Tiphaine Martin
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/coMET |
| git_branch: RELEASE_3_13 |
| git_last_commit: fb8047d |
| git_last_commit_date: 2021-05-19 12:10:24 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:32 -0400 (Fri, 15 Oct 2021).
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 366/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| coMET 1.24.0 (landing page) Tiphaine Martin
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: coMET |
| Version: 1.24.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:coMET.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings coMET_1.24.0.tar.gz |
| StartedAt: 2021-10-14 17:40:57 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 17:51:10 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 612.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: coMET.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:coMET.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings coMET_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/coMET.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘coMET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coMET’ version ‘1.24.0’
* 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 ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 19.2Mb
sub-directories of 1Mb or more:
data 7.9Mb
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'
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 pos_middle_exon pos_snp
snp_chrom snp_pos trackList viewTracks
Consider adding
importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* 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 13.733 0.187 39.132
coMET-package 8.425 0.167 13.148
chromatinHMMAll_UCSC 8.189 0.022 8.217
HistoneAll_UCSC 7.616 0.016 7.637
imprintedGenes_GTEx 7.028 0.029 7.062
* 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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.13-bioc/meat/coMET.Rcheck/00check.log’
for details.
coMET.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL coMET ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, 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:IRanges':
reflect
[1] TRUE
> BiocGenerics:::testPackage("coMET")
RUNIT TEST PROTOCOL -- Thu Oct 14 17:51:00 2021
***********************************************
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
19.279 0.811 20.081
coMET.Rcheck/coMET-Ex.timings
| name | user | system | elapsed | |
| COSMIC_UCSC | 2.382 | 0.076 | 2.460 | |
| ChIPTF_ENCODE | 1.164 | 0.037 | 1.204 | |
| ClinVarCnv_UCSC | 0.810 | 0.082 | 0.893 | |
| ClinVarMain_UCSC | 0.855 | 0.010 | 0.866 | |
| CoreillCNV_UCSC | 0.659 | 0.004 | 0.663 | |
| DNAse_UCSC | 0.780 | 0.005 | 0.786 | |
| DNaseI_FANTOM | 0.818 | 0.008 | 0.827 | |
| DNaseI_RoadMap | 0.328 | 0.004 | 0.333 | |
| GAD_UCSC | 0.741 | 0.005 | 0.746 | |
| GWAScatalog_UCSC | 0.596 | 0.004 | 0.600 | |
| GeneReviews_UCSC | 1.112 | 0.005 | 1.118 | |
| HiCdata2matrix | 0.036 | 0.005 | 0.041 | |
| HistoneAll_UCSC | 7.616 | 0.016 | 7.637 | |
| HistoneOne_UCSC | 0.684 | 0.005 | 0.690 | |
| ISCA_UCSC | 0.833 | 0.007 | 0.841 | |
| TFBS_FANTOM | 0.573 | 0.004 | 0.577 | |
| bindingMotifsBiomart_ENSEMBL | 0.219 | 0.008 | 0.228 | |
| chrUCSC2ENSEMBL | 0.001 | 0.001 | 0.001 | |
| chromHMM_RoadMap | 1.083 | 0.011 | 1.096 | |
| chromatinHMMAll_UCSC | 8.189 | 0.022 | 8.217 | |
| chromatinHMMOne_UCSC | 1.191 | 0.007 | 1.199 | |
| coMET-package | 8.425 | 0.167 | 13.148 | |
| comet | 4.946 | 0.051 | 4.999 | |
| comet.list | 1.354 | 0.014 | 1.368 | |
| comet.web | 13.733 | 0.187 | 39.132 | |
| cpgIslands_UCSC | 0.205 | 0.003 | 0.207 | |
| dgfootprints_RoadMap | 0.898 | 0.010 | 0.909 | |
| eQTL | 2.293 | 0.013 | 2.308 | |
| eQTL_GTEx | 1.806 | 0.007 | 1.814 | |
| gcContent_UCSC | 1.498 | 0.013 | 1.514 | |
| genesName_ENSEMBL | 0.003 | 0.002 | 0.005 | |
| genes_ENSEMBL | 1.398 | 0.004 | 1.403 | |
| imprintedGenes_GTEx | 7.028 | 0.029 | 7.062 | |
| interestGenes_ENSEMBL | 1.245 | 0.005 | 1.251 | |
| interestTranscript_ENSEMBL | 1.481 | 0.004 | 1.486 | |
| knownGenes_UCSC | 1.660 | 0.005 | 1.665 | |
| metQTL | 1.988 | 0.046 | 2.037 | |
| miRNATargetRegionsBiomart_ENSEMBL | 0.088 | 0.004 | 0.092 | |
| otherRegulatoryRegionsBiomart_ENSEMBL | 0.141 | 0.006 | 0.148 | |
| psiQTL_GTEx | 1.870 | 0.023 | 1.893 | |
| refGenes_UCSC | 1.618 | 0.006 | 1.624 | |
| regulationBiomart_ENSEMBL | 0.570 | 0.003 | 0.573 | |
| regulatoryEvidenceBiomart_ENSEMBL | 0.241 | 0.010 | 0.252 | |
| regulatoryFeaturesBiomart_ENSEMBL | 0.225 | 0.010 | 0.235 | |
| regulatorySegmentsBiomart_ENSEMBL | 0.235 | 0.009 | 0.244 | |
| repeatMasker_UCSC | 1.018 | 0.003 | 1.022 | |
| segmentalDups_UCSC | 0.822 | 0.004 | 0.828 | |
| snpBiomart_ENSEMBL | 0.911 | 0.004 | 0.917 | |
| snpLocations_UCSC | 2.095 | 0.006 | 2.103 | |
| structureBiomart_ENSEMBL | 0.814 | 0.003 | 0.817 | |
| transcript_ENSEMBL | 2.810 | 0.007 | 2.818 | |
| xenorefGenes_UCSC | 1.230 | 0.005 | 1.236 | |