| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-26 06:18:07 -0000 (Fri, 26 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4254 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
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To the developers/maintainers of the diffHic package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/diffHic.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 547/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| diffHic 1.33.0 (landing page) Aaron Lun
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | |||||||||
| Package: diffHic |
| Version: 1.33.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:diffHic.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings diffHic_1.33.0.tar.gz |
| StartedAt: 2023-05-26 04:39:03 -0000 (Fri, 26 May 2023) |
| EndedAt: 2023-05-26 04:39:13 -0000 (Fri, 26 May 2023) |
| EllapsedTime: 10.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: diffHic.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:diffHic.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings diffHic_1.33.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/diffHic.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘diffHic/DESCRIPTION’ ... OK
* this is package ‘diffHic’ version ‘1.33.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
download from 'https://CRAN.R-project.org/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
download from 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
download from 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
download from 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES' failed
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 ‘diffHic’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 16.5Mb
sub-directories of 1Mb or more:
doc 1.3Mb
libs 13.9Mb
* 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 ... NOTE
Problems with news in ‘inst/NEWS.Rd’:
Error writing to connection: No space left on device
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ...Warning in for (i in seq_along(specs)) { :
closing unused connection 4 ()
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 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘diffHic.Rnw’... failed to complete the test
ERROR
Errors in running code in vignettes:
when running code in ‘diffHic.Rnw’
...
> proc.time()
user system elapsed
0.180 0.017 0.192
... incomplete output. Crash?
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... ERROR
Rd conversion errors:
Converting parsed Rd's to LaTeX Warning in close.connection(con) :
Problem closing connection: No space left on device
Warning in close.connection(con) :
Problem closing connection: No space left on device
Warning in close.connection(con) :
Problem closing connection: No space left on device
Warning in close.connection(con) :
Problem closing connection: No space left on device
Warning in close.connection(con) :
Problem closing connection: No space left on device
Error in writeLines(x, con, useBytes = TRUE, ...) :
Error writing to connection: No space left on device
* DONE
Status: 2 ERRORs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/diffHic.Rcheck/00check.log’
for details.
diffHic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL diffHic ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘diffHic’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c binner.cpp -o binner.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c check_input.cpp -o check_input.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c cluster_2d.cpp -o cluster_2d.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c count_background.cpp -o count_background.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c count_connect.cpp -o count_connect.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c count_patch.cpp -o count_patch.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c directionality.cpp -o directionality.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c init.cpp -o init.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c iterative_correction.cpp -o iterative_correction.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c neighbors.cpp -o neighbors.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c pair_stats.cpp -o pair_stats.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c quadrant_bg.cpp -o quadrant_bg.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c report_hic_pairs.cpp -o report_hic_pairs.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c trended_filter.cpp -o trended_filter.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.0/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c utils.cpp -o utils.o g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o diffHic.so binner.o check_input.o cluster_2d.o count_background.o count_connect.o count_patch.o directionality.o init.o iterative_correction.o neighbors.o pair_stats.o quadrant_bg.o report_hic_pairs.o trended_filter.o utils.o /home/biocbuild/R/R-4.3.0/site-library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-diffHic/00new/diffHic/libs ** R ** 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 (diffHic)
diffHic.Rcheck/tests/test-basic.Rout.save
R version 3.5.0 Patched (2018-04-30 r74679) -- "Joy in Playing"
Copyright (C) 2018 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.
Natural language support but running in an English locale
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.
> # These are just placeholders for the real things in inst/tests.
>
> suppressWarnings(suppressPackageStartupMessages(require(diffHic)))
>
> hic.file <- system.file("exdata", "hic_sort.bam", package="diffHic")
> cuts <- readRDS(system.file("exdata", "cuts.rds", package="diffHic"))
> param <- pairParam(fragments=cuts)
>
> # Setting up the parameters
> fout <- "output.h5"
> preparePairs(hic.file, param, file=fout)
$pairs
total marked filtered mapped
32 7 3 22
$same.id
dangling self.circle
4 1
$singles
[1] 2
$chimeras
total mapped multi invalid
12 8 7 5
> head(getPairData(fout, param))
length orientation insert
1 40 1 40
2 80 1 80
3 60 2 54
4 40 3 160
5 20 1 66
6 80 0 114
>
> loadChromos(fout)
anchor1 anchor2
1 chrA chrA
2 chrB chrA
3 chrB chrB
> head(loadData(fout, "chrA", "chrA"))
anchor1.id anchor2.id anchor1.pos anchor2.pos anchor1.len anchor2.len
1 2 1 49 14 -5 10
2 2 1 79 9 -10 10
3 2 1 65 21 10 -10
4 4 1 156 6 -10 -10
5 4 2 141 80 -5 10
6 4 2 154 50 10 10
> head(loadData(fout, "chrA", "chrB"))
anchor1.id anchor2.id anchor1.pos anchor2.pos anchor1.len anchor2.len
1 5 2 19 44 10 -10
2 5 3 14 105 10 -10
3 6 1 65 19 5 10
4 6 2 24 90 -5 5
5 6 3 24 100 -5 -10
6 6 3 24 95 -5 -10
Warning message:
In value[[3L]](cond) : anchor definitions are reversed
>
> # Loading the counts.
> data <- squareCounts(fout, param, width=50, filter=1)
> data
class: InteractionSet
dim: 10 1
metadata(2): param width
assays(1): counts
rownames: NULL
rowData names(0):
colnames: NULL
colData names(1): totals
type: ReverseStrictGInteractions
regions: 6
>
> margins <- marginCounts(fout, param, width=50)
> margins
class: RangedSummarizedExperiment
dim: 6 1
metadata(1): param
assays(1): counts
rownames: NULL
rowData names(1): nfrags
colnames: NULL
colData names(1): totals
> totalCounts(fout, param)
[1] 17
>
> regions <- GRanges("chrA", IRanges(c(1, 100, 150), c(20, 140, 160)))
> connectCounts(fout, param, regions=regions, filter=1L)
class: InteractionSet
dim: 2 1
metadata(1): param
assays(1): counts
rownames: NULL
rowData names(0):
colnames: NULL
colData names(1): totals
type: ReverseStrictGInteractions
regions: 3
>
> # Checking some values.
> head(getArea(data))
[1] 2208 2304 2208 2208 3312 3174
> head(pairdist(data))
[1] 47 140 93 47 NA NA
>
> anchors(data, type="first")
GRanges object with 10 ranges and 1 metadata column:
seqnames ranges strand | nfrags
<Rle> <IRanges> <Rle> | <integer>
[1] chrA 49-94 * | 1
[2] chrA 141-188 * | 1
[3] chrA 141-188 * | 1
[4] chrA 141-188 * | 1
[5] chrB 1-69 * | 2
[6] chrB 1-69 * | 2
[7] chrB 1-69 * | 2
[8] chrB 1-69 * | 2
[9] chrB 70-92 * | 1
[10] chrB 70-92 * | 1
-------
seqinfo: 2 sequences from an unspecified genome
> anchors(data, type="second")
GRanges object with 10 ranges and 1 metadata column:
seqnames ranges strand | nfrags
<Rle> <IRanges> <Rle> | <integer>
[1] chrA 1-48 * | 1
[2] chrA 1-48 * | 1
[3] chrA 49-94 * | 1
[4] chrA 95-140 * | 1
[5] chrA 1-48 * | 1
[6] chrA 49-94 * | 1
[7] chrA 95-140 * | 1
[8] chrB 1-69 * | 2
[9] chrB 1-69 * | 2
[10] chrB 70-92 * | 1
-------
seqinfo: 2 sequences from an unspecified genome
> assay(data)
[,1]
[1,] 3
[2,] 1
[3,] 2
[4,] 1
[5,] 1
[6,] 2
[7,] 3
[8,] 1
[9,] 2
[10,] 1
> regions(data)
GRanges object with 6 ranges and 1 metadata column:
seqnames ranges strand | nfrags
<Rle> <IRanges> <Rle> | <integer>
[1] chrA 1-48 * | 1
[2] chrA 49-94 * | 1
[3] chrA 95-140 * | 1
[4] chrA 141-188 * | 1
[5] chrB 1-69 * | 2
[6] chrB 70-92 * | 1
-------
seqinfo: 2 sequences from an unspecified genome
>
> data$totals
[1] 17
> colData(data)
DataFrame with 1 row and 1 column
totals
<integer>
1 17
> metadata(data)
$param
Genome contains 7 restriction fragments across 2 chromosomes
No discard regions are specified
No limits on chromosomes for read extraction
No cap on the read pairs per pair of restriction fragments
$width
[1] 50
>
> asDGEList(data)
An object of class "DGEList"
$counts
Sample1
1 3
2 1
3 2
4 1
5 1
6 2
7 3
8 1
9 2
10 1
$samples
group lib.size norm.factors
Sample1 1 17 1
> asDGEList(data, lib.size=20)$samples
group lib.size norm.factors
Sample1 1 20 1
> asDGEList(data, norm.factors=2, group="a")$samples
group lib.size norm.factors
Sample1 a 17 2
>
> # Playing around with some bin counts.
> stuff <- correctedContact(data)
> head(stuff$truth)
[1] 1.517032e+04 6.123523e-01 6.123523e-01 8.162749e-01 2.041633e-01
[6] 2.041633e-01
>
> data.large <- squareCounts(fout, param, width=100, filter=1)
> boxed <- boxPairs(larger=data.large, smaller=data)
> head(boxed$indices$larger)
[1] 1 2 3 4 5 6
> head(boxed$indices$smaller)
[1] 1 2 2 3 4 4
>
> head(enrichedPairs(data))
class: InteractionSet
dim: 6 1
metadata(2): param width
assays(5): counts quadrant vertical horizontal surrounding
rownames: NULL
rowData names(4): N.quadrant N.vertical N.horizontal N.surrounding
colnames: NULL
colData names(1): totals
type: ReverseStrictGInteractions
regions: 6
> head(clusterPairs(data, tol=10)$indices[[1]])
[1] 1 2 2 2 3 3
>
> # End.
>
> unlink(fout)
>
> proc.time()
user system elapsed
5.571 0.168 5.757