Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:09 -0400 (Fri, 15 Oct 2021).
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 944/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ISAnalytics 1.2.1 (landing page) Andrea Calabria
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: ISAnalytics |
Version: 1.2.1 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ISAnalytics.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ISAnalytics_1.2.1.tar.gz |
StartedAt: 2021-10-15 00:53:29 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 01:15:11 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 1301.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: ISAnalytics.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ISAnalytics.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ISAnalytics_1.2.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ISAnalytics.Rcheck' * using R version 4.1.1 (2021-08-10) * 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 '1.2.1' * 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 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 ... 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 ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... 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 CIS_grubbs 4.25 0.21 16.25 CIS_volcano_plot 4.22 0.13 14.39 sample_statistics 2.34 0.12 12.41 realign_after_collisions 1.58 0.27 20.32 HSC_population_plot 1.55 0.08 20.77 remove_collisions 1.52 0.11 19.61 HSC_population_size_estimate 1.47 0.08 18.75 separate_quant_matrices 1.23 0.16 10.75 import_parallel_Vispa2Matrices_auto 1.14 0.11 13.74 compute_near_integrations 1.05 0.18 16.75 cumulative_count_union 1.17 0.04 10.78 comparison_matrix 0.94 0.11 20.97 aggregate_values_by_key 0.94 0.03 11.06 import_Vispa2_stats 0.81 0.12 8.26 import_single_Vispa2Matrix 0.72 0.08 8.78 compute_abundance 0.73 0.06 7.88 as_sparse_matrix 0.51 0.18 8.44 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed CIS_grubbs 5.38 0.19 15.74 CIS_volcano_plot 4.44 0.09 14.90 sample_statistics 2.47 0.22 12.53 realign_after_collisions 1.86 0.11 20.88 remove_collisions 1.80 0.09 21.69 HSC_population_size_estimate 1.62 0.09 19.18 HSC_population_plot 1.50 0.07 19.94 compute_near_integrations 1.28 0.09 15.61 separate_quant_matrices 1.22 0.05 10.84 aggregate_values_by_key 1.20 0.06 11.28 cumulative_count_union 1.14 0.11 11.47 comparison_matrix 1.08 0.13 11.14 import_parallel_Vispa2Matrices_auto 1.11 0.03 11.65 import_Vispa2_stats 0.78 0.06 8.15 as_sparse_matrix 0.70 0.09 7.43 compute_abundance 0.70 0.05 8.23 import_single_Vispa2Matrix 0.64 0.08 7.90 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' ERROR Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: == Failed tests ================================================================ -- Error (test-import-im-single.R:155:5): import_single_Vispa2Matrix reads type NEW different params -- Error: Cannot open file for writing: * 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp0SHftc\filee68363848ca.tsv' Backtrace: x 1. \-readr::write_tsv(...) test-import-im-single.R:155:4 2. \-readr::write_delim(...) 3. \-vroom::vroom_write(...) 4. \-vroom:::vroom_write_(...) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 810 ] Error: Test failures Execution halted ** running tests for arch 'x64' ... Running 'testthat.R' ERROR Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: == Failed tests ================================================================ -- Error (test-import-im-single.R:155:5): import_single_Vispa2Matrix reads type NEW different params -- Error: Cannot open file for writing: * 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp4ExIrF\file2278176d1ab8.tsv' Backtrace: x 1. \-readr::write_tsv(...) test-import-im-single.R:155:4 2. \-readr::write_delim(...) 3. \-vroom::vroom_write(...) 4. \-vroom:::vroom_write_(...) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 810 ] Error: Test failures Execution halted * 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 See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ISAnalytics.Rcheck/00check.log' for details.
ISAnalytics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ISAnalytics_1.2.1.tar.gz && rm -rf ISAnalytics.buildbin-libdir && mkdir ISAnalytics.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ISAnalytics.buildbin-libdir ISAnalytics_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ISAnalytics_1.2.1.zip && rm ISAnalytics_1.2.1.tar.gz ISAnalytics_1.2.1.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 83 1906k 83 1592k 0 0 1903k 0 0:00:01 --:--:-- 0:00:01 1902k 100 1906k 100 1906k 0 0 2074k 0 --:--:-- --:--:-- --:--:-- 2074k install for i386 * installing *source* package 'ISAnalytics' ... ** using staged installation ** R ** 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 html aggregate_metadata html aggregate_values_by_key html annotation_IS_vars html as_sparse_matrix html association_file_columns html available_outlier_tests html blood_lineages_default html clinical_relevant_suspicious_genes html comparison_matrix html compute_abundance html compute_near_integrations html cumulative_count_union html date_columns_coll html date_formats html default_iss_file_prefixes html default_meta_agg 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_auto html import_parallel_Vispa2Matrices_interactive html import_single_Vispa2Matrix html known_clinical_oncogenes html mandatory_IS_vars html matching_options html outlier_filter html outliers_by_pool_fragments html quantification_types html realign_after_collisions html reduced_AF_columns html remove_collisions html sample_statistics html separate_quant_matrices html threshold_filter 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_1.2.1.zip * DONE (ISAnalytics) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'ISAnalytics' successfully unpacked and MD5 sums checked
ISAnalytics.Rcheck/tests_i386/testthat.Rout.fail R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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 | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% Identifying collisions... Processing collisions... Finished! You provided a single sequence count as matrix, to re-align other related matrices see ?realign_after_collisions *** Association file import summary *** i For detailed report please set option 'ISAnalytics.widgets' to TRUE * Parsing problems detected: TRUE * Date parsing problems: TRUE * Column problems detected: TRUE * NAs found in important columns: TRUE * File system alignment: skipped *** Association file import summary *** i For detailed report please set option 'ISAnalytics.widgets' to TRUE * Parsing problems detected: TRUE * Date parsing problems: TRUE * Column problems detected: TRUE * NAs found in important columns: TRUE * File system alignment: no problems detected *** Association file import summary *** i For detailed report please set option 'ISAnalytics.widgets' to TRUE * Parsing problems detected: TRUE * Date parsing problems: TRUE * Column problems detected: TRUE * NAs found in important columns: TRUE * File system alignment: problems detected *** Association file import summary *** i For detailed report please set option 'ISAnalytics.widgets' to TRUE * Parsing problems detected: TRUE * Date parsing problems: TRUE * Column problems detected: TRUE * NAs found in important columns: TRUE * File system alignment: skipped *** Association file import summary *** i For detailed report please set option 'ISAnalytics.widgets' to TRUE * Parsing problems detected: TRUE * Date parsing problems: TRUE * Column problems detected: TRUE * NAs found in important columns: TRUE * File system alignment: no problems detected *** Association file import summary *** i For detailed report please set option 'ISAnalytics.widgets' to TRUE * Parsing problems detected: TRUE * Date parsing problems: TRUE * Column problems detected: TRUE * NAs found in important columns: TRUE * File system alignment: no problems detected 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 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 Some files are missing and will be ignored adding: Users/biocbuild/bbs-3.13-bioc/tmpdir/Rtmp0SHftc/filee681f323ef3.tsv (deflated 43%) | | | 0% | |======================================================================| 100% Calculating number of IS for each group... | | | 0% | |======================================================================| 100% == Failed tests ================================================================ -- Error (test-import-im-single.R:155:5): import_single_Vispa2Matrix reads type NEW different params -- Error: Cannot open file for writing: * 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp0SHftc\filee68363848ca.tsv' Backtrace: x 1. \-readr::write_tsv(...) test-import-im-single.R:155:4 2. \-readr::write_delim(...) 3. \-vroom::vroom_write(...) 4. \-vroom:::vroom_write_(...) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 810 ] Error: Test failures Execution halted |
ISAnalytics.Rcheck/tests_x64/testthat.Rout.fail R version 4.1.1 (2021-08-10) -- "Kick Things" 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 | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% Identifying collisions... Processing collisions... Finished! You provided a single sequence count as matrix, to re-align other related matrices see ?realign_after_collisions *** Association file import summary *** i For detailed report please set option 'ISAnalytics.widgets' to TRUE * Parsing problems detected: TRUE * Date parsing problems: TRUE * Column problems detected: TRUE * NAs found in important columns: TRUE * File system alignment: skipped *** Association file import summary *** i For detailed report please set option 'ISAnalytics.widgets' to TRUE * Parsing problems detected: TRUE * Date parsing problems: TRUE * Column problems detected: TRUE * NAs found in important columns: TRUE * File system alignment: no problems detected *** Association file import summary *** i For detailed report please set option 'ISAnalytics.widgets' to TRUE * Parsing problems detected: TRUE * Date parsing problems: TRUE * Column problems detected: TRUE * NAs found in important columns: TRUE * File system alignment: problems detected *** Association file import summary *** i For detailed report please set option 'ISAnalytics.widgets' to TRUE * Parsing problems detected: TRUE * Date parsing problems: TRUE * Column problems detected: TRUE * NAs found in important columns: TRUE * File system alignment: skipped *** Association file import summary *** i For detailed report please set option 'ISAnalytics.widgets' to TRUE * Parsing problems detected: TRUE * Date parsing problems: TRUE * Column problems detected: TRUE * NAs found in important columns: TRUE * File system alignment: no problems detected *** Association file import summary *** i For detailed report please set option 'ISAnalytics.widgets' to TRUE * Parsing problems detected: TRUE * Date parsing problems: TRUE * Column problems detected: TRUE * NAs found in important columns: TRUE * File system alignment: no problems detected 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 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 Some files are missing and will be ignored adding: Users/biocbuild/bbs-3.13-bioc/tmpdir/Rtmp4ExIrF/file22781f7875.tsv (deflated 43%) | | | 0% | |======================================================================| 100% Calculating number of IS for each group... | | | 0% | |======================================================================| 100% == Failed tests ================================================================ -- Error (test-import-im-single.R:155:5): import_single_Vispa2Matrix reads type NEW different params -- Error: Cannot open file for writing: * 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp4ExIrF\file2278176d1ab8.tsv' Backtrace: x 1. \-readr::write_tsv(...) test-import-im-single.R:155:4 2. \-readr::write_delim(...) 3. \-vroom::vroom_write(...) 4. \-vroom:::vroom_write_(...) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 810 ] Error: Test failures Execution halted |
ISAnalytics.Rcheck/examples_i386/ISAnalytics-Ex.timings
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ISAnalytics.Rcheck/examples_x64/ISAnalytics-Ex.timings
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