Kasper Daniel Hansen
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/bsseq |
| Branch: RELEASE_3_6 |
| Last Commit: 9efd7a9 |
| Last Changed Date: 2017-10-30 12:39:45 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:21:55 -0400 (Thu, 12 Apr 2018).
| Package 163/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| bsseq 1.14.0 Kasper Daniel Hansen
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: bsseq |
| Version: 1.14.0 |
| Command: rm -rf bsseq.buildbin-libdir bsseq.Rcheck && mkdir bsseq.buildbin-libdir bsseq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bsseq.buildbin-libdir bsseq_1.14.0.tar.gz >bsseq.Rcheck\00install.out 2>&1 && cp bsseq.Rcheck\00install.out bsseq-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=bsseq.buildbin-libdir --install="check:bsseq-install.out" --force-multiarch --no-vignettes --timings bsseq_1.14.0.tar.gz |
| StartedAt: 2018-04-11 22:37:35 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:44:31 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 416.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: bsseq.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### rm -rf bsseq.buildbin-libdir bsseq.Rcheck && mkdir bsseq.buildbin-libdir bsseq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bsseq.buildbin-libdir bsseq_1.14.0.tar.gz >bsseq.Rcheck\00install.out 2>&1 && cp bsseq.Rcheck\00install.out bsseq-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=bsseq.buildbin-libdir --install="check:bsseq-install.out" --force-multiarch --no-vignettes --timings bsseq_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/bsseq.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bsseq/DESCRIPTION' ... OK
* this is package 'bsseq' version '1.14.0'
* package encoding: UTF-8
* 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 'bsseq' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/BSseq-class.Rd:137: missing file link 'setRealizationBackend'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/BSseq.Rd:34: missing file link 'DelayedMatrix'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/BSseqStat-class.Rd:27: missing file link 'DelayedMatrix'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/BSseqTstat-class.Rd:27: missing file link 'DelayedMatrix'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/fisherTests.Rd:55: missing file link 'mclapply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/read.bismark.Rd:37: missing file link 'setRealizationBackend'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/bsseq.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
data 2.7Mb
doc 1.8Mb
* 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 ... NOTE
Namespace in Imports field not imported from: 'HDF5Array'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
BSmooth.tstat 10.64 1.36 13.16
getMeth 4.10 0.97 5.06
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
BSmooth.tstat 8.44 1.33 9.76
* 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: 1 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/bsseq.Rcheck/00check.log'
for details.
bsseq.Rcheck/00install.out
install for i386
* installing *source* package 'bsseq' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'bsseq'
finding HTML links ... done
BS.chr22 html
BSmooth html
BSmooth.fstat html
BSmooth.tstat html
BSseq-class html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/BSseq-class.Rd:137: missing file link 'setRealizationBackend'
BSseq html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/BSseq.Rd:34: missing file link 'DelayedMatrix'
BSseqStat-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/BSseqStat-class.Rd:27: missing file link 'DelayedMatrix'
BSseqTstat-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/BSseqTstat-class.Rd:27: missing file link 'DelayedMatrix'
computeStat html
data.frame2GRanges html
dmrFinder html
fisherTests html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/fisherTests.Rd:55: missing file link 'mclapply'
getCoverage html
getMeth html
getStats html
goodnessOfFit html
hasGRanges-class html
internals html
plotRegion html
read.bismark html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/read.bismark.Rd:37: missing file link 'setRealizationBackend'
read.bsmooth html
read.umtab html
smoothSds html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'bsseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bsseq' as bsseq_1.14.0.zip
* DONE (bsseq)
In R CMD INSTALL
In R CMD INSTALL
|
bsseq.Rcheck/tests_i386/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("bsseq") || stop("unable to load bsseq")
Loading required package: bsseq
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
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
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
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
[1] TRUE
> BiocGenerics:::testPackage("bsseq")
Loading required package: rhdf5
RUNIT TEST PROTOCOL -- Wed Apr 11 22:43:42 2018
***********************************************
Number of test functions: 19
Number of errors: 0
Number of failures: 0
1 Test Suite :
bsseq RUnit Tests - 19 test functions, 0 errors, 0 failures
Number of test functions: 19
Number of errors: 0
Number of failures: 0
>
>
> proc.time()
user system elapsed
27.65 1.12 45.56
|
bsseq.Rcheck/tests_x64/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-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("bsseq") || stop("unable to load bsseq")
Loading required package: bsseq
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
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
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
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
[1] TRUE
> BiocGenerics:::testPackage("bsseq")
Loading required package: rhdf5
RUNIT TEST PROTOCOL -- Wed Apr 11 22:44:27 2018
***********************************************
Number of test functions: 19
Number of errors: 0
Number of failures: 0
1 Test Suite :
bsseq RUnit Tests - 19 test functions, 0 errors, 0 failures
Number of test functions: 19
Number of errors: 0
Number of failures: 0
>
>
> proc.time()
user system elapsed
37.75 1.03 44.42
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bsseq.Rcheck/examples_i386/bsseq-Ex.timings
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bsseq.Rcheck/examples_x64/bsseq-Ex.timings
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