Multiple platform build/check report for BioC 3.9 - CHECK report for bsseq on merida2

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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_1.19.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/bsseq.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.19.3’
* 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 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
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘bsseq-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BSseq-class
> ### Title: Class BSseq
> ### Aliases: BSseq-class [,BSseq-method combine,BSseq,BSseq-method
> ###   combineList length,BSseq-method pData,BSseq-method
> ###   pData<-,BSseq,data.frame-method pData<-,BSseq,DataFrame-method
> ###   sampleNames,BSseq-method sampleNames<-,BSseq,ANY-method
> ###   updateObject,BSseq-method assays,BSseq-method assayNames,BSseq-method
> ###   show,BSseq-method getBSseq collapseBSseq strandCollapse orderBSseq
> ###   chrSelectBSseq hasBeenSmoothed
> ### Keywords: classes
> 
> ### ** Examples
> 
> M <- matrix(1:9, 3,3)
> colnames(M) <- c("A1", "A2", "A3")
> BStest <- BSseq(pos = 1:3, chr = c("chr1", "chr2", "chr1"), M = M, Cov = M + 2)
> chrSelectBSseq(BStest, seqnames = "chr1", order = TRUE)
An object of type 'BSseq' with
  2 methylation loci
  3 samples
has not been smoothed
All assays are in-memory
> collapseBSseq(BStest, group = c("A", "A", "B"))
An object of type 'BSseq' with
  3 methylation loci
  2 samples
has not been smoothed
All assays are in-memory
> 
> #-------------------------------------------------------------------------------
> # An example using a HDF5-backed BSseq object
> #
> hdf5_BStest <- realize(BStest, "HDF5Array")
Loading required package: rhdf5
> chrSelectBSseq(hdf5_BStest, seqnames = "chr1", order = TRUE)
An object of type 'BSseq' with
  2 methylation loci
  3 samples
has not been smoothed
Some assays are HDF5Array-backed
> collapseBSseq(
+     BSseq = hdf5_BStest,
+     group = c("A", "A", "B"),
+     BACKEND = "HDF5Array",
+     type = "integer")
Error in .local(x, group, reorder, na.rm, ...) : 
  unused arguments (BPPARAM = BPPARAM, filepath = h5_path, name = "M", chunkdim = chunkdim, level = level, type = type)
Calls: collapseBSseq -> colsum -> colsum
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
     })
  4: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
         e$call <- cl.i
         stop(e)
     })
  5: tryCatchList(expr, classes, parentenv, handlers)
  6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 159 SKIPPED: 7 FAILED: 1
  1. Error: strandCollapse() works on good input (@test_BSseq-class.R#59) 
  
  Error: testthat unit tests failed
  Execution halted
* 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 ERRORs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/bsseq.Rcheck/00check.log’
for details.

Installation output

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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/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhdf5lib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhdf5lib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhdf5lib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.cpp -o utils.o
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
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
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/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
* DONE (bsseq)

Tests output


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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, 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, rowsum

> test_check("bsseq")
── 1. Error: strandCollapse() works on good input (@test_BSseq-class.R#59)  ────
unused arguments (BPPARAM = BPPARAM, filepath = h5_path, name = "Cov", chunkdim = chunkdim, level = level, type = type)
1: expect_equivalent_SE(SE1 = strandCollapse(bsseq_pos, type = "integer"), SE2 = unstrand(bsseq_pos)) at testthat/test_BSseq-class.R:59
2: stopifnot(is(SE1, "SummarizedExperiment"), is(SE2, "SummarizedExperiment")) at /Users/biocbuild/bbs-3.9-bioc/meat/bsseq.Rcheck/tests/testthat/helper_make_test_data.R:12
3: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), 
       error = function(e) {
           e$call <- cl.i
           stop(e)
       }), warning = function(w) {
       w$call <- cl.i
       w
   })
4: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
       e$call <- cl.i
       stop(e)
   })
5: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: value[[3L]](cond)

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 159 SKIPPED: 7 FAILED: 1
1. Error: strandCollapse() works on good input (@test_BSseq-class.R#59) 

Error: testthat unit tests failed
Execution halted

name	user	system	elapsed
BS.chr22	3.092	0.146	3.251
BSmooth	0.000	0.000	0.001
BSmooth.fstat	0.000	0.001	0.000
BSmooth.tstat	7.687	0.985	8.727

CHECK report for bsseq on merida2

Summary

Command output

Installation output

Tests output

Example timings