Tiphaine Martin
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/coMET |
| Branch: RELEASE_3_6 |
| Last Commit: 0162ac1 |
| Last Changed Date: 2017-11-21 11:08:39 -0400 (Tue, 21 Nov 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:13:07 -0400 (Thu, 12 Apr 2018).
| Package 278/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| coMET 1.10.2 Tiphaine Martin
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: coMET |
| Version: 1.10.2 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings coMET_1.10.2.tar.gz |
| StartedAt: 2018-04-11 22:28:25 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:36:53 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 508.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: coMET.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings coMET_1.10.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/coMET.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 ‘1.10.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘grid’ ‘biomaRt’ ‘Gviz’ ‘psych’ ‘ggbio’ ‘trackViewer’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 28.0Mb
sub-directories of 1Mb or more:
data 9.7Mb
doc 7.1Mb
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 loading without being on the library search path ... 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
chromHMM_RoadMap: no visible binding for global variable
'chromosome_stop'
chromHMM_RoadMap: no visible binding for global variable
'chromosome_start'
chromHMM_RoadMap: no visible binding for global variable
'chromosome_name'
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 pos_middle_exon pos_snp snp_chrom
snp_pos
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
comet.web 11.832 0.148 90.657
coMET-package 5.940 0.072 39.367
* 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
‘/home/biocbuild/bbs-3.6-bioc/meat/coMET.Rcheck/00check.log’
for details.
coMET.Rcheck/00install.out
* installing *source* package ‘coMET’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (coMET)
coMET.Rcheck/tests/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-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
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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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
Loading required package: ggbio
Loading required package: ggplot2
Attaching package: 'ggplot2'
The following objects are masked from 'package:psych':
%+%, alpha
Need specific help about ggbio? try mailing
the maintainer or visit http://tengfei.github.com/ggbio/
Attaching package: 'ggbio'
The following objects are masked from 'package:ggplot2':
geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
xlim
The following object is masked from 'package:psych':
rescale
Loading required package: trackViewer
[1] TRUE
> BiocGenerics:::testPackage("coMET")
RUNIT TEST PROTOCOL -- Wed Apr 11 22:36:48 2018
***********************************************
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
13.208 0.244 14.130
coMET.Rcheck/coMET-Ex.timings
| name | user | system | elapsed | |
| COSMIC_UCSC | 1.772 | 0.004 | 1.779 | |
| ChIPTF_ENCODE | 0.460 | 0.000 | 0.461 | |
| ClinVarCnv_UCSC | 0.788 | 0.000 | 0.791 | |
| ClinVarMain_UCSC | 0.328 | 0.000 | 0.330 | |
| CoreillCNV_UCSC | 0.356 | 0.000 | 0.358 | |
| DNAse_UCSC | 0.428 | 0.000 | 0.429 | |
| DNaseI_FANTOM | 0.624 | 0.004 | 0.630 | |
| DNaseI_RoadMap | 0.284 | 0.000 | 0.286 | |
| GAD_UCSC | 0.296 | 0.000 | 0.294 | |
| GWAScatalog_UCSC | 0.244 | 0.000 | 0.243 | |
| GeneReviews_UCSC | 0.512 | 0.000 | 0.513 | |
| HiCdata2matrix | 0.028 | 0.004 | 0.069 | |
| HistoneAll_UCSC | 3.012 | 0.000 | 3.015 | |
| HistoneOne_UCSC | 0.276 | 0.000 | 0.274 | |
| ISCA_UCSC | 0.000 | 0.000 | 0.001 | |
| TFBS_FANTOM | 0.256 | 0.004 | 0.258 | |
| bindingMotifsBiomart_ENSEMBL | 0.196 | 0.004 | 0.201 | |
| chrUCSC2ENSEMBL | 0 | 0 | 0 | |
| chromHMM_RoadMap | 0.880 | 0.000 | 0.886 | |
| chromatinHMMAll_UCSC | 3.492 | 0.000 | 3.496 | |
| chromatinHMMOne_UCSC | 0.608 | 0.004 | 0.610 | |
| coMET-package | 5.940 | 0.072 | 39.367 | |
| comet | 4.040 | 0.004 | 4.046 | |
| comet.list | 0.916 | 0.000 | 0.916 | |
| comet.web | 11.832 | 0.148 | 90.657 | |
| cpgIslands_UCSC | 0.208 | 0.000 | 0.209 | |
| dgfootprints_RoadMap | 0.588 | 0.012 | 0.601 | |
| eQTL | 0.976 | 0.000 | 0.978 | |
| eQTL_GTEx | 1.056 | 0.000 | 1.057 | |
| gcContent_UCSC | 0.292 | 0.000 | 0.291 | |
| genesName_ENSEMBL | 0.004 | 0.000 | 0.004 | |
| genes_ENSEMBL | 0.66 | 0.00 | 0.66 | |
| imprintedGenes_GTEx | 3.144 | 0.012 | 3.424 | |
| interestGenes_ENSEMBL | 0.548 | 0.000 | 0.546 | |
| interestTranscript_ENSEMBL | 0.660 | 0.004 | 0.666 | |
| knownGenes_UCSC | 0.784 | 0.000 | 0.784 | |
| metQTL | 0.896 | 0.004 | 0.899 | |
| miRNATargetRegionsBiomart_ENSEMBL | 0.112 | 0.000 | 0.110 | |
| otherRegulatoryRegionsBiomart_ENSEMBL | 0.132 | 0.000 | 0.132 | |
| psiQTL_GTEx | 0.868 | 0.004 | 0.871 | |
| refGenes_UCSC | 0.764 | 0.000 | 0.765 | |
| regulationBiomart_ENSEMBL | 0.252 | 0.000 | 0.254 | |
| regulatoryEvidenceBiomart_ENSEMBL | 0.192 | 0.000 | 0.190 | |
| regulatoryFeaturesBiomart_ENSEMBL | 0.216 | 0.000 | 0.216 | |
| regulatorySegmentsBiomart_ENSEMBL | 0.248 | 0.004 | 0.252 | |
| repeatMasker_UCSC | 0.532 | 0.000 | 0.530 | |
| segmentalDups_UCSC | 0.376 | 0.000 | 0.375 | |
| snpBiomart_ENSEMBL | 0.416 | 0.000 | 0.416 | |
| snpLocations_UCSC | 1.096 | 0.000 | 1.101 | |
| structureBiomart_ENSEMBL | 0.460 | 0.000 | 0.465 | |
| transcript_ENSEMBL | 1.400 | 0.020 | 1.422 | |
| xenorefGenes_UCSC | 0.484 | 0.004 | 0.489 | |