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This page was generated on 2024-06-14 12:02 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
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

Package 938/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCDCPlus 1.13.0  (landing page)
Merve Sahin
Snapshot Date: 2024-06-13 14:00 -0400 (Thu, 13 Jun 2024)
git_url: https://git.bioconductor.org/packages/HiCDCPlus
git_branch: devel
git_last_commit: e393345
git_last_commit_date: 2024-04-30 11:31:16 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for HiCDCPlus on nebbiolo2

To the developers/maintainers of the HiCDCPlus package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiCDCPlus.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: HiCDCPlus
Version: 1.13.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HiCDCPlus.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HiCDCPlus_1.13.0.tar.gz
StartedAt: 2024-06-14 00:26:15 -0400 (Fri, 14 Jun 2024)
EndedAt: 2024-06-14 00:32:13 -0400 (Fri, 14 Jun 2024)
EllapsedTime: 358.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: HiCDCPlus.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HiCDCPlus.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HiCDCPlus_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/HiCDCPlus.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘HiCDCPlus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCDCPlus’ version ‘1.13.0’
* 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 ‘HiCDCPlus’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs      1.6Mb
* 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 code 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 ... 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
construct_features          7.233  0.760   7.993
HTClist2gi_list             6.759  0.456   7.215
construct_features_chr      4.808  0.664   5.473
HiCDCPlus_parallel          0.404  0.012  14.098
construct_features_parallel 0.014  0.000  23.418
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘HiCDCPlus.Rmd’ using rmarkdown
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-06-14T00:32:02,710]  [Globals.java:138] [main]  Development mode is enabled
Using 1 CPU thread(s) for primary task
Using 10 CPU thread(s) for secondary task
Not including fragment map
Start preprocess
Writing header
Writing body
java.lang.NumberFormatException: For input string: "score"
	at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2054)
	at java.base/jdk.internal.math.FloatingDecimal.parseFloat(FloatingDecimal.java:122)
	at java.base/java.lang.Float.parseFloat(Float.java:455)
	at juicebox.tools.utils.original.mnditerator.MNDLineParser.updatePairScoreIfNeeded(MNDLineParser.java:88)
	at juicebox.tools.utils.original.mnditerator.MNDFileParser.parseShortFormat(MNDFileParser.java:105)
	at juicebox.tools.utils.original.mnditerator.MNDFileParser.parse(MNDFileParser.java:87)
	at juicebox.tools.utils.original.mnditerator.GenericPairIterator.advance(GenericPairIterator.java:56)
	at juicebox.tools.utils.original.mnditerator.AsciiPairIterator.<init>(AsciiPairIterator.java:55)
	at juicebox.tools.utils.original.mnditerator.PairIterator.getIterator(PairIterator.java:54)
	at juicebox.tools.utils.original.Preprocessor.computeWholeGenomeMatrix(Preprocessor.java:583)
	at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:674)
	at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:436)
	at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:165)
	at juicebox.tools.HiCTools.main(HiCTools.java:94)
Warning: stack imbalance in '$', 37 then 34

 *** caught segfault ***
address (nil), cause 'unknown'
Segmentation fault (core dumped)

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/HiCDCPlus.Rcheck/00check.log’
for details.


Installation output

HiCDCPlus.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL HiCDCPlus
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘HiCDCPlus’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c straw.cpp -o straw.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o HiCDCPlus.so RcppExports.o straw.o -lz -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-HiCDCPlus/00new/HiCDCPlus/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (HiCDCPlus)

Tests output

HiCDCPlus.Rcheck/tests/runTests.Rout


R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> BiocGenerics:::testPackage("HiCDCPlus")
Loading required package: BSgenome
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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, aperm, append,
    as.data.frame, basename, cbind, 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, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

The following object is masked from 'package:BiocIO':

    FileForFormat



RUNIT TEST PROTOCOL -- Fri Jun 14 00:31:34 2024 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
HiCDCPlus RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 10.535   0.488  11.015 

Example timings

HiCDCPlus.Rcheck/HiCDCPlus-Ex.timings

nameusersystemelapsed
HTClist2gi_list6.7590.4567.215
HiCDCPlus3.0070.1643.171
HiCDCPlus_chr1.7860.0441.830
HiCDCPlus_parallel 0.404 0.01214.098
add_1D_features0.0760.0000.076
add_2D_features0.2670.0000.267
add_hic_counts0.3680.0440.412
construct_features7.2330.7607.993
construct_features_chr4.8080.6645.473
construct_features_parallel 0.014 0.00023.418
expand_1D_features0.0910.0120.104
extract_hic_eigenvectors2.3760.1501.646
generate_binned_gi_list0.2450.0040.249
generate_bintolen_gi_list0.4100.0280.439
generate_df_gi_list0.2070.0120.219
get_chr_sizes0.1740.0120.185
get_chrs0.1970.0160.213
get_enzyme_cutsites1.4920.1081.600
gi_list2HTClist0.4000.0440.444
gi_list_Dthreshold.detect0.2350.0090.245
gi_list_binsize_detect0.1960.0290.225
gi_list_read0.3140.0360.349
gi_list_topdom1.8980.2932.176
gi_list_validate0.2090.0090.218
gi_list_write0.2290.0080.236
hic2icenorm_gi_list1.0640.5241.588
hicdc2hic2.1130.2041.425
hicdcdiff2.3370.4252.772