Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-08-15 13:21:33 -0400 (Mon, 15 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4365
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4118
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4183
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

CHECK results for HiCDCPlus on palomino3


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? 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 893/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCDCPlus 1.4.2  (landing page)
Merve Sahin
Snapshot Date: 2022-08-14 13:55:13 -0400 (Sun, 14 Aug 2022)
git_url: https://git.bioconductor.org/packages/HiCDCPlus
git_branch: RELEASE_3_15
git_last_commit: 70d7860
git_last_commit_date: 2022-06-06 10:44:47 -0400 (Mon, 06 Jun 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: HiCDCPlus
Version: 1.4.2
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HiCDCPlus.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings HiCDCPlus_1.4.2.tar.gz
StartedAt: 2022-08-15 01:38:27 -0400 (Mon, 15 Aug 2022)
EndedAt: 2022-08-15 01:45:08 -0400 (Mon, 15 Aug 2022)
EllapsedTime: 401.6 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCDCPlus.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HiCDCPlus.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings HiCDCPlus_1.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/HiCDCPlus.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.4.2'
* 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 '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 for x64 is not available
File 'F:/biocbuild/bbs-3.15-bioc/R/library/HiCDCPlus/libs/x64/HiCDCPlus.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
construct_features          13.00   2.44   15.58
construct_features_chr      11.27   2.40   13.67
HTClist2gi_list              7.93   0.78   11.21
hicdcdiff                    5.05   0.84   10.53
HiCDCPlus_parallel           0.89   0.01   15.28
construct_features_parallel  0.01   0.00   27.62
* 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
  'F:/biocbuild/bbs-3.15-bioc/meat/HiCDCPlus.Rcheck/00check.log'
for details.



Installation output

HiCDCPlus.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL HiCDCPlus
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'HiCDCPlus' ...
** using staged installation
** libs
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c straw.cpp -o straw.o
g++ -shared -s -static-libgcc -o HiCDCPlus.dll tmp.def RcppExports.o straw.o -lz -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-HiCDCPlus/00new/HiCDCPlus/libs/x64
** 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
** 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 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 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.

> 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, 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

Attaching package: 'IRanges'

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

    windows

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 -- Mon Aug 15 01:44:55 2022 
*********************************************** 
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 
  10.50    0.62   11.14 

Example timings

HiCDCPlus.Rcheck/HiCDCPlus-Ex.timings

nameusersystemelapsed
HTClist2gi_list 7.93 0.7811.21
HiCDCPlus2.390.113.58
HiCDCPlus_chr2.480.113.74
HiCDCPlus_parallel 0.89 0.0115.28
add_1D_features0.140.000.14
add_2D_features0.320.100.41
add_hic_counts0.850.202.12
construct_features13.00 2.4415.58
construct_features_chr11.27 2.4013.67
construct_features_parallel 0.01 0.0027.62
expand_1D_features0.160.000.16
extract_hic_eigenvectors0.290.081.84
generate_binned_gi_list0.250.050.30
generate_bintolen_gi_list0.560.181.54
generate_df_gi_list0.270.040.29
get_chr_sizes0.230.030.27
get_chrs0.270.030.30
get_enzyme_cutsites3.780.053.82
gi_list2HTClist0.790.071.89
gi_list_Dthreshold.detect0.280.020.29
gi_list_binsize_detect0.220.010.23
gi_list_read0.360.040.44
gi_list_topdom2.830.264.56
gi_list_validate0.230.050.28
gi_list_write0.280.030.33
hic2icenorm_gi_list1.850.223.08
hicdc2hic1.230.253.44
hicdcdiff 5.05 0.8410.53