenceBiomart_ENSEMBL | 0.197 | 0.004 | 0.200 | |
| regulatoryFeaturesBiomart_ENSEMBL | 0.195 | 0.004 | 0.198 | |
| regulatorySegmentsBiomart_ENSEMBL | 0.203 | 0.012 | 0.215 | |
| repeatMasker_UCSC | 0.757 | 0.052 | 0.810 | |
| segmentalDups_UCSC | 0.626 | 0.000 | 0.627 | |
| setColors | 0.001 | 0.000 | 0.000 | |
| snpBiomart_ENSEMBL | 0.656 | 0.008 | 0.664 | |
| snpLocations_UCSC | 1.731 | 0.012 | 1.744 | |
| structureBiomart_ENSEMBL | 0.589 | 0.012 | 0.600 | |
| transcript_ENSEMBL | 1.869 | 0.000 | 1.869 | |
| xenorefGenes_UCSC | 0.928 | 0.004 | 0.931 | |