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This page was generated on 2022-01-19 13:06:44 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 tokay2


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 868/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCDCPlus 1.2.0  (landing page)
Merve Sahin
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/HiCDCPlus
git_branch: RELEASE_3_14
git_last_commit: d706a7e
git_last_commit_date: 2021-10-26 13:07:04 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: HiCDCPlus
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HiCDCPlus.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings HiCDCPlus_1.2.0.tar.gz
StartedAt: 2022-01-18 20:56:40 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 21:08:16 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 696.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: HiCDCPlus.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HiCDCPlus.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings HiCDCPlus_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/HiCDCPlus.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HiCDCPlus/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HiCDCPlus' version '1.2.0'
* 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 whether package 'HiCDCPlus' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs      2.2Mb
* 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 ... 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/HiCDCPlus/libs/i386/HiCDCPlus.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-3.14-bioc/R/library/HiCDCPlus/libs/x64/HiCDCPlus.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 'HiCDCPlus-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hicdcdiff
> ### Title: hicdcdiff
> ### Aliases: hicdcdiff
> 
> ### ** Examples
> 
> outputdir<-paste0(tempdir(check=TRUE),'/')
> hicdcdiff(input_paths=list(NSD2=c(
+ system.file("extdata", "GSE131651_NSD2_LOW_arima_example.hic",
+ package = "HiCDCPlus"),
+ system.file("extdata", "GSE131651_NSD2_HIGH_arima_example.hic",
+ package = "HiCDCPlus")),
+ TKO=c(system.file("extdata", "GSE131651_TKOCTCF_new_example.hic",
+ package = "HiCDCPlus"),
+ system.file("extdata", "GSE131651_NTKOCTCF_new_example.hic",
+ package = "HiCDCPlus"))),
+ filter_file=system.file("extdata", "GSE131651_analysis_indices.txt.gz",
+ package = "HiCDCPlus"),
+          chrs='chr22',
+          output_path=outputdir,
+          fitType = 'mean',
+          binsize=50000,
+          diagnostics=FALSE)
WARN [2022-01-18T21:04:37,546]  [Globals.java:138] [main]  Development mode is enabled
WARN [2022-01-18T21:04:40,879]  [Globals.java:138] [main]  Development mode is enabled
Joining, by = c("Dband", "chr", "startI", "startJ")
WARN [2022-01-18T21:04:45,040]  [Globals.java:138] [main]  Development mode is enabled
Joining, by = c("Dband", "chr", "startI", "startJ")
WARN [2022-01-18T21:04:50,602]  [Globals.java:138] [main]  Development mode is enabled
Joining, by = c("Dband", "chr", "startI", "startJ")
Joining, by = "Dband"
converting counts to integer mode
Error: memory exhausted (limit reached?)
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
construct_features          10.12   1.86   12.53
construct_features_chr       8.68   1.88   10.64
hicdcdiff                    8.76   0.99   17.00
HTClist2gi_list              8.86   0.39   12.61
gi_list_topdom               4.64   0.64    9.82
hic2icenorm_gi_list          2.70   0.95    6.05
hicdc2hic                    3.10   0.39    8.38
HiCDCPlus                    3.18   0.11    5.47
HiCDCPlus_chr                2.85   0.01    5.05
HiCDCPlus_parallel           1.12   0.08   14.44
extract_hic_eigenvectors     0.85   0.04   10.99
construct_features_parallel  0.05   0.00   23.13
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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 ERROR, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/HiCDCPlus.Rcheck/00check.log'
for details.


Installation output

HiCDCPlus.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/HiCDCPlus_1.2.0.tar.gz && rm -rf HiCDCPlus.buildbin-libdir && mkdir HiCDCPlus.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HiCDCPlus.buildbin-libdir HiCDCPlus_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL HiCDCPlus_1.2.0.zip && rm HiCDCPlus_1.2.0.tar.gz HiCDCPlus_1.2.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1010k  100 1010k    0     0  3213k      0 --:--:-- --:--:-- --:--:-- 3226k

install for i386

* installing *source* package 'HiCDCPlus' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c straw.cpp -o straw.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o HiCDCPlus.dll tmp.def RcppExports.o straw.o -lz -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/HiCDCPlus.buildbin-libdir/00LOCK-HiCDCPlus/00new/HiCDCPlus/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'HiCDCPlus'
    finding HTML links ... done
    HTClist2gi_list                         html  
    HiCDCPlus                               html  
    HiCDCPlus_chr                           html  
    HiCDCPlus_parallel                      html  
    add_1D_features                         html  
    add_2D_features                         html  
    add_hic_counts                          html  
    add_hicpro_allvalidpairs_counts         html  
    add_hicpro_matrix_counts                html  
    construct_features                      html  
    construct_features_chr                  html  
    construct_features_parallel             html  
    expand_1D_features                      html  
    extract_hic_eigenvectors                html  
    generate_binned_gi_list                 html  
    generate_bintolen_gi_list               html  
    generate_df_gi_list                     html  
    get_chr_sizes                           html  
    get_chrs                                html  
    get_enzyme_cutsites                     html  
    gi_list2HTClist                         html  
    gi_list_Dthreshold.detect               html  
    gi_list_binsize_detect                  html  
    gi_list_read                            html  
    gi_list_topdom                          html  
    gi_list_validate                        html  
    gi_list_write                           html  
    hic2icenorm_gi_list                     html  
    hicdc2hic                               html  
    hicdcdiff                               html  
    straw                                   html  
    straw_dump                              html  
*** 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

install for x64

* installing *source* package 'HiCDCPlus' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c straw.cpp -o straw.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o HiCDCPlus.dll tmp.def RcppExports.o straw.o -lz -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/HiCDCPlus.buildbin-libdir/HiCDCPlus/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HiCDCPlus' as HiCDCPlus_1.2.0.zip
* DONE (HiCDCPlus)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'HiCDCPlus' successfully unpacked and MD5 sums checked

Tests output

HiCDCPlus.Rcheck/tests_i386/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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.

> 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 -- Tue Jan 18 21:07:56 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 
   8.31    0.98    9.26 

HiCDCPlus.Rcheck/tests_x64/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 -- Tue Jan 18 21:08:07 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 
  10.43    0.48   10.92 

Example timings

HiCDCPlus.Rcheck/examples_i386/HiCDCPlus-Ex.timings

nameusersystemelapsed
HTClist2gi_list 7.51 0.7314.74
HiCDCPlus2.840.464.82
HiCDCPlus_chr2.690.154.19
HiCDCPlus_parallel 1.18 0.0515.28
add_1D_features0.130.120.25
add_2D_features0.470.020.49
add_hic_counts1.280.065.34
construct_features10.69 1.9512.72
construct_features_chr8.761.159.90
construct_features_parallel 0.02 0.0327.33
expand_1D_features0.230.000.24
extract_hic_eigenvectors 1.69 0.0713.18
generate_binned_gi_list0.330.070.40
generate_bintolen_gi_list0.580.292.32
generate_df_gi_list0.210.000.22
get_chr_sizes0.160.020.17
get_chrs0.160.020.17
get_enzyme_cutsites2.400.102.51
gi_list2HTClist1.160.833.81
gi_list_Dthreshold.detect0.210.080.30
gi_list_binsize_detect0.190.030.22
gi_list_read0.390.020.47
gi_list_topdom4.940.677.25
gi_list_validate0.360.050.41
gi_list_write0.450.000.45
hic2icenorm_gi_list2.750.795.05
hicdc2hic 2.51 1.8318.93

HiCDCPlus.Rcheck/examples_x64/HiCDCPlus-Ex.timings

nameusersystemelapsed
HTClist2gi_list 8.86 0.3912.61
HiCDCPlus3.180.115.47
HiCDCPlus_chr2.850.015.05
HiCDCPlus_parallel 1.12 0.0814.44
add_1D_features0.190.000.18
add_2D_features0.420.080.50
add_hic_counts1.500.032.97
construct_features10.12 1.8612.53
construct_features_chr 8.68 1.8810.64
construct_features_parallel 0.05 0.0023.13
expand_1D_features0.210.000.21
extract_hic_eigenvectors 0.85 0.0410.99
generate_binned_gi_list0.360.020.37
generate_bintolen_gi_list0.590.281.88
generate_df_gi_list0.240.030.26
get_chr_sizes0.20.00.2
get_chrs0.190.000.19
get_enzyme_cutsites2.110.062.17
gi_list2HTClist1.130.082.89
gi_list_Dthreshold.detect0.350.020.36
gi_list_binsize_detect0.340.010.36
gi_list_read0.580.000.61
gi_list_topdom4.640.649.82
gi_list_validate0.340.020.36
gi_list_write0.310.030.34
hic2icenorm_gi_list2.700.956.05
hicdc2hic3.100.398.38
hicdcdiff 8.76 0.9917.00