Tiphaine Martin
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/coMET |
| Branch: RELEASE_3_11 |
| Last Commit: ed93a9c |
| Last Changed Date: 2020-04-27 14:46:05 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:21 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE coMET PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 353/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| coMET 1.20.0 Tiphaine Martin
| malbec2 | Linux (Ubuntu 18.04.4 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: 1.20.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:coMET.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings coMET_1.20.0.tar.gz |
| StartedAt: 2020-10-17 02:50:30 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 03:06:46 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 976.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: coMET.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:coMET.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings coMET_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/coMET.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'coMET/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'coMET' version '1.20.0'
* 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 whether package 'coMET' can be installed ... OK
* checking installed package size ... NOTE
installed size is 19.4Mb
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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
comet.web 15.98 0.23 61.64
coMET-package 6.30 0.39 18.91
imprintedGenes_GTEx 4.82 0.06 5.09
COSMIC_UCSC 1.96 0.11 9.03
ChIPTF_ENCODE 0.88 0.25 7.53
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
comet.web 18.70 0.14 62.58
coMET-package 6.05 0.05 18.42
HistoneAll_UCSC 5.60 0.00 5.60
imprintedGenes_GTEx 5.42 0.05 5.47
comet 5.33 0.06 5.39
chromatinHMMAll_UCSC 5.13 0.00 5.12
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.11-bioc/meat/coMET.Rcheck/00check.log'
for details.
coMET.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/coMET_1.20.0.tar.gz && rm -rf coMET.buildbin-libdir && mkdir coMET.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=coMET.buildbin-libdir coMET_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL coMET_1.20.0.zip && rm coMET_1.20.0.tar.gz coMET_1.20.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 12.6M 100 12.6M 0 0 36.9M 0 --:--:-- --:--:-- --:--:-- 37.5M
install for i386
* installing *source* package 'coMET' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'coMET'
finding HTML links ... done
COSMIC_UCSC html
ChIPTF_ENCODE html
ClinVarCnv_UCSC html
ClinVarMain_UCSC html
CoreillCNV_UCSC html
DNAse_UCSC html
DNaseI_FANTOM html
DNaseI_RoadMap html
GAD_UCSC html
GWAScatalog_UCSC html
GeneReviews_UCSC html
HiCdata2matrix html
HistoneAll_UCSC html
HistoneOne_UCSC html
ISCA_UCSC html
TFBS_FANTOM html
bindingMotifsBiomart_ENSEMBL html
check.configVar html
check.configVar.cometlist html
check.format.mydata html
chrUCSC2ENSEMBL html
chromHMM_RoadMap html
chromatinHMMAll_UCSC html
chromatinHMMOne_UCSC html
coMET-package html
comet html
comet.list html
comet.web html
compute.cormatrix html
cpgIslands_UCSC html
cpgPvalue html
create.color.bar html
create.color.list html
create.color.list.large html
create.symbol.list html
create.symbol.list.large html
create.tracks.user html
create.tracks.web html
createList.trackUser html
datasets html
dgfootprints_RoadMap html
draw.legend html
draw.name.genes.web html
draw.name.tracks.web html
draw.plot.annotation html
draw.plot.axis.data html
draw.plot.comet html
draw.plot.comet.nopval html
draw.plot.comet.web html
draw.plot.cormatrix.plot html
draw.plot.grid.mydata html
draw.plot.grid.mydata.large html
draw.plot.grid.mydata.names html
draw.plot.grid.setup html
draw.plot.linesconnection html
draw.plot.mydata.ggbio html
eQTL html
eQTL_GTEx html
fix.values html
fix.values.generic html
fix.values.large html
gcContent_UCSC html
genesName_ENSEMBL html
genes_ENSEMBL html
imprintedGenes_GTEx html
interestGenes_ENSEMBL html
interestTranscript_ENSEMBL html
knownGenes_UCSC html
metQTL html
miRNATargetRegionsBiomart_ENSEMBL html
otherRegulatoryRegionsBiomart_ENSEMBL html
printPlot.comet html
printPlot.comet.nopval html
printPlot.comet.web html
psiQTL_GTEx html
read.config html
read.file.cormatrix html
read.file.mydata html
read.file.mydata.large html
refGenes_UCSC html
regulationBiomart_ENSEMBL html
regulatoryEvidenceBiomart_ENSEMBL html
regulatoryFeaturesBiomart_ENSEMBL html
regulatorySegmentsBiomart_ENSEMBL html
repeatMasker_UCSC html
retrieve.data html
segmentalDups_UCSC html
set.image.parameters html
snpBiomart_ENSEMBL html
snpLocations_UCSC html
structureBiomart_ENSEMBL html
transcript_ENSEMBL html
xenorefGenes_UCSC html
** 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
install for x64
* installing *source* package 'coMET' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'coMET' as coMET_1.20.0.zip
* DONE (coMET)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'coMET' successfully unpacked and MD5 sums checked
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coMET.Rcheck/tests_i386/runTests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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 -- Sat Oct 17 03:06:15 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
13.26 1.28 17.73
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coMET.Rcheck/tests_x64/runTests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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 -- Sat Oct 17 03:06:35 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
14.54 0.57 18.82
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coMET.Rcheck/examples_i386/coMET-Ex.timings
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coMET.Rcheck/examples_x64/coMET-Ex.timings
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