Package: cola

Version: 0.99.14

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cola.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings cola_0.99.14.tar.gz

StartedAt: 2019-04-09 01:55:57 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:58:08 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 131.4 seconds

RetCode: 1

Status:  ERROR

CheckDir: cola.Rcheck

Warnings: NA

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cola.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings cola_0.99.14.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/cola.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cola/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cola' version '0.99.14'
* 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 'cola' 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 ... WARNING
Codoc mismatches from documentation object 'hierarchical_partition':
hierarchical_partition
  Code: function(data, top_value_method = "MAD", partition_method =
                 "kmeans", concordance_cutoff = 0.9, PAC_cutoff = 0.2,
                 silhouette_cutoff = 0.5, min_samples = 6,
                 min_signatures = 50, max_k = 4, verbose = TRUE,
                 mc.cores = 1, ...)
  Docs: function(data, top_value_method = "MAD", partition_method =
                 "kmeans", concordance_cutoff = 0.9, PAC_cutoff = 0.2,
                 silhouette_cutoff = 0.5, min_samples = 6, max_k = 4,
                 verbose = TRUE, mc.cores = 1, ...)
  Argument names in code not in docs:
    min_signatures
  Mismatches in argument names (first 3):
    Position: 8 Code: min_signatures Docs: max_k
    Position: 9 Code: max_k Docs: verbose
    Position: 10 Code: verbose Docs: mc.cores

* 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 line endings in C/C++/Fortran sources/headers ... 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-3.9-bioc/R/library/cola/libs/i386/cola.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-3.9-bioc/R/library/cola/libs/x64/cola.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' ... ERROR
Running examples in 'cola-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: register_top_value_methods
> ### Title: Register user-defined top-value methods
> ### Aliases: register_top_value_methods
> 
> ### ** Examples
> 
> all_top_value_methods()
[1] "sd"  "cv"  "MAD" "ATC"
> register_top_value_methods(
+     ATC_spearman = function(mat) ATC(mat, method = "spearman"),
+     ATC_multicore = function(mat) ATC(mat, mc.cores = 2)
+ )
Error in mclapply(ind_list, function(ind) { : 
  'mc.cores' > 1 is not supported on Windows
Calls: register_top_value_methods -> <Anonymous> -> ATC -> mclapply
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'cola-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: register_top_value_methods
> ### Title: Register user-defined top-value methods
> ### Aliases: register_top_value_methods
> 
> ### ** Examples
> 
> all_top_value_methods()
[1] "sd"  "cv"  "MAD" "ATC"
> register_top_value_methods(
+     ATC_spearman = function(mat) ATC(mat, method = "spearman"),
+     ATC_multicore = function(mat) ATC(mat, mc.cores = 2)
+ )
Error in mclapply(ind_list, function(ind) { : 
  'mc.cores' > 1 is not supported on Windows
Calls: register_top_value_methods -> <Anonymous> -> ATC -> mclapply
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.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 ERRORs, 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/cola.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/cola_0.99.14.tar.gz && rm -rf cola.buildbin-libdir && mkdir cola.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cola.buildbin-libdir cola_0.99.14.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL cola_0.99.14.zip && rm cola_0.99.14.tar.gz cola_0.99.14.zip
###
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100  883k  100  883k    0     0  12.0M      0 --:--:-- --:--:-- --:--:-- 13.2M

install for i386

* installing *source* package 'cola' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cal_consensus_mat.cpp -o cal_consensus_mat.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o cola.dll tmp.def RcppExports.o cal_consensus_mat.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/cola.buildbin-libdir/00LOCK-cola/00new/cola/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cola'
    finding HTML links ... done
    ATC                                     html  
    ConsensusPartition-class                html  
    ConsensusPartitionList-class            html  
    Extract.ConsensusPartitionList          html  
    Extract.HierarchicalPartition           html  
    ExtractExtract.ConsensusPartitionList   html  
    ExtractExtract.HierarchicalPartition    html  
    HierarchicalPartition-class             html  
    PAC                                     html  
    adjust_matrix                           html  
    adjust_outlier                          html  
    all_leaves-HierarchicalPartition-method
                                            html  
    all_nodes-HierarchicalPartition-method
                                            html  
    all_partition_methods                   html  
    all_top_value_methods                   html  
    cola                                    html  
    cola_report-ConsensusPartition-method   html  
    cola_report-ConsensusPartitionList-method
                                            html  
    cola_report-HierarchicalPartition-method
                                            html  
    cola_report-dispatch                    html  
    cola_rh                                 html  
    cola_rl                                 html  
    collect_classes-ConsensusPartition-method
                                            html  
    collect_classes-ConsensusPartitionList-method
                                            html  
    collect_classes-HierarchicalPartition-method
                                            html  
    collect_classes-dispatch                html  
    collect_plots-ConsensusPartition-method
                                            html  
    collect_plots-ConsensusPartitionList-method
                                            html  
    collect_plots-dispatch                  html  
    concordance                             html  
    consensus_heatmap-ConsensusPartition-method
                                            html  
    consensus_partition                     html  
    correspond_between_rankings             html  
    correspond_between_two_rankings         html  
    dimension_reduction-ConsensusPartition-method
                                            html  
    dimension_reduction-HierarchicalPartition-method
                                            html  
    dimension_reduction-dispatch            html  
    dimension_reduction-matrix-method       html  
    get_anno-ConsensusPartition-method      html  
    get_anno-ConsensusPartitionList-method
                                            html  
    get_anno-HierarchicalPartition-method   html  
    get_anno-dispatch                       html  
    get_anno_col-ConsensusPartition-method
                                            html  
    get_anno_col-ConsensusPartitionList-method
                                            html  
    get_anno_col-HierarchicalPartition-method
                                            html  
    get_anno_col-dispatch                   html  
    get_classes-ConsensusPartition-method   html  
    get_classes-ConsensusPartitionList-method
                                            html  
    get_classes-HierarchicalPartition-method
                                            html  
    get_classes-dispatch                    html  
    get_consensus-ConsensusPartition-method
                                            html  
    get_matrix-ConsensusPartition-method    html  
    get_matrix-ConsensusPartitionList-method
                                            html  
    get_matrix-HierarchicalPartition-method
                                            html  
    get_matrix-dispatch                     html  
    get_membership-ConsensusPartition-method
                                            html  
    get_membership-ConsensusPartitionList-method
                                            html  
    get_membership-dispatch                 html  
    get_param-ConsensusPartition-method     html  
    get_signatures-ConsensusPartition-method
                                            html  
    get_signatures-HierarchicalPartition-method
                                            html  
    get_signatures-dispatch                 html  
    get_stats-ConsensusPartition-method     html  
    get_stats-ConsensusPartitionList-method
                                            html  
    get_stats-dispatch                      html  
    guess_best_k-ConsensusPartition-method
                                            html  
    guess_best_k-ConsensusPartitionList-method
                                            html  
    guess_best_k-HierarchicalPartition-method
                                            html  
    guess_best_k-dispatch                   html  
    hierarchical_partition                  html  
    knitr_add_tab_item                      html  
    knitr_insert_tabs                       html  
    max_depth-HierarchicalPartition-method
                                            html  
    membership_heatmap-ConsensusPartition-method
                                            html  
    plot_ecdf-ConsensusPartition-method     html  
    register_NMF                            html  
    register_SOM                            html  
    register_partition_methods              html  
    register_top_value_methods              html  
    relabel_class                           html  
    remove_partition_methods                html  
    remove_top_value_methods                html  
    run_all_consensus_partition_methods     html  
    select_partition_number-ConsensusPartition-method
                                            html  
    show-ConsensusPartition-method          html  
    show-ConsensusPartitionList-method      html  
    show-HierarchicalPartition-method       html  
    show-dispatch                           html  
    submit_to_david                         html  
    test_between_factors                    html  
    test_to_known_factors-ConsensusPartition-method
                                            html  
    test_to_known_factors-ConsensusPartitionList-method
                                            html  
    test_to_known_factors-HierarchicalPartition-method
                                            html  
    test_to_known_factors-dispatch          html  
    top_elements_overlap                    html  
    top_rows_heatmap-ConsensusPartitionList-method
                                            html  
    top_rows_heatmap-dispatch               html  
    top_rows_heatmap-matrix-method          html  
    top_rows_overlap-ConsensusPartitionList-method
                                            html  
    top_rows_overlap-dispatch               html  
    top_rows_overlap-matrix-method          html  
    venn_euler                              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 'cola' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cal_consensus_mat.cpp -o cal_consensus_mat.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o cola.dll tmp.def RcppExports.o cal_consensus_mat.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/cola.buildbin-libdir/cola/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cola' as cola_0.99.14.zip
* DONE (cola)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'cola' successfully unpacked and MD5 sums checked

R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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.

> library(testthat)
> suppressWarnings(suppressPackageStartupMessages(library(cola)))
> 
> test_check("cola")
== testthat results  ===========================================================
OK: 1 SKIPPED: 0 FAILED: 0
> 
> 
> proc.time()
   user  system elapsed 
   1.18    0.21    1.39 

R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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.

> library(testthat)
> suppressWarnings(suppressPackageStartupMessages(library(cola)))
> 
> test_check("cola")
== testthat results  ===========================================================
OK: 1 SKIPPED: 0 FAILED: 0
> 
> 
> proc.time()
   user  system elapsed 
   1.12    0.10    1.21