Andrea Calabria
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/ISAnalytics |
| git_branch: master |
| git_last_commit: 780bce0 |
| git_last_commit_date: 2022-01-13 08:34:52 -0400 (Thu, 13 Jan 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:50 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 959/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ISAnalytics 1.5.3 (landing page) Andrea Calabria
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ISAnalytics |
| Version: 1.5.3 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ISAnalytics.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ISAnalytics_1.5.3.tar.gz |
| StartedAt: 2022-03-17 19:23:38 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:30:29 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 411.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ISAnalytics.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ISAnalytics.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ISAnalytics_1.5.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ISAnalytics.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.5.3'
* 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
sharing_venn 21.58 0.39 21.96
comparison_matrix 0.87 0.17 12.07
import_Vispa2_stats 0.76 0.19 6.56
iss_source 0.89 0.04 6.36
import_parallel_Vispa2Matrices 0.84 0.08 12.40
import_single_Vispa2Matrix 0.44 0.19 7.30
compute_near_integrations 0.32 0.02 6.56
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/ISAnalytics.Rcheck/00check.log'
for details.
ISAnalytics.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ISAnalytics
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-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
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
* DONE (ISAnalytics)
Making 'packages.html' ... done
ISAnalytics.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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: biocbuild/bbs-3.15-bioc/tmpdir/RtmpqCoP7Y/file25387b744f2.tsv (deflated 43%)
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|======================================================================| 100%
Calculating number of IS for each group...
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|======================================================================| 100%
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| | 0%
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|=================================== | 50%
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|======================================================================| 100%
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| | 0%
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|=================================== | 50%
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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
62.50 4.09 231.35
ISAnalytics.Rcheck/ISAnalytics-Ex.timings
| name | user | system | elapsed | |
| CIS_grubbs | 1.14 | 0.00 | 1.14 | |
| CIS_volcano_plot | 1.44 | 0.00 | 1.44 | |
| HSC_population_plot | 0.73 | 0.03 | 5.00 | |
| HSC_population_size_estimate | 0.45 | 0.00 | 4.53 | |
| aggregate_metadata | 0.10 | 0.02 | 0.11 | |
| aggregate_values_by_key | 0.05 | 0.00 | 0.05 | |
| annotation_IS_vars | 0 | 0 | 0 | |
| annotation_issues | 0.03 | 0.00 | 0.03 | |
| as_sparse_matrix | 0.04 | 0.00 | 0.05 | |
| association_file_columns | 0 | 0 | 0 | |
| available_outlier_tests | 0 | 0 | 0 | |
| blood_lineages_default | 0.02 | 0.00 | 0.01 | |
| circos_genomic_density | 0 | 0 | 0 | |
| clinical_relevant_suspicious_genes | 0 | 0 | 0 | |
| comparison_matrix | 0.87 | 0.17 | 12.07 | |
| compute_abundance | 0.04 | 0.00 | 0.03 | |
| compute_near_integrations | 0.32 | 0.02 | 6.56 | |
| cumulative_count_union | 0.13 | 0.01 | 0.14 | |
| cumulative_is | 0.08 | 0.00 | 0.08 | |
| date_columns_coll | 0 | 0 | 0 | |
| date_formats | 0 | 0 | 0 | |
| default_iss_file_prefixes | 0 | 0 | 0 | |
| default_meta_agg | 0.01 | 0.00 | 0.01 | |
| default_report_path | 0 | 0 | 0 | |
| default_stats | 0.02 | 0.00 | 0.02 | |
| generate_Vispa2_launch_AF | 0.03 | 0.00 | 0.03 | |
| generate_blank_association_file | 0 | 0 | 0 | |
| import_Vispa2_stats | 0.76 | 0.19 | 6.56 | |
| import_association_file | 0.27 | 0.14 | 0.32 | |
| import_parallel_Vispa2Matrices | 0.84 | 0.08 | 12.40 | |
| import_single_Vispa2Matrix | 0.44 | 0.19 | 7.30 | |
| integration_alluvial_plot | 2.78 | 0.03 | 2.81 | |
| is_sharing | 1.14 | 0.03 | 1.17 | |
| iss_source | 0.89 | 0.04 | 6.36 | |
| known_clinical_oncogenes | 0.02 | 0.00 | 0.02 | |
| mandatory_IS_vars | 0 | 0 | 0 | |
| matching_options | 0 | 0 | 0 | |
| outlier_filter | 0.72 | 0.00 | 3.70 | |
| outliers_by_pool_fragments | 0.44 | 0.00 | 3.25 | |
| purity_filter | 0.55 | 0.00 | 0.54 | |
| quantification_types | 0 | 0 | 0 | |
| realign_after_collisions | 0.42 | 0.02 | 3.30 | |
| reduced_AF_columns | 0 | 0 | 0 | |
| refGene_table_cols | 0 | 0 | 0 | |
| remove_collisions | 0.41 | 0.03 | 3.06 | |
| sample_statistics | 1.07 | 0.08 | 1.16 | |
| separate_quant_matrices | 0.02 | 0.00 | 0.02 | |
| sharing_heatmap | 2.30 | 0.09 | 2.39 | |
| sharing_venn | 21.58 | 0.39 | 21.96 | |
| threshold_filter | 0.04 | 0.00 | 0.05 | |
| top_abund_tableGrob | 0.36 | 0.00 | 0.36 | |
| top_integrations | 0.03 | 0.00 | 0.03 | |
| unzip_file_system | 0.02 | 0.00 | 0.02 | |