Multiple platform build/check report for BioC 3.14 - CHECK results for HelloRanges on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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: HelloRanges

Version: 1.20.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HelloRanges.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings HelloRanges_1.20.0.tar.gz

StartedAt: 2022-04-12 21:03:39 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 21:11:36 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 476.7 seconds

RetCode: 1

Status: ERROR

CheckDir: HelloRanges.Rcheck

Warnings: NA

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HelloRanges.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings HelloRanges_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/HelloRanges.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HelloRanges/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HelloRanges' version '1.20.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomicRanges',
  'Biostrings', 'BSgenome', 'GenomicFeatures', 'VariantAnnotation',
  'Rsamtools', 'GenomicAlignments', 'rtracklayer', 'GenomeInfoDb',
  'SummarizedExperiment'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'HelloRanges' 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
* 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 ... NOTE
Packages in Depends field not imported from:
  'BSgenome' 'GenomicAlignments' 'GenomicFeatures' 'VariantAnnotation'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'BiocGenerics:::testPackage' 'IRanges:::subgrouping'
  'S4Vectors:::make_zero_col_DataFrame'
  See the note in ?`:::` about the use of this operator.
* 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 ... WARNING
Missing link or links in documentation object 'bedtools_getfasta.Rd':
  '[rtracklayer]{import}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'HelloRanges_unit_tests.R'
 ERROR
Running the tests in 'tests/HelloRanges_unit_tests.R' failed.
Last 13 lines of output:
  HelloRanges RUnit Tests - 17 test functions, 0 errors, 1 failure
  FAILURE in test_genomecov: Error in checkIdentical(exp, eval(r)) : FALSE 
   
  
  Test files with failing tests
  
     test_genomecov.R 
       test_genomecov 
  
  
  Error in BiocGenerics:::testPackage("HelloRanges") : 
    unit tests failed for package HelloRanges
  Calls: <Anonymous> -> <Anonymous>
  In addition: There were 17 warnings (use warnings() to see them)
  Execution halted
** running tests for arch 'x64' ...
  Running 'HelloRanges_unit_tests.R'
 ERROR
Running the tests in 'tests/HelloRanges_unit_tests.R' failed.
Last 13 lines of output:
  HelloRanges RUnit Tests - 17 test functions, 0 errors, 1 failure
  FAILURE in test_genomecov: Error in checkIdentical(exp, eval(r)) : FALSE 
   
  
  Test files with failing tests
  
     test_genomecov.R 
       test_genomecov 
  
  
  Error in BiocGenerics:::testPackage("HelloRanges") : 
    unit tests failed for package HelloRanges
  Calls: <Anonymous> -> <Anonymous>
  In addition: There were 17 warnings (use warnings() to see them)
  Execution halted
* 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 ERRORs, 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/HelloRanges.Rcheck/00check.log'
for details.

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##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/HelloRanges_1.20.0.tar.gz && rm -rf HelloRanges.buildbin-libdir && mkdir HelloRanges.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HelloRanges.buildbin-libdir HelloRanges_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL HelloRanges_1.20.0.zip && rm HelloRanges_1.20.0.tar.gz HelloRanges_1.20.0.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
 85 1131k   85  970k    0     0  1735k      0 --:--:-- --:--:-- --:--:-- 1735k
100 1131k  100 1131k    0     0  1886k      0 --:--:-- --:--:-- --:--:-- 1885k

install for i386

* installing *source* package 'HelloRanges' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'HelloRanges'
    finding HTML links ... done
    argparse                                html  
    bedtools_closest                        html  
    bedtools_complement                     html  
    bedtools_coverage                       html  
    bedtools_flank                          html  
    bedtools_genomecov                      html  
    bedtools_getfasta                       html  
    bedtools_groupby                        html  
    bedtools_intersect                      html  
    bedtools_jaccard                        html  
    bedtools_makewindows                    html  
    bedtools_map                            html  
    bedtools_merge                          html  
    finding level-2 HTML links ... done

    bedtools_multiinter                     html  
    bedtools_nuc                            html  
    bedtools_shift                          html  
    bedtools_slop                           html  
    bedtools_subtract                       html  
    bedtools_unionbedg                      html  
    distmode                                html  
    pair                                    html  
** 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 'HelloRanges' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HelloRanges' as HelloRanges_1.20.0.zip
* DONE (HelloRanges)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'HelloRanges' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.

> require("HelloRanges") || stop("unable to load HelloRanges package")
Loading required package: HelloRanges
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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BSgenome
Loading required package: rtracklayer
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: VariantAnnotation
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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

    rowMedians

Loading required package: SummarizedExperiment
Loading required package: Rsamtools

Attaching package: 'VariantAnnotation'

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

    tabulate

Loading required package: GenomicAlignments
[1] TRUE
> HelloRanges:::.test()
Timing stopped at: 2.09 0.01 3.03
Error in checkIdentical(exp, eval(r)) : FALSE 
 
In addition: There were 13 warnings (use warnings() to see them)


RUNIT TEST PROTOCOL -- Tue Apr 12 21:10:28 2022 
*********************************************** 
Number of test functions: 17 
Number of errors: 0 
Number of failures: 1 

 
1 Test Suite : 
HelloRanges RUnit Tests - 17 test functions, 0 errors, 1 failure
FAILURE in test_genomecov: Error in checkIdentical(exp, eval(r)) : FALSE 
 

Test files with failing tests

   test_genomecov.R 
     test_genomecov 


Error in BiocGenerics:::testPackage("HelloRanges") : 
  unit tests failed for package HelloRanges
Calls: <Anonymous> -> <Anonymous>
In addition: There were 17 warnings (use warnings() to see them)
Execution halted


R version 4.1.3 (2022-03-10) -- "One Push-Up"
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.

> require("HelloRanges") || stop("unable to load HelloRanges package")
Loading required package: HelloRanges
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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BSgenome
Loading required package: rtracklayer
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: VariantAnnotation
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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

    rowMedians

Loading required package: SummarizedExperiment
Loading required package: Rsamtools

Attaching package: 'VariantAnnotation'

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

    tabulate

Loading required package: GenomicAlignments
[1] TRUE
> HelloRanges:::.test()
Timing stopped at: 1.86 0.01 1.88
Error in checkIdentical(exp, eval(r)) : FALSE 
 
In addition: There were 13 warnings (use warnings() to see them)


RUNIT TEST PROTOCOL -- Tue Apr 12 21:11:25 2022 
*********************************************** 
Number of test functions: 17 
Number of errors: 0 
Number of failures: 1 

 
1 Test Suite : 
HelloRanges RUnit Tests - 17 test functions, 0 errors, 1 failure
FAILURE in test_genomecov: Error in checkIdentical(exp, eval(r)) : FALSE 
 

Test files with failing tests

   test_genomecov.R 
     test_genomecov 


Error in BiocGenerics:::testPackage("HelloRanges") : 
  unit tests failed for package HelloRanges
Calls: <Anonymous> -> <Anonymous>
In addition: There were 17 warnings (use warnings() to see them)
Execution halted

name	user	system	elapsed
bedtools_closest	0.28	0.00	0.28
bedtools_complement	0.02	0.00	0.01
bedtools_coverage	0.10	0.00	0.11
bedtools_flank	0.10	0.03	0.13
bedtools_genomecov	0.09	0.06	0.15
bedtools_getfasta	0.05	0.02	0.07
bedtools_groupby	0.03	0.03	0.06
bedtools_intersect	0.38	0.16	0.53
bedtools_jaccard	0.07	0.03	0.11
bedtools_makewindows	0.07	0.00	0.07
bedtools_map	0.14	0.00	0.14
bedtools_merge	0.14	0.00	0.14
bedtools_multiinter	0.06	0.00	0.06
bedtools_nuc	0.03	0.00	0.03
bedtools_shift	0.05	0.00	0.05
bedtools_slop	0.06	0.00	0.06
bedtools_subtract	0.08	0.00	0.08
bedtools_unionbedg	0.05	0.00	0.05
distmode	0	0	0

name	user	system	elapsed
bedtools_closest	0.44	0.00	0.43
bedtools_complement	0.02	0.00	0.02
bedtools_coverage	0.13	0.00	0.12
bedtools_flank	0.09	0.00	0.09
bedtools_genomecov	0.13	0.00	0.13
bedtools_getfasta	0.04	0.00	0.05
bedtools_groupby	0.93	0.00	0.92
bedtools_intersect	0.39	0.00	0.39
bedtools_jaccard	0.09	0.00	0.09
bedtools_makewindows	0.09	0.00	0.10
bedtools_map	0.18	0.00	0.17
bedtools_merge	0.18	0.00	0.19
bedtools_multiinter	0.08	0.00	0.07
bedtools_nuc	0.06	0.00	0.07
bedtools_shift	0.05	0.00	0.04
bedtools_slop	0.08	0.00	0.08
bedtools_subtract	0.11	0.00	0.11
bedtools_unionbedg	0.06	0.00	0.06
distmode	0	0	0

CHECK results for HelloRanges on tokay2

Summary

Command output

Installation output

Tests output

Example timings