Kasper Daniel Hansen
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/bsseq |
| Branch: RELEASE_3_9 |
| Last Commit: 07e398b |
| Last Changed Date: 2019-05-02 11:53:37 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:50:18 -0400 (Wed, 16 Oct 2019).
| Package 191/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| bsseq 1.20.0 Kasper Daniel Hansen
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: bsseq |
| Version: 1.20.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bsseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bsseq_1.20.0.tar.gz |
| StartedAt: 2019-10-16 01:03:27 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:13:29 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 601.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: bsseq.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bsseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bsseq_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/bsseq.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bsseq/DESCRIPTION’ ... OK
* this is package ‘bsseq’ version ‘1.20.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘bsseq’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.9Mb
sub-directories of 1Mb or more:
data 6.5Mb
* 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
* 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
Missing object imported by a ':::' call: ‘DelayedArray:::.normarg_grid’
Unexported objects imported by ':::' calls:
‘BiocGenerics:::replaceSlots’
‘DelayedArray:::get_verbose_block_processing’
‘GenomicRanges:::.extract_groups_from_GenomicRanges’
‘GenomicRanges:::.get_circle_length’
‘GenomicRanges:::extraColumnSlotNames’ ‘HDF5Array:::.create_dir’
‘HDF5Array:::.replace_dir’ ‘HDF5Array:::.shorten_assay2h5_links’
‘IRanges:::.shift_ranges_in_groups_to_first_circle’
‘S4Vectors:::make_zero_col_DataFrame’ ‘S4Vectors:::new_DataFrame’
‘S4Vectors:::normalize_names_replacement_value’
‘S4Vectors:::numeric2integer’ ‘S4Vectors:::sapply_isNULL’
‘data.table:::funique’
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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getMeth 12.885 4.972 17.896
getCoverage 11.985 0.960 12.962
BSmooth.tstat 9.978 2.102 12.109
findLoci 6.215 1.199 7.421
BSseq-class 5.183 1.575 6.132
goodnessOfFit 4.262 1.205 5.486
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/bsseq.Rcheck/00check.log’
for details.
bsseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL bsseq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘bsseq’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c check_M_and_Cov.cpp -o check_M_and_Cov.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c init.cpp -o init.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o bsseq.so check_M_and_Cov.o init.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-bsseq/00new/bsseq/libs ** R ** data *** moving datasets to lazyload DB Registered S3 method overwritten by 'R.oo': method from throw.default R.methodsS3 ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (bsseq)
bsseq.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(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, 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
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
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, rowsum
> test_check("bsseq")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 131 | SKIPPED: 7 | WARNINGS: 4 | FAILED: 0 ]
>
> proc.time()
user system elapsed
100.728 26.876 143.120
bsseq.Rcheck/bsseq-Ex.timings
| name | user | system | elapsed | |
| BS.chr22 | 3.981 | 0.325 | 4.307 | |
| BSmooth | 0.001 | 0.001 | 0.001 | |
| BSmooth.fstat | 0 | 0 | 0 | |
| BSmooth.tstat | 9.978 | 2.102 | 12.109 | |
| BSseq-class | 5.183 | 1.575 | 6.132 | |
| BSseq | 0.885 | 0.159 | 1.045 | |
| FWGRanges-class | 0.004 | 0.002 | 0.006 | |
| computeStat | 0.000 | 0.000 | 0.001 | |
| data.frame2GRanges | 0.034 | 0.008 | 0.041 | |
| dmrFinder | 1.878 | 0.548 | 2.431 | |
| findLoci | 6.215 | 1.199 | 7.421 | |
| fisherTests | 0.413 | 0.013 | 0.426 | |
| getCoverage | 11.985 | 0.960 | 12.962 | |
| getMeth | 12.885 | 4.972 | 17.896 | |
| getStats | 0.589 | 0.258 | 0.846 | |
| goodnessOfFit | 4.262 | 1.205 | 5.486 | |
| hasGRanges-class | 0.001 | 0.001 | 0.003 | |
| read.bismark | 2.339 | 0.190 | 0.575 | |
| read.umtab | 0.002 | 0.003 | 0.001 | |
| smoothSds | 0.002 | 0.002 | 0.001 | |