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CHECK report for bsseq on malbec2

This page was generated on 2019-04-09 11:32:46 -0400 (Tue, 09 Apr 2019).

Package 188/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bsseq 1.19.3
Kasper Daniel Hansen
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/bsseq
Branch: master
Last Commit: d9114c7
Last Changed Date: 2019-01-31 17:38:18 -0400 (Thu, 31 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ ERROR ]
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: bsseq
Version: 1.19.3
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:bsseq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings bsseq_1.19.3.tar.gz
StartedAt: 2019-04-08 23:08:07 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:14:03 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 356.4 seconds
RetCode: 1
Status:  ERROR 
CheckDir: bsseq.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:bsseq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings bsseq_1.19.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/bsseq.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 10.2Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
    libs   2.6Mb
* 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:
  3: is(SE1, "SummarizedExperiment")
  4: strandCollapse(bsseq_pos, type = "integer")
  5: rowsum(x = assay(BSseq, "M", withDimnames = FALSE), group = group, reorder = TRUE, 
         BPPARAM = BPPARAM, filepath = h5_path, name = "Cov", chunkdim = chunkdim, level = level, 
         type = type)
  6: rowsum(x = assay(BSseq, "M", withDimnames = FALSE), group = group, reorder = TRUE, 
         BPPARAM = BPPARAM, filepath = h5_path, name = "Cov", chunkdim = chunkdim, level = level, 
         type = type)
  
  ══ 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/bsseq.Rcheck/00check.log’
for details.


Installation output

bsseq.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL bsseq
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘bsseq’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c check_M_and_Cov.cpp -o check_M_and_Cov.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o bsseq.so check_M_and_Cov.o init.o utils.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
installing to /home/biocbuild/bbs-3.9-bioc/R/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.fail


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 /home/biocbuild/bbs-3.9-bioc/meat/bsseq.Rcheck/tests/testthat/helper_make_test_data.R:12
3: is(SE1, "SummarizedExperiment")
4: strandCollapse(bsseq_pos, type = "integer")
5: rowsum(x = assay(BSseq, "M", withDimnames = FALSE), group = group, reorder = TRUE, 
       BPPARAM = BPPARAM, filepath = h5_path, name = "Cov", chunkdim = chunkdim, level = level, 
       type = type)
6: rowsum(x = assay(BSseq, "M", withDimnames = FALSE), group = group, reorder = TRUE, 
       BPPARAM = BPPARAM, filepath = h5_path, name = "Cov", chunkdim = chunkdim, level = level, 
       type = type)

══ 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

Example timings

bsseq.Rcheck/bsseq-Ex.timings

nameusersystemelapsed
BS.chr223.4590.1083.581
BSmooth000
BSmooth.fstat0.0000.0000.001
BSmooth.tstat 8.244 0.42810.219