Farhad Shokoohi
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/DMCHMM |
| Branch: RELEASE_3_8 |
| Last Commit: 5f583ec |
| Last Changed Date: 2018-10-30 11:42:06 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:28:13 -0400 (Sat, 13 Apr 2019).
| Package 419/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DMCHMM 1.4.0 Farhad Shokoohi
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: DMCHMM |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DMCHMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DMCHMM_1.4.0.tar.gz |
| StartedAt: 2019-04-13 01:50:58 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 02:03:49 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 770.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: DMCHMM.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DMCHMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DMCHMM_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DMCHMM.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DMCHMM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DMCHMM' version '1.4.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
NOTE
Depends: includes the non-default packages:
'SummarizedExperiment' 'S4Vectors' 'BiocParallel' 'GenomicRanges'
'IRanges' 'fdrtool'
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 whether package 'DMCHMM' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'DMCHMM'
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DMCHMM.Rcheck/00install.out' for details.
* 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
.findDMCs : .mfun3: no visible binding for global variable 'Weights'
findDMCs,BSDMCs : .mfun3: no visible binding for global variable
'Weights'
Undefined global functions or variables:
Weights
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'methVars' 'methVars<-'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
manhattanDMCs-method 55.16 0.17 55.33
findDMCs-method 54.81 0.16 54.96
qqDMCs-method 46.43 0.03 46.45
methHMMCMC-method 45.82 0.05 45.87
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
qqDMCs-method 66.88 0.04 66.92
findDMCs-method 65.22 0.05 65.26
methHMMCMC-method 64.88 0.06 64.97
manhattanDMCs-method 61.36 0.06 61.42
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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: 2 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/DMCHMM.Rcheck/00check.log'
for details.
DMCHMM.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/DMCHMM_1.4.0.tar.gz && rm -rf DMCHMM.buildbin-libdir && mkdir DMCHMM.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DMCHMM.buildbin-libdir DMCHMM_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL DMCHMM_1.4.0.zip && rm DMCHMM_1.4.0.tar.gz DMCHMM_1.4.0.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
100 540k 100 540k 0 0 2313k 0 --:--:-- --:--:-- --:--:-- 2349k
install for i386
* installing *source* package 'DMCHMM' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'DMCHMM'
** help
*** installing help indices
converting help for package 'DMCHMM'
finding HTML links ... done
BSDMCs-class html
BSData-class html
finding level-2 HTML links ... done
DMCHMM-package html
cBSDMCs-method html
cBSData-method html
combine-method html
data html
findDMCs-method html
manhattanDMCs-method html
methHMEM-method html
methHMMCMC-method html
methLevels-method html
methReads-method html
methStates-method html
params html
qqDMCs-method html
readBismark-method html
totalReads-method html
writeBED-method html
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'DMCHMM'
In R CMD INSTALL
install for x64
* installing *source* package 'DMCHMM' ...
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'DMCHMM'
* MD5 sums
packaged installation of 'DMCHMM' as DMCHMM_1.4.0.zip
* DONE (DMCHMM)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'DMCHMM' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
DMCHMM.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> library(testthat)
> library(DMCHMM)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
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, colMeans, colSums, colnames,
dirname, 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
Loading required package: S4Vectors
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: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply
Loading required package: fdrtool
DMCHMM package, Version 1.4.0, Released 2018-09-02
A pipeline for identifying differentially methylated CpG sites
using Hidden Markov Model in bisulfite sequencing data.
BugReports: https://github.com/shokoohi/DMCHMM/issues
Attaching package: 'DMCHMM'
The following object is masked from 'package:Biobase':
combine
The following object is masked from 'package:BiocGenerics':
combine
Warning message:
replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'DMCHMM'
>
> test_check("DMCHMM")
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== testthat results ===========================================================
OK: 2 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
11.78 0.79 12.57
|
DMCHMM.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> library(testthat)
> library(DMCHMM)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
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, colMeans, colSums, colnames,
dirname, 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
Loading required package: S4Vectors
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: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply
Loading required package: fdrtool
DMCHMM package, Version 1.4.0, Released 2018-09-02
A pipeline for identifying differentially methylated CpG sites
using Hidden Markov Model in bisulfite sequencing data.
BugReports: https://github.com/shokoohi/DMCHMM/issues
Attaching package: 'DMCHMM'
The following object is masked from 'package:Biobase':
combine
The following object is masked from 'package:BiocGenerics':
combine
Warning message:
replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'DMCHMM'
>
> test_check("DMCHMM")
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|========= | 12%
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|================== | 25%
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|========================== | 38%
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|=================================== | 50%
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|============================================ | 62%
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|==================================================== | 75%
|
|============================================================= | 88%
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|======================================================================| 100%
== testthat results ===========================================================
OK: 2 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
12.28 0.40 12.67
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DMCHMM.Rcheck/examples_i386/DMCHMM-Ex.timings
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DMCHMM.Rcheck/examples_x64/DMCHMM-Ex.timings
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