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CHECK report for bsseq on celaya2

This page was generated on 2019-10-16 12:50:18 -0400 (Wed, 16 Oct 2019).

Package 191/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bsseq 1.20.0
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)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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###
### Running 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
###
##############################################################################
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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.



Installation output

bsseq.Rcheck/00install.out

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###
### 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)

Tests output

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 

Example timings

bsseq.Rcheck/bsseq-Ex.timings

nameusersystemelapsed
BS.chr223.9810.3254.307
BSmooth0.0010.0010.001
BSmooth.fstat000
BSmooth.tstat 9.978 2.10212.109
BSseq-class5.1831.5756.132
BSseq0.8850.1591.045
FWGRanges-class0.0040.0020.006
computeStat0.0000.0000.001
data.frame2GRanges0.0340.0080.041
dmrFinder1.8780.5482.431
findLoci6.2151.1997.421
fisherTests0.4130.0130.426
getCoverage11.985 0.96012.962
getMeth12.885 4.97217.896
getStats0.5890.2580.846
goodnessOfFit4.2621.2055.486
hasGRanges-class0.0010.0010.003
read.bismark2.3390.1900.575
read.umtab0.0020.0030.001
smoothSds0.0020.0020.001