Multiple platform build/check report for BioC 3.12 - CHECK report for metagene2 on tokay1

Package: metagene2

Version: 1.6.1

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagene2.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings metagene2_1.6.1.tar.gz

StartedAt: 2021-05-06 04:25:37 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 04:35:37 -0400 (Thu, 06 May 2021)

EllapsedTime: 600.1 seconds

RetCode: 0

Status: OK

CheckDir: metagene2.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagene2.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings metagene2_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/metagene2.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'metagene2/DESCRIPTION' ... OK
* this is package 'metagene2' version '1.6.1'
* 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 'metagene2' 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 ... 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 Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* 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
plot_metagene 7.61    0.1     7.7
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
plot_metagene  7.3   0.03    7.33
* 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: OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/metagene2_1.6.1.tar.gz && rm -rf metagene2.buildbin-libdir && mkdir metagene2.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metagene2.buildbin-libdir metagene2_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL metagene2_1.6.1.zip && rm metagene2_1.6.1.tar.gz metagene2_1.6.1.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
100 1440k  100 1440k    0     0  11.0M      0 --:--:-- --:--:-- --:--:-- 11.1M

install for i386

* installing *source* package 'metagene2' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'metagene2'
    finding HTML links ... done
    Bam_Handler                             html  
    as_is_region_order                      html  
    coverage_order                          html  
    get_demo_bam_files                      html  
    get_demo_design                         html  
    get_demo_metagene                       html  
    get_demo_region_filenames               html  
    get_demo_regions                        html  
    get_demo_rna_bam_files                  html  
    get_demo_rna_regions                    html  
    metagene2                               html  
    metagene2_heatmap                       html  
    plot_metagene                           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 'metagene2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metagene2' as metagene2_1.6.1.zip
* DONE (metagene2)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'metagene2' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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.

> ## Run all tests in the metagene package
> BiocGenerics:::testPackage("metagene2")

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


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    windows

region_name is missing from the new metadata. Recreating it.
region_name is missing from the new metadata. Recreating it.
region_name is missing from the new metadata. Recreating it.
Replace region_metadata with metadata which would result in a different region split. All caches at the 'split_regions' step will be invalidated, and split_by will be reset to its default value.


RUNIT TEST PROTOCOL -- Thu May 06 04:33:21 2021 
*********************************************** 
Number of test functions: 128 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
metagene2 RUnit Tests - 128 test functions, 0 errors, 0 failures
Number of test functions: 128 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In checkIdentical(obs, warning(exp)) : 

Some bam files have discrepancies in their seqnames.

This could be caused by chromosome names present only in a subset of the bam files (i.e.: chrY in some bam files, but absent in others.

This could also be caused by discrepancies in the seqlevels style (i.e.: UCSC:chr1 versus NCBI:1)


2: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 100 out-of-bound ranges located on sequence
  chr1. Note that ranges located on a sequence whose length is unknown
  (NA) or on a circular sequence are not considered out-of-bound (use
  seqlengths() and isCircular() to get the lengths and circularity flags
  of the underlying sequences). You can use trim() to trim these ranges.
  See ?`trim,GenomicRanges-method` for more information.
3: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 200 out-of-bound ranges located on sequence
  chr1. Note that ranges located on a sequence whose length is unknown
  (NA) or on a circular sequence are not considered out-of-bound (use
  seqlengths() and isCircular() to get the lengths and circularity flags
  of the underlying sequences). You can use trim() to trim these ranges.
  See ?`trim,GenomicRanges-method` for more information.
4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 600 out-of-bound ranges located on sequence
  chr1. Note that ranges located on a sequence whose length is unknown
  (NA) or on a circular sequence are not considered out-of-bound (use
  seqlengths() and isCircular() to get the lengths and circularity flags
  of the underlying sequences). You can use trim() to trim these ranges.
  See ?`trim,GenomicRanges-method` for more information.
> #BiocGenerics:::testPackage("metagene2", pattern="^test_demo.*\\.R$")
> 
> proc.time()
   user  system elapsed 
 107.90    2.46  114.15


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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.

> ## Run all tests in the metagene package
> BiocGenerics:::testPackage("metagene2")

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


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    windows

region_name is missing from the new metadata. Recreating it.
region_name is missing from the new metadata. Recreating it.
region_name is missing from the new metadata. Recreating it.
Replace region_metadata with metadata which would result in a different region split. All caches at the 'split_regions' step will be invalidated, and split_by will be reset to its default value.


RUNIT TEST PROTOCOL -- Thu May 06 04:35:30 2021 
*********************************************** 
Number of test functions: 128 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
metagene2 RUnit Tests - 128 test functions, 0 errors, 0 failures
Number of test functions: 128 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In checkIdentical(obs, warning(exp)) : 

Some bam files have discrepancies in their seqnames.

This could be caused by chromosome names present only in a subset of the bam files (i.e.: chrY in some bam files, but absent in others.

This could also be caused by discrepancies in the seqlevels style (i.e.: UCSC:chr1 versus NCBI:1)


2: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 100 out-of-bound ranges located on sequence
  chr1. Note that ranges located on a sequence whose length is unknown
  (NA) or on a circular sequence are not considered out-of-bound (use
  seqlengths() and isCircular() to get the lengths and circularity flags
  of the underlying sequences). You can use trim() to trim these ranges.
  See ?`trim,GenomicRanges-method` for more information.
3: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 200 out-of-bound ranges located on sequence
  chr1. Note that ranges located on a sequence whose length is unknown
  (NA) or on a circular sequence are not considered out-of-bound (use
  seqlengths() and isCircular() to get the lengths and circularity flags
  of the underlying sequences). You can use trim() to trim these ranges.
  See ?`trim,GenomicRanges-method` for more information.
4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 600 out-of-bound ranges located on sequence
  chr1. Note that ranges located on a sequence whose length is unknown
  (NA) or on a circular sequence are not considered out-of-bound (use
  seqlengths() and isCircular() to get the lengths and circularity flags
  of the underlying sequences). You can use trim() to trim these ranges.
  See ?`trim,GenomicRanges-method` for more information.
> #BiocGenerics:::testPackage("metagene2", pattern="^test_demo.*\\.R$")
> 
> proc.time()
   user  system elapsed 
 121.46    3.03  128.15

name	user	system	elapsed
Bam_Handler	0.11	0.00	0.11
as_is_region_order	3.41	0.22	3.64
coverage_order	2.20	0.25	2.45
get_demo_bam_files	0	0	0
get_demo_design	0	0	0
get_demo_metagene	1.61	0.11	1.72
get_demo_region_filenames	0.11	0.00	0.11
get_demo_regions	0.10	0.00	0.09
get_demo_rna_bam_files	0	0	0
get_demo_rna_regions	0.11	0.00	0.11
metagene2	1.57	0.10	1.68
metagene2_heatmap	3.71	0.18	3.89
plot_metagene	7.61	0.10	7.70

name	user	system	elapsed
Bam_Handler	0.09	0.00	0.09
as_is_region_order	3.13	0.11	3.24
coverage_order	2.78	0.13	2.91
get_demo_bam_files	0	0	0
get_demo_design	0	0	0
get_demo_metagene	2.22	0.15	2.37
get_demo_region_filenames	0.13	0.00	0.13
get_demo_regions	0.09	0.00	0.09
get_demo_rna_bam_files	0	0	0
get_demo_rna_regions	0.11	0.00	0.11
metagene2	1.89	0.08	1.97
metagene2_heatmap	3.97	0.08	4.05
plot_metagene	7.30	0.03	7.33

CHECK report for metagene2 on tokay1

Summary

Command output

Installation output

Tests output

Example timings