Kasper Daniel Hansen
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/bsseq |
| Branch: RELEASE_3_7 |
| Last Commit: 8494740 |
| Last Changed Date: 2018-06-12 23:43:44 -0400 (Tue, 12 Jun 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:36:24 -0400 (Wed, 17 Oct 2018).
| Package 170/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| bsseq 1.16.1 Kasper Daniel Hansen
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: bsseq |
| Version: 1.16.1 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bsseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings bsseq_1.16.1.tar.gz |
| StartedAt: 2018-10-17 00:50:57 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 00:58:52 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 475.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: bsseq.Rcheck |
| Warnings: 2 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bsseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings bsseq_1.16.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/bsseq.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.16.1'
* 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-3.7-bioc/tmpdir/RtmpCaCHJ8/R.INSTALL12b45891282d/bsseq/man/BSseq-class.Rd:137: file link 'setRealizationBackend' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCaCHJ8/R.INSTALL12b45891282d/bsseq/man/BSseq.Rd:34: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCaCHJ8/R.INSTALL12b45891282d/bsseq/man/BSseqStat-class.Rd:27: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCaCHJ8/R.INSTALL12b45891282d/bsseq/man/BSseqTstat-class.Rd:27: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCaCHJ8/R.INSTALL12b45891282d/bsseq/man/fisherTests.Rd:55: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCaCHJ8/R.INSTALL12b45891282d/bsseq/man/read.bismark.Rd:37: file link 'setRealizationBackend' in package 'DelayedArray' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/bsseq.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 8.7Mb
sub-directories of 1Mb or more:
data 7.7Mb
* 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
Unexported objects imported by ':::' calls:
'DelayedArray:::RealizationSink'
'DelayedArray:::get_max_block_length'
'DelayedArray:::get_spacings_for_linear_capped_length_blocks'
See the note in ?`:::` about the use of this operator.
* 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 ... WARNING
Undocumented S4 methods:
generic 'dimnames' and siglist 'arrayRealizationSink'
All user-level objects in a package (including S4 classes and methods)
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 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 or elapsed time > 5s
user system elapsed
getMeth 13.37 1.55 15.05
getCoverage 12.49 0.69 13.20
BSmooth.tstat 7.59 1.22 8.84
BS.chr22 2.64 0.11 11.21
dmrFinder 1.97 0.17 10.74
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getMeth 12.90 1.39 14.29
getCoverage 13.02 0.92 14.00
BSmooth.tstat 7.58 1.04 8.62
read.bismark 0.74 0.26 8.12
* 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: 2 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/bsseq.Rcheck/00check.log'
for details.
bsseq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/bsseq_1.16.1.tar.gz && rm -rf bsseq.buildbin-libdir && mkdir bsseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bsseq.buildbin-libdir bsseq_1.16.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL bsseq_1.16.1.zip && rm bsseq_1.16.1.tar.gz bsseq_1.16.1.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 2283k 100 2283k 0 0 22.4M 0 --:--:-- --:--:-- --:--:-- 24.2M
install for i386
* installing *source* package 'bsseq' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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-3.7-bioc/tmpdir/RtmpCaCHJ8/R.INSTALL12b45891282d/bsseq/man/BSseq-class.Rd:137: file link 'setRealizationBackend' in package 'DelayedArray' does not exist and so has been treated as a topic
BSseq html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCaCHJ8/R.INSTALL12b45891282d/bsseq/man/BSseq.Rd:34: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
BSseqStat-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCaCHJ8/R.INSTALL12b45891282d/bsseq/man/BSseqStat-class.Rd:27: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
BSseqTstat-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCaCHJ8/R.INSTALL12b45891282d/bsseq/man/BSseqTstat-class.Rd:27: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
computeStat html
data.frame2GRanges html
dmrFinder html
fisherTests html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCaCHJ8/R.INSTALL12b45891282d/bsseq/man/fisherTests.Rd:55: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
getCoverage html
getMeth html
getStats html
goodnessOfFit html
hasGRanges-class html
internals html
plotRegion html
read.bismark html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCaCHJ8/R.INSTALL12b45891282d/bsseq/man/read.bismark.Rd:37: file link 'setRealizationBackend' in package 'DelayedArray' does not exist and so has been treated as a topic
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_1.16.1.zip
* DONE (bsseq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'bsseq' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
bsseq.Rcheck/tests_i386/runTests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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, 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: 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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
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
[1] TRUE
> BiocGenerics:::testPackage("bsseq")
Loading required package: rhdf5
RUNIT TEST PROTOCOL -- Wed Oct 17 00:57:49 2018
***********************************************
Number of test functions: 17
Number of errors: 0
Number of failures: 0
1 Test Suite :
bsseq RUnit Tests - 17 test functions, 0 errors, 0 failures
Number of test functions: 17
Number of errors: 0
Number of failures: 0
>
>
> proc.time()
user system elapsed
48.40 2.07 55.51
|
bsseq.Rcheck/tests_x64/runTests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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, 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: 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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
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
[1] TRUE
> BiocGenerics:::testPackage("bsseq")
Loading required package: rhdf5
RUNIT TEST PROTOCOL -- Wed Oct 17 00:58:47 2018
***********************************************
Number of test functions: 17
Number of errors: 0
Number of failures: 0
1 Test Suite :
bsseq RUnit Tests - 17 test functions, 0 errors, 0 failures
Number of test functions: 17
Number of errors: 0
Number of failures: 0
>
>
> proc.time()
user system elapsed
50.25 1.84 56.79
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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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