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This page was generated on 2021-11-26 15:04:54 -0500 (Fri, 26 Nov 2021).

CHECK results for ISAnalytics on nebbiolo2

To the developers/maintainers of the ISAnalytics package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ISAnalytics.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 956/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ISAnalytics 1.4.1  (landing page)
Andrea Calabria
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/ISAnalytics
git_branch: RELEASE_3_14
git_last_commit: 0fed8b9
git_last_commit_date: 2021-10-28 05:05:55 -0500 (Thu, 28 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ISAnalytics
Version: 1.4.1
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ISAnalytics_1.4.1.tar.gz
StartedAt: 2021-11-25 09:53:53 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 09:56:24 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 151.7 seconds
RetCode: 0
Status:   OK  
CheckDir: ISAnalytics.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ISAnalytics_1.4.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/ISAnalytics.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ISAnalytics/DESCRIPTION’ ... OK
* this is package ‘ISAnalytics’ version ‘1.4.1’
* 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 for sufficient/correct file permissions ... 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
* 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
.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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
sharing_venn 23.776  0.416  24.168
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/ISAnalytics.Rcheck/00check.log’
for details.



Installation output

ISAnalytics.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL ISAnalytics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘ISAnalytics’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** 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
* DONE (ISAnalytics)

Tests output

ISAnalytics.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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

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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: tmp/RtmpBizMIx/file5050c36428b8c.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 0 | SKIP 0 | PASS 765 ]
> 
> proc.time()
   user  system elapsed 
 46.092   9.408  48.677 

Example timings

ISAnalytics.Rcheck/ISAnalytics-Ex.timings

nameusersystemelapsed
CIS_grubbs1.4090.0331.441
CIS_volcano_plot1.5360.0241.560
HSC_population_plot1.0880.2560.949
HSC_population_size_estimate0.6500.1260.806
aggregate_metadata0.4780.0800.127
aggregate_values_by_key0.0550.0000.055
annotation_IS_vars000
as_sparse_matrix0.0430.0000.043
association_file_columns000
available_outlier_tests000
blood_lineages_default0.0150.0030.018
circos_genomic_density000
clinical_relevant_suspicious_genes0.010.000.01
comparison_matrix1.3930.7241.286
compute_abundance0.0410.0040.045
compute_near_integrations2.4781.8361.214
cumulative_count_union0.1200.0120.132
cumulative_is0.1130.0070.107
date_columns_coll000
date_formats000
default_iss_file_prefixes000
default_meta_agg0.0120.0040.016
default_report_path0.0030.0000.002
default_stats0.0010.0000.000
generate_Vispa2_launch_AF0.0250.0040.027
generate_blank_association_file0.0030.0040.007
import_Vispa2_stats0.5090.1690.555
import_association_file0.1760.0560.216
import_parallel_Vispa2Matrices1.2950.8091.231
import_single_Vispa2Matrix0.8140.4930.616
integration_alluvial_plot3.9520.6822.886
is_sharing1.1110.0031.109
iss_source1.6080.3581.339
known_clinical_oncogenes0.0070.0040.011
mandatory_IS_vars0.0010.0000.000
matching_options000
outlier_filter0.7310.1320.767
outliers_by_pool_fragments0.4290.1180.431
purity_filter0.4220.0040.426
quantification_types0.0010.0000.000
realign_after_collisions0.6470.2050.549
reduced_AF_columns0.0010.0000.000
refGene_table_cols000
remove_collisions0.7250.2050.565
sample_statistics1.0820.1031.185
separate_quant_matrices0.0190.0000.020
sharing_heatmap2.7560.1122.862
sharing_venn23.776 0.41624.168
threshold_filter0.0470.0080.055
top_abund_tableGrob0.4680.0000.468
top_integrations0.0310.0000.031
unzip_file_system0.0040.0000.004