Multiple platform build/check report for BioC 3.8 - CHECK report for metagene on tokay1

Package: metagene

Version: 2.14.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagene.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings metagene_2.14.0.tar.gz

StartedAt: 2019-04-13 03:39:08 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 03:49:08 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 600.4 seconds

RetCode: 1

Status: ERROR

CheckDir: metagene.Rcheck

Warnings: NA

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagene.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings metagene_2.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/metagene.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '2.14.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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:
    Bam file C:/Users/biocbuild/bbs-3.8-bioc/R/library/metagene/extdata/align1_rep1.bam not found.
  
  Test files with failing tests
  
     test_metagene.R 
       test.metagene_get_table_check_copy_of_table 
       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:
    Bam file C:/Users/biocbuild/bbs-3.8-bioc/R/library/metagene/extdata/align1_rep1.bam not found.
  
  Test files with failing tests
  
     test_metagene.R 
       test.metagene_get_table_check_copy_of_table 
       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-3.8-bioc/meat/metagene.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/metagene_2.14.0.tar.gz && rm -rf metagene.buildbin-libdir && mkdir metagene.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metagene.buildbin-libdir metagene_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL metagene_2.14.0.zip && rm metagene_2.14.0.tar.gz metagene_2.14.0.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
100 4870k  100 4870k    0     0  58.8M      0 --:--:-- --:--:-- --:--:-- 61.7M

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_2.14.0.zip
* DONE (metagene)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'metagene' successfully unpacked and MD5 sums checked
In R CMD INSTALL


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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
Timing stopped at: 0.38 0 0.39
Error in `[.data.table`(tab, , `:=`(c, 1:5)) : 
  Supplied 5 items to be assigned to 50000 items of column 'c'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code.
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
Timing stopped at: 0.13 0 0.13
Error in private$check_bam_file(bam_file) : 
  Bam file C:/Users/biocbuild/bbs-3.8-bioc/R/library/metagene/extdata/align1_rep1.bam not found.
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 -- Sat Apr 13 03:47:09 2019 
*********************************************** 
Number of test functions: 205 
Number of errors: 2 
Number of failures: 0 

 
1 Test Suite : 
metagene RUnit Tests - 205 test functions, 2 errors, 0 failures
ERROR in test.metagene_get_table_check_copy_of_table: Error in `[.data.table`(tab, , `:=`(c, 1:5)) : 
  Supplied 5 items to be assigned to 50000 items of column 'c'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code.
ERROR in test.metagene_initialize_valid_named_bam_files: Error in private$check_bam_file(bam_file) : 
  Bam file C:/Users/biocbuild/bbs-3.8-bioc/R/library/metagene/extdata/align1_rep1.bam not found.

Test files with failing tests

   test_metagene.R 
     test.metagene_get_table_check_copy_of_table 
     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 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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
Timing stopped at: 0.45 0 0.45
Error in `[.data.table`(tab, , `:=`(c, 1:5)) : 
  Supplied 5 items to be assigned to 50000 items of column 'c'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code.
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
Timing stopped at: 0.13 0 0.12
Error in private$check_bam_file(bam_file) : 
  Bam file C:/Users/biocbuild/bbs-3.8-bioc/R/library/metagene/extdata/align1_rep1.bam not found.
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 -- Sat Apr 13 03:49:03 2019 
*********************************************** 
Number of test functions: 205 
Number of errors: 2 
Number of failures: 0 

 
1 Test Suite : 
metagene RUnit Tests - 205 test functions, 2 errors, 0 failures
ERROR in test.metagene_get_table_check_copy_of_table: Error in `[.data.table`(tab, , `:=`(c, 1:5)) : 
  Supplied 5 items to be assigned to 50000 items of column 'c'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code.
ERROR in test.metagene_initialize_valid_named_bam_files: Error in private$check_bam_file(bam_file) : 
  Bam file C:/Users/biocbuild/bbs-3.8-bioc/R/library/metagene/extdata/align1_rep1.bam not found.

Test files with failing tests

   test_metagene.R 
     test.metagene_get_table_check_copy_of_table 
     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	0.19	0.01	0.53
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	0	0
get_demo_design	0.00	0.02	0.02
get_demo_metagene	1.57	0.45	2.56
get_demo_regions	0	0	0
get_promoters_txdb	0	0	0
metagene	0.24	0.02	0.25
permutation_test	0	0	0
plot_metagene	0.83	0.08	0.91
promoters_hg18	0	0	0
promoters_hg19	0.01	0.00	0.01
promoters_mm10	0	0	0
promoters_mm9	0	0	0
write_bed_file_filter_result	0	0	0

name	user	system	elapsed
Bam_Handler	0.91	0.02	0.92
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	0	0
get_demo_design	0	0	0
get_demo_metagene	1.56	0.09	1.65
get_demo_regions	0	0	0
get_promoters_txdb	0	0	0
metagene	0.25	0.02	0.27
permutation_test	0	0	0
plot_metagene	0.61	0.08	0.69
promoters_hg18	0.00	0.01	0.02
promoters_hg19	0	0	0
promoters_mm10	0	0	0
promoters_mm9	0.00	0.02	0.01
write_bed_file_filter_result	0	0	0

CHECK report for metagene on tokay1

Summary

Command output

Installation output

Tests output

Example timings