Multiple platform build/check report for BioC 3.7 - CHECK report for metagene on tokay2

Package: metagene

Version: 2.12.2

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagene.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings metagene_2.12.2.tar.gz

StartedAt: 2018-10-17 03:11:38 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 03:22:08 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 630.4 seconds

RetCode: 1

Status: ERROR

CheckDir: metagene.Rcheck

Warnings: NA

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagene.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings metagene_2.12.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/metagene.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'metagene/DESCRIPTION' ... OK
* this is package 'metagene' version '2.12.2'
* 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 'metagene' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'similaRpeak'
A package should be listed in only one of these fields.
* 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 ... NOTE
avoid_gaps_update: no visible binding for global variable 'value'
avoid_gaps_update: no visible binding for global variable 'bam'
avoid_gaps_update: no visible binding for global variable 'tab'
avoid_gaps_update: no visible binding for global variable 'nuc'
permutation_test: no visible global function definition for '.'
permutation_test: no visible binding for global variable 'value'
plot_metagene: no visible binding for global variable 'bin'
plot_metagene: no visible binding for global variable 'value'
plot_metagene: no visible binding for global variable 'qinf'
plot_metagene: no visible binding for global variable 'qsup'
plot_metagene: no visible binding for global variable 'group'
plot_metagene: no visible binding for global variable 'nuc'
plot_metagene: no visible binding for global variable 'design'
plot_metagene: no visible binding for global variable 'nuctot'
Undefined global functions or variables:
  . bam bin design group nuc nuctot qinf qsup tab value
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... 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
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
  ERROR in test.metagene_initialize_valid_named_bam_files: Error in private$check_bam_file(bam_file) : 
    Bam file C:/Users/biocbuild/bbs-3.7-bioc/R/library/metagene/extdata/align1_rep1.bam not found.
  
  Test files with failing tests
  
     test_metagene.R 
       test.metagene_initialize_valid_named_bam_files 
  
  
  Error in BiocGenerics:::testPackage("metagene") : 
    unit tests failed for package metagene
  In addition: Warning message:
  In `[<-`(`*tmp*`, design_name, value = new("SimpleRleList", elementType = "Rle",  :
    implicit list embedding of S4 objects is deprecated
  Execution halted
** running tests for arch 'x64' ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
  ERROR in test.metagene_initialize_valid_named_bam_files: Error in private$check_bam_file(bam_file) : 
    Bam file C:/Users/biocbuild/bbs-3.7-bioc/R/library/metagene/extdata/align1_rep1.bam not found.
  
  Test files with failing tests
  
     test_metagene.R 
       test.metagene_initialize_valid_named_bam_files 
  
  
  Error in BiocGenerics:::testPackage("metagene") : 
    unit tests failed for package metagene
  In addition: Warning message:
  In `[<-`(`*tmp*`, design_name, value = new("SimpleRleList", elementType = "Rle",  :
    implicit list embedding of S4 objects is deprecated
  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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/metagene.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/metagene_2.12.2.tar.gz && rm -rf metagene.buildbin-libdir && mkdir metagene.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metagene.buildbin-libdir metagene_2.12.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL metagene_2.12.2.zip && rm metagene_2.12.2.tar.gz metagene_2.12.2.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 4870k  100 4870k    0     0  47.7M      0 --:--:-- --:--:-- --:--:-- 50.6M

install for i386

* installing *source* package 'metagene' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'metagene'
    finding HTML links ... done
    Bam_Handler                             html  
    avoid_gaps_update                       html  
    bed_file_filter                         html  
    exon_by_gene_with_observed_transcripts
                                            html  
    get_demo_bam_files                      html  
    get_demo_design                         html  
    get_demo_metagene                       html  
    get_demo_regions                        html  
    get_promoters_txdb                      html  
    metagene                                html  
    permutation_test                        html  
    plot_metagene                           html  
    promoters_hg18                          html  
    promoters_hg19                          html  
    promoters_mm10                          html  
    promoters_mm9                           html  
    write_bed_file_filter_result            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'metagene' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metagene' as metagene_2.12.2.zip
* DONE (metagene)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'metagene' successfully unpacked and MD5 sums checked
In R CMD INSTALL


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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("metagene")

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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, 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

produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
Timing stopped at: 0.17 0 0.17
Error in private$check_bam_file(bam_file) : 
  Bam file C:/Users/biocbuild/bbs-3.7-bioc/R/library/metagene/extdata/align1_rep1.bam not found.
In addition: 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 normalizePath(path.expand(path), winslash, mustWork) :
  path[1]="NotExistingFile": The system cannot find the file specified
3: In normalizePath(path.expand(path), winslash, mustWork) :
  path[2]="NotExistingFile2": The system cannot find the file specified
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
ChIP-Seq flip/unflip
produce data table : ChIP-Seq
[1] TRUE
Normalization done
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
produce data table : ChIP-Seq
ChIP-Seq flip/unflip
ChIP-Seq flip/unflip
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
[1] TRUE


RUNIT TEST PROTOCOL -- Wed Oct 17 03:20:01 2018 
*********************************************** 
Number of test functions: 205 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
metagene RUnit Tests - 205 test functions, 1 error, 0 failures
ERROR in test.metagene_initialize_valid_named_bam_files: Error in private$check_bam_file(bam_file) : 
  Bam file C:/Users/biocbuild/bbs-3.7-bioc/R/library/metagene/extdata/align1_rep1.bam not found.

Test files with failing tests

   test_metagene.R 
     test.metagene_initialize_valid_named_bam_files 


Error in BiocGenerics:::testPackage("metagene") : 
  unit tests failed for package metagene
In addition: Warning message:
In `[<-`(`*tmp*`, design_name, value = new("SimpleRleList", elementType = "Rle",  :
  implicit list embedding of S4 objects is deprecated
Execution halted


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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("metagene")

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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, 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

produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
Timing stopped at: 0.15 0 0.14
Error in private$check_bam_file(bam_file) : 
  Bam file C:/Users/biocbuild/bbs-3.7-bioc/R/library/metagene/extdata/align1_rep1.bam not found.
In addition: 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 normalizePath(path.expand(path), winslash, mustWork) :
  path[1]="NotExistingFile": The system cannot find the file specified
3: In normalizePath(path.expand(path), winslash, mustWork) :
  path[2]="NotExistingFile2": The system cannot find the file specified
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
ChIP-Seq flip/unflip
produce data table : ChIP-Seq
[1] TRUE
Normalization done
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
produce data table : ChIP-Seq
ChIP-Seq flip/unflip
ChIP-Seq flip/unflip
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
[1] TRUE


RUNIT TEST PROTOCOL -- Wed Oct 17 03:22:02 2018 
*********************************************** 
Number of test functions: 205 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
metagene RUnit Tests - 205 test functions, 1 error, 0 failures
ERROR in test.metagene_initialize_valid_named_bam_files: Error in private$check_bam_file(bam_file) : 
  Bam file C:/Users/biocbuild/bbs-3.7-bioc/R/library/metagene/extdata/align1_rep1.bam not found.

Test files with failing tests

   test_metagene.R 
     test.metagene_initialize_valid_named_bam_files 


Error in BiocGenerics:::testPackage("metagene") : 
  unit tests failed for package metagene
In addition: Warning message:
In `[<-`(`*tmp*`, design_name, value = new("SimpleRleList", elementType = "Rle",  :
  implicit list embedding of S4 objects is deprecated
Execution halted

name	user	system	elapsed
Bam_Handler	0.25	0.04	0.41
avoid_gaps_update	0	0	0
bed_file_filter	0	0	0
exon_by_gene_with_observed_transcripts	0	0	0
get_demo_bam_files	0.00	0.01	0.02
get_demo_design	0	0	0
get_demo_metagene	2.39	0.63	3.56
get_demo_regions	0	0	0
get_promoters_txdb	0	0	0
metagene	0.33	0.00	0.33
permutation_test	0	0	0
plot_metagene	1.05	0.07	1.12
promoters_hg18	0.01	0.00	0.02
promoters_hg19	0	0	0
promoters_mm10	0.00	0.02	0.01
promoters_mm9	0.02	0.00	0.02
write_bed_file_filter_result	0	0	0

name	user	system	elapsed
Bam_Handler	1.03	0.00	1.03
avoid_gaps_update	0.01	0.00	0.02
bed_file_filter	0	0	0
exon_by_gene_with_observed_transcripts	0	0	0
get_demo_bam_files	0	0	0
get_demo_design	0	0	0
get_demo_metagene	1.70	0.13	1.83
get_demo_regions	0	0	0
get_promoters_txdb	0	0	0
metagene	0.28	0.01	0.30
permutation_test	0	0	0
plot_metagene	0.62	0.05	0.67
promoters_hg18	0.00	0.02	0.02
promoters_hg19	0	0	0
promoters_mm10	0	0	0
promoters_mm9	0	0	0
write_bed_file_filter_result	0	0	0

CHECK report for metagene on tokay2

Summary

Command output

Installation output

Tests output

Example timings