Package: bsseq

Version: 1.18.0

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_1.18.0.tar.gz

StartedAt: 2019-04-15 22:42:22 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:49:27 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 424.2 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_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/bsseq.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.18.0’
* 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 12.3Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
    libs   4.8Mb
* 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
* 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:
  ‘BiocGenerics:::replaceSlots’ ‘DelayedArray:::.normarg_grid’
  ‘DelayedArray:::get_verbose_block_processing’
  ‘GenomicRanges:::.extract_groups_from_GenomicRanges’
  ‘GenomicRanges:::.get_circle_length’
  ‘GenomicRanges:::extraColumnSlotNames’ ‘HDF5Array:::.create_dir’
  ‘HDF5Array:::.shorten_h5_paths’
  ‘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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/bsseq/libs/bsseq.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘_rand_r’, possibly from ‘rand_r’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
getMeth       11.865  2.386  14.358
getCoverage   10.148  0.481  10.698
BSmooth.tstat  7.693  1.086   8.844
findLoci       5.746  0.567   6.360
* 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-3.8-bioc/meat/bsseq.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL bsseq
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘bsseq’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -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/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -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/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/include" -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 /Library/Frameworks/R.framework/Versions/3.5/Resources/library/beachmat/lib/libbeachmat.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libsz.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/bsseq/libs
** R
** data
*** moving datasets to lazyload DB
** 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
* DONE (bsseq)

R version 3.5.3 (2019-03-11) -- "Great Truth"
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, 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
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

> test_check("bsseq")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 162 SKIPPED: 7 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 71.154  16.895  95.135 

name	user	system	elapsed
BS.chr22	3.100	0.157	3.273
BSmooth	0.001	0.000	0.000
BSmooth.fstat	0.000	0.001	0.000
BSmooth.tstat	7.693	1.086	8.844
BSseq-class	1.362	0.510	1.532
BSseq	0.660	0.124	0.799
FWGRanges-class	0.003	0.001	0.003
computeStat	0	0	0
data.frame2GRanges	0.025	0.004	0.029
dmrFinder	2.579	0.589	3.194
findLoci	5.746	0.567	6.360
fisherTests	0.399	0.007	0.410
getCoverage	10.148	0.481	10.698
getMeth	11.865	2.386	14.358
getStats	0.447	0.147	0.596
goodnessOfFit	2.561	0.542	3.125
hasGRanges-class	0.000	0.001	0.001
read.bismark	0.993	1.095	0.377
read.umtab	0.001	0.002	0.001
smoothSds	0.000	0.001	0.000