Multiple platform build/check report for BioC 3.14 - CHECK results for ISAnalytics 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: ISAnalytics

Version: 1.4.3

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ISAnalytics.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ISAnalytics_1.4.3.tar.gz

StartedAt: 2022-04-12 21:39:29 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 21:59:07 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 1177.4 seconds

RetCode: 0

Status: OK

CheckDir: ISAnalytics.Rcheck

Warnings: 0

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ISAnalytics.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ISAnalytics_1.4.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ISAnalytics.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 'ISAnalytics/DESCRIPTION' ... OK
* this is package 'ISAnalytics' version '1.4.3'
* package encoding: UTF-8
* 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 'ISAnalytics' 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 ... NOTE
.check_file_system_alignment: no visible binding for global variable
  'Found'
.clean_data: no visible binding for global variable 'alluvia_id'
.count_group_union: no visible binding for global variable
  '..col_groups'
.count_group_union: no visible binding for global variable 'group_id'
.find_in_common : <anonymous>: no visible binding for global variable
  'group_id'
.sh_obtain_lookup: no visible global function definition for '.'
.sh_row_permut: no visible binding for global variable 'shared'
.sh_row_permut: no visible binding for global variable 'is_coord'
.sh_row_permut: no visible global function definition for '.'
.sh_truth_tbl_venn : retrieve_is: no visible binding for global
  variable 'group_id'
.sh_truth_tbl_venn: no visible binding for global variable 'observed'
.sh_truth_tbl_venn: no visible binding for global variable 'group_id'
.sharing_multdf_mult_key: no visible binding for global variable
  'shared'
.sharing_multdf_mult_key : <anonymous>: no visible binding for global
  variable 'is'
.sharing_multdf_mult_key: no visible binding for global variable '.'
.sharing_multdf_single_key: no visible binding for global variable
  'shared'
.sharing_multdf_single_key : <anonymous>: no visible binding for global
  variable 'is'
.sharing_multdf_single_key: no visible binding for global variable '.'
.sharing_singledf_mult_key: no visible binding for global variable
  'shared'
.sharing_singledf_mult_key: no visible binding for global variable 'is'
.sharing_singledf_mult_key: no visible binding for global variable '.'
.sharing_singledf_single_key: no visible binding for global variable
  'is'
.sharing_singledf_single_key: no visible binding for global variable
  'shared'
.sharing_singledf_single_key : <anonymous>: no visible binding for
  global variable 'shared'
.sharing_singledf_single_key : <anonymous>: no visible binding for
  global variable 'is_coord'
.sharing_singledf_single_key : <anonymous>: no visible binding for
  global variable 'group_id'
.sharing_singledf_single_key: no visible binding for global variable
  '.'
.sliding_window: no visible binding for global variable '..mand_vars'
.sliding_window: no visible binding for global variable 'chr_before'
.sliding_window: no visible binding for global variable
  'integration_locus_before'
.sliding_window: no visible binding for global variable 'strand_before'
.sliding_window: no visible binding for global variable '..num_cols'
compute_near_integrations: no visible binding for global variable
  '..mand_vars'
compute_near_integrations: no visible binding for global variable
  'chr_before'
compute_near_integrations: no visible binding for global variable
  'integration_locus_before'
compute_near_integrations: no visible binding for global variable
  'strand_before'
cumulative_is: no visible global function definition for '.'
cumulative_is : <anonymous>: no visible binding for global variable
  'is'
cumulative_is: no visible binding for global variable 'is'
sharing_heatmap : plot_rel_heat: no visible binding for global variable
  '..fill..'
Undefined global functions or variables:
  . ..col_groups ..fill.. ..mand_vars ..num_cols Found alluvia_id
  chr_before group_id integration_locus_before is is_coord observed
  shared strand_before
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
sharing_venn                   24.33   0.53   34.43
comparison_matrix               1.43   0.21   16.18
compute_near_integrations       1.33   0.26   10.28
import_parallel_Vispa2Matrices  1.14   0.14   15.05
import_single_Vispa2Matrix      1.00   0.26    9.41
import_Vispa2_stats             0.92   0.22    8.00
iss_source                      1.09   0.00    8.07
HSC_population_plot             0.87   0.00    7.00
outliers_by_pool_fragments      0.69   0.00    9.08
HSC_population_size_estimate    0.66   0.02    6.52
remove_collisions               0.64   0.01    5.01
realign_after_collisions        0.53   0.00    7.70
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
sharing_venn                   26.24   0.28   26.72
comparison_matrix               1.66   0.20   33.53
import_parallel_Vispa2Matrices  1.32   0.05   15.03
compute_near_integrations       0.95   0.40   11.51
import_single_Vispa2Matrix      0.92   0.35    8.99
iss_source                      1.20   0.01    7.89
import_Vispa2_stats             0.96   0.11    9.55
HSC_population_plot             0.88   0.00    6.65
HSC_population_size_estimate    0.78   0.03    7.25
remove_collisions               0.72   0.01    5.10
realign_after_collisions        0.68   0.04    5.04
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/ISAnalytics.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ISAnalytics_1.4.3.tar.gz && rm -rf ISAnalytics.buildbin-libdir && mkdir ISAnalytics.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ISAnalytics.buildbin-libdir ISAnalytics_1.4.3.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ISAnalytics_1.4.3.zip && rm ISAnalytics_1.4.3.tar.gz ISAnalytics_1.4.3.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
  2 2452k    2 51087    0     0   323k      0  0:00:07 --:--:--  0:00:07  323k
 97 2452k   97 2396k    0     0  2083k      0  0:00:01  0:00:01 --:--:-- 2083k
100 2452k  100 2452k    0     0  2128k      0  0:00:01  0:00:01 --:--:-- 2128k

install for i386

* installing *source* package 'ISAnalytics' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ISAnalytics'
    finding HTML links ... done
    CIS_grubbs                              html  
    CIS_volcano_plot                        html  
    HSC_population_plot                     html  
    HSC_population_size_estimate            html  
    ISAnalytics-deprecated                  html  
    ISAnalytics                             html  
    aggregate_metadata                      html  
    aggregate_values_by_key                 html  
    annotation_IS_vars                      html  
    annotation_issues                       html  
    as_sparse_matrix                        html  
    association_file                        html  
    association_file_columns                html  
    available_outlier_tests                 html  
    blood_lineages_default                  html  
    circos_genomic_density                  html  
    clinical_relevant_suspicious_genes      html  
    comparison_matrix                       html  
    compute_abundance                       html  
    compute_near_integrations               html  
    cumulative_count_union                  html  
    cumulative_is                           html  
    date_columns_coll                       html  
    date_formats                            html  
    default_iss_file_prefixes               html  
    default_meta_agg                        html  
    default_report_path                     html  
    default_stats                           html  
    generate_Vispa2_launch_AF               html  
    generate_blank_association_file         html  
    import_Vispa2_stats                     html  
    import_association_file                 html  
    import_parallel_Vispa2Matrices          html  
    import_parallel_Vispa2Matrices_auto     html  
    import_parallel_Vispa2Matrices_interactive
                                            html  
    import_single_Vispa2Matrix              html  
    integration_alluvial_plot               html  
    integration_matrices                    html  
    is_sharing                              html  
    iss_source                              html  
    known_clinical_oncogenes                html  
    mandatory_IS_vars                       html  
    matching_options                        html  
    outlier_filter                          html  
    outliers_by_pool_fragments              html  
    proto_oncogenes                         html  
    purity_filter                           html  
    quantification_types                    html  
    realign_after_collisions                html  
    reduced_AF_columns                      html  
    refGene_table_cols                      html  
    refGenes_hg19                           html  
    remove_collisions                       html  
    sample_statistics                       html  
    separate_quant_matrices                 html  
    sharing_heatmap                         html  
    sharing_venn                            html  
    threshold_filter                        html  
    top_abund_tableGrob                     html  
    top_integrations                        html  
    unzip_file_system                       html  
*** copying figures
** 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 'ISAnalytics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ISAnalytics' as ISAnalytics_1.4.3.zip
* DONE (ISAnalytics)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ISAnalytics' 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.

> library(testthat)
> library(ISAnalytics)
Loading required package: magrittr

Attaching package: 'magrittr'

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

    equals, is_less_than, not

> 
> test_check("ISAnalytics")
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Warning: found NA concatenatePoolIDSeqRun field
i Check association file for possible issues
Duplicates found for some files
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Some files are missing and will be ignored
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Some files are missing and will be ignored
  adding: Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpuI1ob2/file32c45d046898.tsv (deflated 43%)

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Calculating number of IS for each group...

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Calculating combinations...
Done!
Calculating combinations...
Done!
[ FAIL 0 | WARN 6 | SKIP 1 | PASS 755 ]

== Skipped tests ===============================================================
* On Windows (1)

[ FAIL 0 | WARN 6 | SKIP 1 | PASS 755 ]
> 
> proc.time()
   user  system elapsed 
  72.56    4.21  302.29


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.

> library(testthat)
> library(ISAnalytics)
Loading required package: magrittr

Attaching package: 'magrittr'

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

    equals, is_less_than, not

> 
> test_check("ISAnalytics")
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Warning: found NA concatenatePoolIDSeqRun field
i Check association file for possible issues
Duplicates found for some files
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Some files are missing and will be ignored
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Some files are missing and will be ignored
  adding: Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpWoAmzU/file1eec5fb2116.tsv (deflated 43%)

  |                                                                            
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  |======================================================================| 100%

Calculating number of IS for each group...

  |                                                                            
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  |                                                                            
  |======================================================================| 100%


  |                                                                            
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  |======================================================================| 100%


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  |======================================================================| 100%

Calculating combinations...
Done!
Calculating combinations...
Done!
[ FAIL 0 | WARN 6 | SKIP 1 | PASS 755 ]

== Skipped tests ===============================================================
* On Windows (1)

[ FAIL 0 | WARN 6 | SKIP 1 | PASS 755 ]
> 
> proc.time()
   user  system elapsed 
  79.62    3.62  334.51

name	user	system	elapsed
CIS_grubbs	1.50	0.06	1.57
CIS_volcano_plot	1.66	0.05	1.70
HSC_population_plot	0.87	0.00	7.00
HSC_population_size_estimate	0.66	0.02	6.52
aggregate_metadata	0.23	0.00	0.23
aggregate_values_by_key	0.11	0.00	0.11
annotation_IS_vars	0	0	0
annotation_issues	0.05	0.01	0.06
as_sparse_matrix	0.08	0.00	0.08
association_file_columns	0	0	0
available_outlier_tests	0	0	0
blood_lineages_default	0.03	0.00	0.03
circos_genomic_density	0	0	0
clinical_relevant_suspicious_genes	0.02	0.00	0.02
comparison_matrix	1.43	0.21	16.18
compute_abundance	0.08	0.00	0.08
compute_near_integrations	1.33	0.26	10.28
cumulative_count_union	0.22	0.00	0.22
cumulative_is	0.14	0.00	0.14
date_columns_coll	0	0	0
date_formats	0	0	0
default_iss_file_prefixes	0	0	0
default_meta_agg	0.02	0.00	0.01
default_report_path	0	0	0
default_stats	0	0	0
generate_Vispa2_launch_AF	0.03	0.02	0.05
generate_blank_association_file	0.02	0.00	0.02
import_Vispa2_stats	0.92	0.22	8.00
import_association_file	0.44	0.14	0.53
import_parallel_Vispa2Matrices	1.14	0.14	15.05
import_single_Vispa2Matrix	1.00	0.26	9.41
integration_alluvial_plot	4.36	0.03	4.93
is_sharing	1.69	0.10	1.79
iss_source	1.09	0.00	8.07
known_clinical_oncogenes	0.02	0.00	0.02
mandatory_IS_vars	0	0	0
matching_options	0	0	0
outlier_filter	0.81	0.00	4.45
outliers_by_pool_fragments	0.69	0.00	9.08
purity_filter	0.92	0.00	0.94
quantification_types	0	0	0
realign_after_collisions	0.53	0.00	7.70
reduced_AF_columns	0	0	0
refGene_table_cols	0	0	0
remove_collisions	0.64	0.01	5.01
sample_statistics	1.65	0.11	1.77
separate_quant_matrices	0.04	0.00	0.03
sharing_heatmap	2.73	0.25	2.98
sharing_venn	24.33	0.53	34.43
threshold_filter	0.15	0.00	0.15
top_abund_tableGrob	0.66	0.02	0.67
top_integrations	0.03	0.00	0.03
unzip_file_system	0.00	0.01	0.02

name	user	system	elapsed
CIS_grubbs	1.43	0.00	1.43
CIS_volcano_plot	2.26	0.02	2.28
HSC_population_plot	0.88	0.00	6.65
HSC_population_size_estimate	0.78	0.03	7.25
aggregate_metadata	0.23	0.00	0.24
aggregate_values_by_key	0.11	0.00	0.11
annotation_IS_vars	0	0	0
annotation_issues	0.06	0.00	0.06
as_sparse_matrix	0.08	0.00	0.08
association_file_columns	0	0	0
available_outlier_tests	0	0	0
blood_lineages_default	0.03	0.00	0.03
circos_genomic_density	0	0	0
clinical_relevant_suspicious_genes	0.02	0.00	0.02
comparison_matrix	1.66	0.20	33.53
compute_abundance	0.06	0.02	0.08
compute_near_integrations	0.95	0.40	11.51
cumulative_count_union	0.19	0.00	0.19
cumulative_is	0.12	0.00	0.12
date_columns_coll	0	0	0
date_formats	0	0	0
default_iss_file_prefixes	0	0	0
default_meta_agg	0.02	0.00	0.02
default_report_path	0.00	0.02	0.01
default_stats	0	0	0
generate_Vispa2_launch_AF	0.05	0.00	0.05
generate_blank_association_file	0	0	0
import_Vispa2_stats	0.96	0.11	9.55
import_association_file	0.50	0.07	0.53
import_parallel_Vispa2Matrices	1.32	0.05	15.03
import_single_Vispa2Matrix	0.92	0.35	8.99
integration_alluvial_plot	3.97	0.00	3.96
is_sharing	1.29	0.06	1.36
iss_source	1.20	0.01	7.89
known_clinical_oncogenes	0.02	0.00	0.02
mandatory_IS_vars	0	0	0
matching_options	0	0	0
outlier_filter	0.95	0.01	4.75
outliers_by_pool_fragments	0.80	0.00	4.58
purity_filter	0.94	0.00	0.94
quantification_types	0	0	0
realign_after_collisions	0.68	0.04	5.04
reduced_AF_columns	0	0	0
refGene_table_cols	0	0	0
remove_collisions	0.72	0.01	5.10
sample_statistics	1.86	0.08	1.94
separate_quant_matrices	0.02	0.02	0.03
sharing_heatmap	3.01	0.04	3.06
sharing_venn	26.24	0.28	26.72
threshold_filter	0.17	0.00	0.17
top_abund_tableGrob	0.72	0.00	0.72
top_integrations	0.05	0.00	0.05
unzip_file_system	0.00	0.02	0.01

CHECK results for ISAnalytics on tokay2

Summary

Command output

Installation output

Tests output

Example timings