| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:00:52 -0400 (Tue, 09 Apr 2019).
| Package 188/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| bsseq 1.19.3 Kasper Daniel Hansen
| 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 |
| Package: bsseq |
| Version: 1.19.3 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bsseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings bsseq_1.19.3.tar.gz |
| StartedAt: 2019-04-09 01:29:26 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:40:35 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 669.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: bsseq.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bsseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings bsseq_1.19.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/bsseq.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'bsseq' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSmooth.Rd:38: file link 'getHDF5DumpChunkDim' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSmooth.Rd:40: file link 'getHDF5DumpChunkDim' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSmooth.Rd:43: file link 'getHDF5DumpCompressionLevel' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSmooth.Rd:44: file link 'getHDF5DumpCompressionLevel' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSmooth.Rd:67: file link 'getRealizationBackend' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSseq-class.Rd:137: file link 'setRealizationBackend' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSseq.Rd:34: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSseqStat-class.Rd:27: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSseqTstat-class.Rd:27: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/findLoci.Rd:44: file link 'vmatchPattern' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/findLoci.Rd:45: file link 'vmatchPattern' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/findLoci.Rd:55: file link 'vmatchPattern' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/fisherTests.Rd:55: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/read.bismark.Rd:36: file link 'rowRanges' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/read.bismark.Rd:73: file link 'getHDF5DumpChunkDim' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/read.bismark.Rd:75: file link 'getHDF5DumpChunkDim' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/read.bismark.Rd:78: file link 'getHDF5DumpCompressionLevel' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/read.bismark.Rd:79: file link 'getHDF5DumpCompressionLevel' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/read.bismark.Rd:91: file link 'tempdir' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/read.bismark.Rd:177: file link 'getRealizationBackend' in package 'DelayedArray' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/bsseq.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 9.5Mb
sub-directories of 1Mb or more:
data 6.4Mb
libs 1.9Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/bsseq/libs/i386/bsseq.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/bsseq/libs/x64/bsseq.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (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 ...
** running examples for arch 'i386' ... 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
** running examples for arch 'x64' ... 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 tests for arch 'i386' ...
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: 161 SKIPPED: 7 FAILED: 1
1. Error: strandCollapse() works on good input (@test_BSseq-class.R#59)
Error: testthat unit tests failed
Execution halted
** running tests for arch 'x64' ...
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: 161 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: 4 ERRORs, 1 WARNING, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/bsseq.Rcheck/00check.log'
for details.
bsseq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/bsseq_1.19.3.tar.gz && rm -rf bsseq.buildbin-libdir && mkdir bsseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bsseq.buildbin-libdir bsseq_1.19.3.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL bsseq_1.19.3.zip && rm bsseq_1.19.3.tar.gz bsseq_1.19.3.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 2083k 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2083k 100 2083k 0 0 5775k 0 --:--:-- --:--:-- --:--:-- 5870k
install for i386
* installing *source* package 'bsseq' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c check_M_and_Cov.cpp -o check_M_and_Cov.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o bsseq.dll tmp.def check_M_and_Cov.o init.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/bsseq.buildbin-libdir/00LOCK-bsseq/00new/bsseq/libs/i386
** 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
converting help for package 'bsseq'
finding HTML links ... done
BS.chr22 html
BSmooth html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSmooth.Rd:38: file link 'getHDF5DumpChunkDim' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSmooth.Rd:40: file link 'getHDF5DumpChunkDim' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSmooth.Rd:43: file link 'getHDF5DumpCompressionLevel' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSmooth.Rd:44: file link 'getHDF5DumpCompressionLevel' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSmooth.Rd:67: file link 'getRealizationBackend' in package 'DelayedArray' does not exist and so has been treated as a topic
BSmooth.fstat html
BSmooth.tstat html
BSseq-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSseq-class.Rd:137: file link 'setRealizationBackend' in package 'DelayedArray' does not exist and so has been treated as a topic
BSseq html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSseq.Rd:34: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
BSseqStat-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSseqStat-class.Rd:27: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
BSseqTstat-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSseqTstat-class.Rd:27: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
FWGRanges-class html
computeStat html
data.frame2GRanges html
dmrFinder html
findLoci html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/findLoci.Rd:44: file link 'vmatchPattern' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/findLoci.Rd:45: file link 'vmatchPattern' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/findLoci.Rd:55: file link 'vmatchPattern' in package 'Biostrings' does not exist and so has been treated as a topic
fisherTests html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/fisherTests.Rd:55: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
getCoverage html
getMeth html
getStats html
goodnessOfFit html
hasGRanges-class html
internals html
plotRegion html
read.bismark html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/read.bismark.Rd:36: file link 'rowRanges' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/read.bismark.Rd:73: file link 'getHDF5DumpChunkDim' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/read.bismark.Rd:75: file link 'getHDF5DumpChunkDim' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/read.bismark.Rd:78: file link 'getHDF5DumpCompressionLevel' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/read.bismark.Rd:79: file link 'getHDF5DumpCompressionLevel' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/read.bismark.Rd:91: file link 'tempdir' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/read.bismark.Rd:177: file link 'getRealizationBackend' in package 'DelayedArray' does not exist and so has been treated as a topic
read.bsmooth html
read.umtab html
smoothSds html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'bsseq' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c check_M_and_Cov.cpp -o check_M_and_Cov.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o bsseq.dll tmp.def check_M_and_Cov.o init.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/bsseq.buildbin-libdir/bsseq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bsseq' as bsseq_1.19.3.zip
* DONE (bsseq)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'bsseq' successfully unpacked and MD5 sums checked
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bsseq.Rcheck/tests_i386/testthat.Rout.fail
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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 C:\Users\biocbuild\bbs-3.9-bioc\meat\bsseq.Rcheck\tests_i386\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: 161 SKIPPED: 7 FAILED: 1
1. Error: strandCollapse() works on good input (@test_BSseq-class.R#59)
Error: testthat unit tests failed
Execution halted
|
bsseq.Rcheck/tests_x64/testthat.Rout.fail
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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 C:\Users\biocbuild\bbs-3.9-bioc\meat\bsseq.Rcheck\tests_x64\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: 161 SKIPPED: 7 FAILED: 1
1. Error: strandCollapse() works on good input (@test_BSseq-class.R#59)
Error: testthat unit tests failed
Execution halted
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bsseq.Rcheck/examples_i386/bsseq-Ex.timings
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bsseq.Rcheck/examples_x64/bsseq-Ex.timings
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