| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:08:12 -0400 (Wed, 13 Apr 2022).
| 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 | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 956/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ISAnalytics 1.4.3 (landing page) Andrea Calabria
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ISAnalytics |
| Version: 1.4.3 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ISAnalytics_1.4.3.tar.gz |
| StartedAt: 2022-04-12 14:36:08 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 14:41:36 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 327.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ISAnalytics.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ISAnalytics_1.4.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ISAnalytics.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 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
.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 43.514 0.328 43.903
integration_alluvial_plot 8.487 1.262 5.791
compute_near_integrations 5.120 4.565 2.676
iss_source 5.564 0.769 4.013
sharing_heatmap 5.053 0.062 5.123
* 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
‘/Users/biocbuild/bbs-3.14-bioc/meat/ISAnalytics.Rcheck/00check.log’
for details.
ISAnalytics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ISAnalytics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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)
ISAnalytics.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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: tmp/RtmpJcTCCg/filef712122b0a5a.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 0 | PASS 772 ]
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 772 ]
>
> proc.time()
user system elapsed
124.875 15.865 128.196
ISAnalytics.Rcheck/ISAnalytics-Ex.timings
| name | user | system | elapsed | |
| CIS_grubbs | 2.851 | 0.076 | 2.935 | |
| CIS_volcano_plot | 3.392 | 0.026 | 3.421 | |
| HSC_population_plot | 2.714 | 0.501 | 2.119 | |
| HSC_population_size_estimate | 2.213 | 0.487 | 1.722 | |
| aggregate_metadata | 0.234 | 0.025 | 0.259 | |
| aggregate_values_by_key | 0.126 | 0.012 | 0.138 | |
| annotation_IS_vars | 0.001 | 0.000 | 0.001 | |
| annotation_issues | 0.069 | 0.004 | 0.073 | |
| as_sparse_matrix | 0.069 | 0.003 | 0.072 | |
| association_file_columns | 0.001 | 0.002 | 0.003 | |
| available_outlier_tests | 0.000 | 0.001 | 0.000 | |
| blood_lineages_default | 0.037 | 0.001 | 0.037 | |
| circos_genomic_density | 0.001 | 0.000 | 0.000 | |
| clinical_relevant_suspicious_genes | 0.023 | 0.000 | 0.023 | |
| comparison_matrix | 2.817 | 1.070 | 2.730 | |
| compute_abundance | 0.077 | 0.010 | 0.087 | |
| compute_near_integrations | 5.120 | 4.565 | 2.676 | |
| cumulative_count_union | 0.351 | 0.168 | 0.363 | |
| cumulative_is | 0.198 | 0.020 | 0.218 | |
| date_columns_coll | 0 | 0 | 0 | |
| date_formats | 0.000 | 0.000 | 0.001 | |
| default_iss_file_prefixes | 0 | 0 | 0 | |
| default_meta_agg | 0.03 | 0.00 | 0.03 | |
| default_report_path | 0.003 | 0.000 | 0.003 | |
| default_stats | 0.001 | 0.000 | 0.002 | |
| generate_Vispa2_launch_AF | 0.066 | 0.004 | 0.069 | |
| generate_blank_association_file | 0.010 | 0.001 | 0.012 | |
| import_Vispa2_stats | 0.810 | 0.353 | 0.839 | |
| import_association_file | 0.389 | 0.077 | 0.447 | |
| import_parallel_Vispa2Matrices | 2.622 | 1.139 | 2.325 | |
| import_single_Vispa2Matrix | 1.231 | 1.518 | 1.148 | |
| integration_alluvial_plot | 8.487 | 1.262 | 5.791 | |
| is_sharing | 2.198 | 0.045 | 2.247 | |
| iss_source | 5.564 | 0.769 | 4.013 | |
| known_clinical_oncogenes | 0.019 | 0.002 | 0.021 | |
| mandatory_IS_vars | 0 | 0 | 0 | |
| matching_options | 0 | 0 | 0 | |
| outlier_filter | 1.238 | 0.326 | 1.358 | |
| outliers_by_pool_fragments | 0.656 | 0.256 | 0.727 | |
| purity_filter | 1.314 | 0.056 | 1.371 | |
| quantification_types | 0.000 | 0.001 | 0.000 | |
| realign_after_collisions | 1.813 | 0.730 | 1.313 | |
| reduced_AF_columns | 0.000 | 0.000 | 0.001 | |
| refGene_table_cols | 0.000 | 0.000 | 0.001 | |
| remove_collisions | 1.866 | 0.747 | 1.385 | |
| sample_statistics | 2.405 | 0.223 | 2.634 | |
| separate_quant_matrices | 0.034 | 0.003 | 0.038 | |
| sharing_heatmap | 5.053 | 0.062 | 5.123 | |
| sharing_venn | 43.514 | 0.328 | 43.903 | |
| threshold_filter | 0.131 | 0.001 | 0.131 | |
| top_abund_tableGrob | 0.866 | 0.006 | 0.873 | |
| top_integrations | 0.056 | 0.001 | 0.058 | |
| unzip_file_system | 0.005 | 0.016 | 0.021 | |