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This page was generated on 2021-10-15 15:05:42 -0400 (Fri, 15 Oct 2021).

CHECK results for HiCDCPlus on nebbiolo1

To the developers/maintainers of the HiCDCPlus package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 858/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCDCPlus 1.0.0  (landing page)
Merve Sahin
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/HiCDCPlus
git_branch: RELEASE_3_13
git_last_commit: c666131
git_last_commit_date: 2021-05-19 12:59:52 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: HiCDCPlus
Version: 1.0.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:HiCDCPlus.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings HiCDCPlus_1.0.0.tar.gz
StartedAt: 2021-10-14 10:10:13 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:15:48 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 335.4 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCDCPlus.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:HiCDCPlus.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings HiCDCPlus_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/HiCDCPlus.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCDCPlus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCDCPlus’ version ‘1.0.0’
* 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
* checking installed package size ... OK
* 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 ... 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
extract_hic_eigenvectors    12.133  0.188  10.243
construct_features           7.670  3.835  11.505
hicdc2hic                    9.883  0.495   3.192
HTClist2gi_list              8.142  0.240   8.384
construct_features_chr       5.357  2.816   8.174
HiCDCPlus_parallel           0.609  0.024  15.622
construct_features_parallel  0.014  0.036  26.279
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/HiCDCPlus.Rcheck/00check.log’
for details.



Installation output

HiCDCPlus.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL HiCDCPlus
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘HiCDCPlus’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/lib -L/usr/local/lib -o HiCDCPlus.so RcppExports.o straw.o -lz -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> BiocGenerics:::testPackage("HiCDCPlus")
Loading required package: BSgenome
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, 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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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: rtracklayer


RUNIT TEST PROTOCOL -- Thu Oct 14 10:15:45 2021 
*********************************************** 
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 
 10.053   0.514  10.553 

Example timings

HiCDCPlus.Rcheck/HiCDCPlus-Ex.timings

nameusersystemelapsed
HTClist2gi_list8.1420.2408.384
HiCDCPlus2.4600.0842.545
HiCDCPlus_chr2.6420.0712.713
HiCDCPlus_parallel 0.609 0.02415.622
add_1D_features0.1230.0000.124
add_2D_features0.6120.0600.680
add_hic_counts0.6020.0400.642
construct_features 7.670 3.83511.505
construct_features_chr5.3572.8168.174
construct_features_parallel 0.014 0.03626.279
expand_1D_features0.1880.0000.187
extract_hic_eigenvectors12.133 0.18810.243
generate_binned_gi_list0.2990.0140.313
generate_bintolen_gi_list0.4670.0600.527
generate_df_gi_list0.2830.0120.295
get_chr_sizes0.2720.0120.284
get_chrs0.2360.0080.244
get_enzyme_cutsites2.9500.1643.114
gi_list2HTClist0.5650.0040.570
gi_list_Dthreshold.detect0.3030.0280.330
gi_list_binsize_detect0.3310.0080.338
gi_list_read0.4760.0040.479
gi_list_topdom2.6440.1122.737
gi_list_validate0.3010.0080.309
gi_list_write0.3100.0120.322
hic2icenorm_gi_list2.8630.0202.885
hicdc2hic9.8830.4953.192
hicdcdiff3.5660.0243.594