Tiphaine Martin
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/coMET |
| Branch: RELEASE_3_10 |
| Last Commit: 9eef045 |
| Last Changed Date: 2019-10-29 13:09:08 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:41:16 -0400 (Wed, 15 Apr 2020).
| Package 342/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| coMET 1.18.0 Tiphaine Martin
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: coMET |
| Version: 1.18.0 |
| 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_1.18.0.tar.gz |
| StartedAt: 2020-04-15 01:23:10 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:32:49 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 578.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: coMET.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/coMET.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.18.0’
* 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 18.8Mb
sub-directories of 1Mb or more:
data 7.5Mb
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 or elapsed time > 5s
user system elapsed
comet.web 8.307 0.128 53.947
chromatinHMMAll_UCSC 6.330 0.027 6.370
HistoneAll_UCSC 6.010 0.014 6.047
coMET-package 5.864 0.064 19.780
imprintedGenes_GTEx 5.160 0.061 5.508
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.10-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/3.6/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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 -- Wed Apr 15 01:32:42 2020
***********************************************
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
16.036 0.792 16.933
coMET.Rcheck/coMET-Ex.timings
| name | user | system | elapsed | |
| COSMIC_UCSC | 2.207 | 0.047 | 2.260 | |
| ChIPTF_ENCODE | 1.375 | 0.112 | 1.488 | |
| ClinVarCnv_UCSC | 0.712 | 0.100 | 0.815 | |
| ClinVarMain_UCSC | 0.643 | 0.024 | 0.671 | |
| CoreillCNV_UCSC | 0.615 | 0.004 | 0.624 | |
| DNAse_UCSC | 0.625 | 0.003 | 0.628 | |
| DNaseI_FANTOM | 0.701 | 0.010 | 0.711 | |
| DNaseI_RoadMap | 0.298 | 0.005 | 0.304 | |
| GAD_UCSC | 0.628 | 0.003 | 0.635 | |
| GWAScatalog_UCSC | 0.513 | 0.003 | 0.516 | |
| GeneReviews_UCSC | 0.977 | 0.006 | 0.987 | |
| HiCdata2matrix | 0.034 | 0.004 | 0.038 | |
| HistoneAll_UCSC | 6.010 | 0.014 | 6.047 | |
| HistoneOne_UCSC | 0.485 | 0.003 | 0.489 | |
| ISCA_UCSC | 0.785 | 0.060 | 0.849 | |
| TFBS_FANTOM | 0.446 | 0.003 | 0.449 | |
| bindingMotifsBiomart_ENSEMBL | 0.258 | 0.010 | 0.269 | |
| chrUCSC2ENSEMBL | 0.001 | 0.000 | 0.000 | |
| chromHMM_RoadMap | 0.953 | 0.038 | 0.996 | |
| chromatinHMMAll_UCSC | 6.330 | 0.027 | 6.370 | |
| chromatinHMMOne_UCSC | 0.786 | 0.004 | 0.790 | |
| coMET-package | 5.864 | 0.064 | 19.780 | |
| comet | 4.262 | 0.040 | 4.324 | |
| comet.list | 1.281 | 0.015 | 1.306 | |
| comet.web | 8.307 | 0.128 | 53.947 | |
| cpgIslands_UCSC | 0.234 | 0.003 | 0.236 | |
| dgfootprints_RoadMap | 1.105 | 0.024 | 1.138 | |
| eQTL | 1.710 | 0.009 | 1.731 | |
| eQTL_GTEx | 1.624 | 0.008 | 1.648 | |
| gcContent_UCSC | 1.366 | 0.052 | 1.423 | |
| genesName_ENSEMBL | 0.004 | 0.002 | 0.004 | |
| genes_ENSEMBL | 1.122 | 0.016 | 1.149 | |
| imprintedGenes_GTEx | 5.160 | 0.061 | 5.508 | |
| interestGenes_ENSEMBL | 0.969 | 0.008 | 0.983 | |
| interestTranscript_ENSEMBL | 1.089 | 0.008 | 1.105 | |
| knownGenes_UCSC | 1.331 | 0.004 | 1.350 | |
| metQTL | 1.540 | 0.010 | 1.574 | |
| miRNATargetRegionsBiomart_ENSEMBL | 0.091 | 0.003 | 0.097 | |
| otherRegulatoryRegionsBiomart_ENSEMBL | 0.183 | 0.009 | 0.193 | |
| psiQTL_GTEx | 1.444 | 0.006 | 1.470 | |
| refGenes_UCSC | 1.165 | 0.004 | 1.180 | |
| regulationBiomart_ENSEMBL | 0.472 | 0.003 | 0.477 | |
| regulatoryEvidenceBiomart_ENSEMBL | 0.267 | 0.007 | 0.278 | |
| regulatoryFeaturesBiomart_ENSEMBL | 0.284 | 0.007 | 0.294 | |
| regulatorySegmentsBiomart_ENSEMBL | 0.286 | 0.007 | 0.300 | |
| repeatMasker_UCSC | 0.804 | 0.003 | 0.818 | |
| segmentalDups_UCSC | 0.610 | 0.002 | 0.621 | |
| snpBiomart_ENSEMBL | 0.703 | 0.003 | 0.711 | |
| snpLocations_UCSC | 1.560 | 0.005 | 1.575 | |
| structureBiomart_ENSEMBL | 0.597 | 0.004 | 0.603 | |
| transcript_ENSEMBL | 2.095 | 0.012 | 2.122 | |
| xenorefGenes_UCSC | 0.791 | 0.003 | 0.803 | |