Multiple platform build/check report for BioC 3.13 - CHECK results for HiCDCPlus on tokay2

Package: HiCDCPlus

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HiCDCPlus.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings HiCDCPlus_1.0.0.tar.gz

StartedAt: 2021-10-15 00:23:17 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 00:35:46 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 749.4 seconds

RetCode: 0

Status: OK

CheckDir: HiCDCPlus.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HiCDCPlus.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings HiCDCPlus_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/HiCDCPlus.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.0.0'
* 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 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-3.13-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-3.13-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' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
hicdcdiff                    8.83  32.40   49.70
construct_features          11.81   2.02   13.99
construct_features_chr      11.45   1.87   13.33
HTClist2gi_list              8.17   1.14   37.64
hicdc2hic                    2.74   3.40   11.25
gi_list_topdom               4.21   0.79    6.35
hic2icenorm_gi_list          2.80   1.03    5.21
extract_hic_eigenvectors     1.54   0.02   13.42
HiCDCPlus_parallel           1.26   0.11   14.30
construct_features_parallel  0.02   0.00   24.94
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
construct_features          10.30   1.83   12.53
construct_features_chr       8.25   2.04   10.30
HTClist2gi_list              9.50   0.44   11.38
hicdcdiff                    8.46   1.38   16.34
gi_list_topdom               4.68   0.89    7.05
HiCDCPlus                    3.36   0.16    5.55
HiCDCPlus_chr                3.02   0.03    5.18
hicdc2hic                    2.24   0.37    6.37
HiCDCPlus_parallel           1.38   0.01   16.34
extract_hic_eigenvectors     0.87   0.06   11.44
construct_features_parallel  0.03   0.00   22.31
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/HiCDCPlus.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/HiCDCPlus_1.0.0.tar.gz && rm -rf HiCDCPlus.buildbin-libdir && mkdir HiCDCPlus.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HiCDCPlus.buildbin-libdir HiCDCPlus_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL HiCDCPlus_1.0.0.zip && rm HiCDCPlus_1.0.0.tar.gz HiCDCPlus_1.0.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 1010k    0  1136    0     0  13867      0  0:01:14 --:--:--  0:01:14 13853
100 1010k  100 1010k    0     0  2236k      0 --:--:-- --:--:-- --:--:-- 2235k

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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/HiCDCPlus.buildbin-libdir/HiCDCPlus/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HiCDCPlus' as HiCDCPlus_1.0.0.zip
* DONE (HiCDCPlus)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'HiCDCPlus' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
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
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

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 -- Fri Oct 15 00:35:08 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 
   8.70    0.79    9.46


R version 4.1.1 (2021-08-10) -- "Kick Things"
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
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

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 -- Fri Oct 15 00:35:19 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 
  10.15    0.46   10.61

name	user	system	elapsed
HTClist2gi_list	8.17	1.14	37.64
HiCDCPlus	2.95	0.50	4.92
HiCDCPlus_chr	2.84	0.34	4.34
HiCDCPlus_parallel	1.26	0.11	14.30
add_1D_features	0.20	0.11	0.31
add_2D_features	0.44	0.03	0.47
add_hic_counts	1.30	0.02	2.83
construct_features	11.81	2.02	13.99
construct_features_chr	11.45	1.87	13.33
construct_features_parallel	0.02	0.00	24.94
expand_1D_features	0.18	0.00	0.19
extract_hic_eigenvectors	1.54	0.02	13.42
generate_binned_gi_list	0.29	0.06	0.37
generate_bintolen_gi_list	0.84	0.28	1.86
generate_df_gi_list	0.33	0.00	0.33
get_chr_sizes	0.22	0.00	0.21
get_chrs	0.29	0.02	0.30
get_enzyme_cutsites	3.32	0.09	3.42
gi_list2HTClist	1.55	1.50	4.58
gi_list_Dthreshold.detect	0.33	0.06	0.39
gi_list_binsize_detect	0.27	0.00	0.27
gi_list_read	0.41	0.02	0.45
gi_list_topdom	4.21	0.79	6.35
gi_list_validate	0.36	0.02	0.37
gi_list_write	0.44	0.02	0.45
hic2icenorm_gi_list	2.80	1.03	5.21
hicdc2hic	2.74	3.40	11.25
hicdcdiff	8.83	32.40	49.70

name	user	system	elapsed
HTClist2gi_list	9.50	0.44	11.38
HiCDCPlus	3.36	0.16	5.55
HiCDCPlus_chr	3.02	0.03	5.18
HiCDCPlus_parallel	1.38	0.01	16.34
add_1D_features	0.20	0.00	0.21
add_2D_features	0.55	0.02	0.56
add_hic_counts	1.40	0.05	3.34
construct_features	10.30	1.83	12.53
construct_features_chr	8.25	2.04	10.30
construct_features_parallel	0.03	0.00	22.31
expand_1D_features	0.24	0.00	0.24
extract_hic_eigenvectors	0.87	0.06	11.44
generate_binned_gi_list	0.25	0.00	0.25
generate_bintolen_gi_list	0.67	0.38	1.78
generate_df_gi_list	0.28	0.05	0.33
get_chr_sizes	0.29	0.04	0.34
get_chrs	0.28	0.00	0.28
get_enzyme_cutsites	2.38	0.07	2.44
gi_list2HTClist	1.37	0.03	3.56
gi_list_Dthreshold.detect	0.30	0.04	0.34
gi_list_binsize_detect	0.30	0.02	0.32
gi_list_read	0.43	0.00	0.45
gi_list_topdom	4.68	0.89	7.05
gi_list_validate	0.37	0.05	0.42
gi_list_write	0.38	0.01	0.39
hic2icenorm_gi_list	2.76	0.74	5.00
hicdc2hic	2.24	0.37	6.37
hicdcdiff	8.46	1.38	16.34

CHECK results for HiCDCPlus on tokay2

Summary

Command output

Installation output

Tests output

Example timings