Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:58 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the autonomics package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/autonomics.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 102/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
autonomics 1.0.1 (landing page) Aditya Bhagwat
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: autonomics |
Version: 1.0.1 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:autonomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings autonomics_1.0.1.tar.gz |
StartedAt: 2021-10-14 19:43:37 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 20:00:30 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 1013.0 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: autonomics.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:autonomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings autonomics_1.0.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/autonomics.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 'autonomics/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'autonomics' version '1.0.1' * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. * checking for portable file names ... OK * checking whether package 'autonomics' 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 ... WARNING Undocumented code objects: 'translate' All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * 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' ... ERROR Running examples in 'autonomics-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: read_affymetrix > ### Title: Read affymetrix microarray > ### Aliases: read_affymetrix > > ### ** Examples > > require(magrittr) Loading required package: magrittr > url <- paste0('http://www.bioconductor.org/help/publications/2003/', + 'Chiaretti/chiaretti2/T33.tgz') > localfile <- file.path('~/autonomicscache', basename(url)) > if (!file.exists(localfile)){ + download.file(url, destfile = localfile) + untar(localfile, exdir = path.expand('~/autonomicscache')) + } Error in download.file(url, destfile = localfile) : cannot open destfile '~/autonomicscache/T33.tgz', reason 'No such file or directory' Execution halted ** running examples for arch 'x64' ... ERROR Running examples in 'autonomics-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: read_affymetrix > ### Title: Read affymetrix microarray > ### Aliases: read_affymetrix > > ### ** Examples > > require(magrittr) Loading required package: magrittr > url <- paste0('http://www.bioconductor.org/help/publications/2003/', + 'Chiaretti/chiaretti2/T33.tgz') > localfile <- file.path('~/autonomicscache', basename(url)) > if (!file.exists(localfile)){ + download.file(url, destfile = localfile) + untar(localfile, exdir = path.expand('~/autonomicscache')) + } Error in download.file(url, destfile = localfile) : cannot open destfile '~/autonomicscache/T33.tgz', reason 'No such file or directory' Execution halted * 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: 2 ERRORs, 1 WARNING, 1 NOTE See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/autonomics.Rcheck/00check.log' for details.
autonomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/autonomics_1.0.1.tar.gz && rm -rf autonomics.buildbin-libdir && mkdir autonomics.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=autonomics.buildbin-libdir autonomics_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL autonomics_1.0.1.zip && rm autonomics_1.0.1.tar.gz autonomics_1.0.1.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 2 9411k 2 222k 0 0 723k 0 0:00:13 --:--:-- 0:00:13 723k 46 9411k 46 4409k 0 0 3416k 0 0:00:02 0:00:01 0:00:01 3415k 100 9411k 100 9411k 0 0 4202k 0 0:00:02 0:00:02 --:--:-- 4205k install for i386 * installing *source* package 'autonomics' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Note: wrong number of arguments to '/' ** help *** installing help indices converting help for package 'autonomics' finding HTML links ... done AUTONOMICS_DATASETS html MAXQUANT_PATTERNS_PEPCOUNTS html MAXQUANT_PATTERNS_QUANTITY html TESTS html add_smiles html analysis html analyze html assert_is_valid_sumexp html biplot html biplot_corrections html biplot_covariates html center html contrast_subgroup_cols html contrastdefs html counts html counts2cpm html counts2tpm html cpm html create_design html create_sfile html default_formula html default_sfile html download_data html download_gtf html dt2mat html explore_imputations html explore_transformations html extract_features html extract_rectangle html fdata html filter_exprs_replicated_in_some_subgroup html filter_features html filter_medoid html filter_replicated html filter_samples html fit_limma html flevels html fnames html formula2str html fvalues html fvars html guess_maxquant_quantity html guess_sep html halfnormimpute html impute_systematic_nondetects html invert html is_imputed html is_sig html limma html log2counts html log2countsratios html log2cpm html log2cpmratios html log2tpm html log2tpmratios html log2transform html make_volcano_dt html matrix2sumexp html merge_sdata html merge_sfile html message_df html occupancies html pca html plot_boxplots html plot_contrastogram html plot_data html plot_densities html plot_detections html plot_features html plot_venn html plot_violins html plot_volcano html preprocess_rnaseq_counts html proteingroups html read_affymetrix html read_metabolon html read_proteingroups html read_rectangles html read_rnaseq_counts html read_somascan html rm_singleton_samples html scaledlibsizes html sdata html slevels html snames html split_by_svar html split_extract html standardize_maxquant_snames html subgroup_matrix html subtract_baseline html sumexp2mae html sumexp_to_long_dt html summarize_fit html svalues html svars html tpm html values html venn_detects html weights html zero_to_na html ** 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 'autonomics' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'autonomics' as autonomics_1.0.1.zip * DONE (autonomics) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'autonomics' successfully unpacked and MD5 sums checked
autonomics.Rcheck/tests_i386/testthat.Rout 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(autonomics) Attaching package: 'autonomics' The following object is masked from 'package:stats': biplot > > test_check("autonomics") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 102 ] > > proc.time() user system elapsed 122.37 4.37 124.75 |
autonomics.Rcheck/tests_x64/testthat.Rout 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(autonomics) Attaching package: 'autonomics' The following object is masked from 'package:stats': biplot > > test_check("autonomics") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 102 ] > > proc.time() user system elapsed 126.70 2.75 127.70 |
autonomics.Rcheck/examples_i386/autonomics-Ex.timings
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autonomics.Rcheck/examples_x64/autonomics-Ex.timings
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