Kamal Kishore
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/compEpiTools |
| Branch: RELEASE_3_10 |
| Last Commit: 10eba89 |
| Last Changed Date: 2019-10-29 13:09:03 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:23:29 -0400 (Wed, 15 Apr 2020).
| Package 346/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| compEpiTools 1.20.0 Kamal Kishore
| 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: compEpiTools |
| Version: 1.20.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:compEpiTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings compEpiTools_1.20.0.tar.gz |
| StartedAt: 2020-04-15 02:16:33 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 02:27:32 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 659.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: compEpiTools.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:compEpiTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings compEpiTools_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/compEpiTools.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'compEpiTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'compEpiTools' 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 'compEpiTools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* 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
TSS: no visible global function definition for 'end<-'
TSS: no visible global function definition for 'start<-'
findLncRNA: no visible global function definition for 'start<-'
findLncRNA: no visible global function definition for 'end<-'
findLncRNA: no visible global function definition for 'IRanges'
stallingIndex : getBound: no visible global function definition for
'start<-'
stallingIndex : getBound: no visible global function definition for
'end<-'
stallingIndex: no visible global function definition for 'IRanges'
topGOres : <anonymous>: no visible global function definition for
'ggplot'
topGOres : <anonymous>: no visible global function definition for 'aes'
topGOres : <anonymous>: no visible binding for global variable
'Significant'
topGOres : <anonymous>: no visible binding for global variable 'P_val'
topGOres : <anonymous>: no visible global function definition for
'geom_bar'
topGOres : <anonymous>: no visible global function definition for
'coord_flip'
topGOres : <anonymous>: no visible global function definition for
'ylab'
ucsc2GRanges: no visible global function definition for 'IRanges'
GR2fasta,GRanges: no visible global function definition for
'seqlengths'
GR2fasta,GRanges: no visible global function definition for
'seqlengths<-'
GR2fasta,GRanges: no visible global function definition for 'trim'
GRangesInPromoters,GRanges: no visible global function definition for
'start<-'
GRannotate,GRanges: no visible global function definition for 'start<-'
GRannotate,GRanges: no visible global function definition for 'end<-'
GRcoverageSummit,GRanges: no visible global function definition for
'start<-'
GRcoverageSummit,GRanges: no visible global function definition for
'end<-'
GRmidpoint,GRanges: no visible global function definition for 'start<-'
GRmidpoint,GRanges: no visible global function definition for 'end<-'
GRsetwidth,GRanges: no visible global function definition for 'start<-'
GRsetwidth,GRanges: no visible global function definition for 'end<-'
countOverlapsInBins,GRanges: no visible global function definition for
'IRanges'
featuresLength,TxDb: no visible global function definition for 'reduce'
getPromoterClass,TxDb: no visible binding for global variable 'txdb'
getPromoterClass,TxDb: no visible global function definition for
'start<-'
getPromoterClass,TxDb: no visible global function definition for
'stopCluster'
makeGtfFromDb,TxDb: no visible global function definition for 'reduce'
matchEnhancers,GRanges: no visible global function definition for
'distanceToNearest'
matchEnhancers,GRanges: no visible global function definition for
'IRanges'
Undefined global functions or variables:
IRanges P_val Significant aes coord_flip distanceToNearest end<-
geom_bar ggplot reduce seqlengths seqlengths<- start<- stopCluster
trim txdb ylab
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
topGOres 35.97 0.06 36.04
makeGtfFromDb 6.91 0.14 7.07
simplifyGOterms 1.03 0.12 7.50
getPromoterClass-methods 0.72 0.03 19.30
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
topGOres 42.76 0.20 43.05
makeGtfFromDb 5.75 0.17 5.92
getPromoterClass-methods 1.14 0.05 20.96
* 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: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/compEpiTools.Rcheck/00check.log'
for details.
compEpiTools.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/compEpiTools_1.20.0.tar.gz && rm -rf compEpiTools.buildbin-libdir && mkdir compEpiTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=compEpiTools.buildbin-libdir compEpiTools_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL compEpiTools_1.20.0.zip && rm compEpiTools_1.20.0.tar.gz compEpiTools_1.20.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2066k 100 2066k 0 0 18.6M 0 --:--:-- --:--:-- --:--:-- 19.4M
install for i386
* installing *source* package 'compEpiTools' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
converting help for package 'compEpiTools'
finding HTML links ... done
GR2fasta-methods html
GRanges2ucsc-methods html
GRangesInPromoters-methods html
GRannotate-methods html
GRannotateSimple html
GRbaseCoverage-methods html
GRcoverage-methods html
GRcoverageSummit-methods html
GRenrichment-methods html
GRmidpoint-methods html
GRsetwidth html
TSS html
compEpiTools-package html
countOverlapsInBins-methods html
distanceFromTSS-methods html
enhancers html
findLncRNA html
getPromoterClass-methods html
finding level-2 HTML links ... done
heatmapData html
heatmapPlot html
makeGtfFromDb html
matchEnhancers html
overlapOfGRanges-methods html
palette2d html
plotStallingIndex html
simplifyGOterms html
stallingIndex html
topGOres html
ucsc2GRanges html
unionMaxScore-methods html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package can be loaded from final location
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'compEpiTools' ...
** testing if installed package can be loaded
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'compEpiTools' as compEpiTools_1.20.0.zip
* DONE (compEpiTools)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'compEpiTools' successfully unpacked and MD5 sums checked
|
compEpiTools.Rcheck/examples_i386/compEpiTools-Ex.timings
|
compEpiTools.Rcheck/examples_x64/compEpiTools-Ex.timings
|