Tiphaine Martin
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/coMET |
| Branch: RELEASE_3_9 |
| Last Commit: 3b430a9 |
| Last Changed Date: 2019-05-02 11:53:52 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:54:47 -0400 (Wed, 16 Oct 2019).
| Package 325/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| coMET 1.16.0 Tiphaine Martin
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: coMET |
| Version: 1.16.0 |
| 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_1.16.0.tar.gz |
| StartedAt: 2019-10-16 01:41:07 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:53:27 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 739.7 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_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/coMET.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.16.0’
* 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 : : 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 8.902 0.180 54.949
coMET-package 7.213 0.344 20.310
chromatinHMMAll_UCSC 6.949 0.031 6.983
HistoneAll_UCSC 6.343 0.021 6.367
imprintedGenes_GTEx 5.256 0.093 5.673
comet 4.899 0.115 5.018
* 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-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 Oct 16 01:53:16 2019
***********************************************
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
20.318 1.790 22.059
coMET.Rcheck/coMET-Ex.timings
| name | user | system | elapsed | |
| COSMIC_UCSC | 2.645 | 0.050 | 2.697 | |
| ChIPTF_ENCODE | 1.832 | 0.220 | 2.053 | |
| ClinVarCnv_UCSC | 0.850 | 0.147 | 0.997 | |
| ClinVarMain_UCSC | 0.820 | 0.095 | 0.915 | |
| CoreillCNV_UCSC | 0.614 | 0.007 | 0.621 | |
| DNAse_UCSC | 0.681 | 0.008 | 0.690 | |
| DNaseI_FANTOM | 0.886 | 0.018 | 0.905 | |
| DNaseI_RoadMap | 0.351 | 0.018 | 0.368 | |
| GAD_UCSC | 0.726 | 0.008 | 0.734 | |
| GWAScatalog_UCSC | 0.511 | 0.007 | 0.519 | |
| GeneReviews_UCSC | 0.819 | 0.006 | 0.827 | |
| HiCdata2matrix | 0.036 | 0.005 | 0.041 | |
| HistoneAll_UCSC | 6.343 | 0.021 | 6.367 | |
| HistoneOne_UCSC | 0.539 | 0.008 | 0.547 | |
| ISCA_UCSC | 0.705 | 0.010 | 0.715 | |
| TFBS_FANTOM | 0.555 | 0.005 | 0.560 | |
| bindingMotifsBiomart_ENSEMBL | 0.355 | 0.014 | 0.369 | |
| chrUCSC2ENSEMBL | 0.000 | 0.000 | 0.001 | |
| chromHMM_RoadMap | 0.941 | 0.017 | 0.959 | |
| chromatinHMMAll_UCSC | 6.949 | 0.031 | 6.983 | |
| chromatinHMMOne_UCSC | 1.031 | 0.009 | 1.042 | |
| coMET-package | 7.213 | 0.344 | 20.310 | |
| comet | 4.899 | 0.115 | 5.018 | |
| comet.list | 1.827 | 0.037 | 1.866 | |
| comet.web | 8.902 | 0.180 | 54.949 | |
| cpgIslands_UCSC | 0.288 | 0.006 | 0.296 | |
| dgfootprints_RoadMap | 1.509 | 0.062 | 1.571 | |
| eQTL | 1.730 | 0.016 | 1.748 | |
| eQTL_GTEx | 2.282 | 0.090 | 2.374 | |
| gcContent_UCSC | 1.618 | 0.033 | 1.652 | |
| genesName_ENSEMBL | 0.007 | 0.004 | 0.011 | |
| genes_ENSEMBL | 1.188 | 0.019 | 1.209 | |
| imprintedGenes_GTEx | 5.256 | 0.093 | 5.673 | |
| interestGenes_ENSEMBL | 1.042 | 0.021 | 1.064 | |
| interestTranscript_ENSEMBL | 1.220 | 0.016 | 1.236 | |
| knownGenes_UCSC | 1.435 | 0.008 | 1.445 | |
| metQTL | 1.858 | 0.016 | 1.895 | |
| miRNATargetRegionsBiomart_ENSEMBL | 0.130 | 0.005 | 0.135 | |
| otherRegulatoryRegionsBiomart_ENSEMBL | 0.261 | 0.022 | 0.284 | |
| psiQTL_GTEx | 1.658 | 0.011 | 1.670 | |
| refGenes_UCSC | 1.097 | 0.007 | 1.104 | |
| regulationBiomart_ENSEMBL | 0.533 | 0.006 | 0.538 | |
| regulatoryEvidenceBiomart_ENSEMBL | 0.371 | 0.013 | 0.385 | |
| regulatoryFeaturesBiomart_ENSEMBL | 0.391 | 0.013 | 0.405 | |
| regulatorySegmentsBiomart_ENSEMBL | 0.395 | 0.014 | 0.410 | |
| repeatMasker_UCSC | 0.928 | 0.005 | 0.933 | |
| segmentalDups_UCSC | 0.607 | 0.004 | 0.611 | |
| snpBiomart_ENSEMBL | 0.692 | 0.007 | 0.700 | |
| snpLocations_UCSC | 1.461 | 0.006 | 1.467 | |
| structureBiomart_ENSEMBL | 0.674 | 0.005 | 0.680 | |
| transcript_ENSEMBL | 2.455 | 0.019 | 2.475 | |
| xenorefGenes_UCSC | 0.701 | 0.008 | 0.710 | |