Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:06:11 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 99/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
autonomics 1.2.0 (landing page) Aditya Bhagwat
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: autonomics |
Version: 1.2.0 |
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:autonomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings autonomics_1.2.0.tar.gz |
StartedAt: 2022-04-12 15:47:09 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 16:09:46 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 1356.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: autonomics.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:autonomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings autonomics_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/autonomics.Rcheck' * using R version 4.1.3 (2022-03-10) * 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 '1.2.0' * 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 ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in documentation object 'normimpute' 'ref' 'pos' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * 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 read_rnaseq_counts 22.15 0.86 22.57 pca 15.64 0.09 15.73 is_sig 13.05 0.11 13.00 filter_medoid 12.36 0.15 12.78 explore_imputations 11.50 0.14 11.50 biplot_covariates 11.06 0.17 11.24 plot_detections 11.01 0.19 10.86 read_somascan 10.67 0.19 10.85 read_rectangles 9.60 0.39 10.32 fit_limma 8.88 0.03 8.86 summarize_fit 7.32 0.47 7.52 read_metabolon 7.50 0.16 7.65 sumexp_to_long_dt 6.16 0.24 6.09 biplot_corrections 6.05 0.19 6.23 analyze 5.44 0.25 7.72 explore_transformations 5.36 0.13 5.40 read_proteingroups 5.36 0.12 5.33 plot_violins 5.19 0.08 5.26 plot_venn 5.17 0.08 5.22 add_smiles 3.05 0.22 5.89 counts 2.99 0.11 19.87 download_data 2.79 0.14 9.42 merge_sfile 2.64 0.25 30.36 center 2.59 0.25 162.87 analysis 2.30 0.19 16.36 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed read_rnaseq_counts 20.43 0.84 20.89 is_sig 12.39 0.08 12.34 filter_medoid 12.03 0.05 12.07 pca 11.64 0.07 11.72 explore_imputations 11.48 0.13 11.47 read_somascan 10.07 0.08 10.55 read_rectangles 9.28 0.42 9.70 plot_detections 8.50 0.22 8.44 fit_limma 8.28 0.05 8.29 biplot_covariates 7.68 0.13 7.81 read_metabolon 7.18 0.11 7.60 summarize_fit 6.36 0.25 6.44 read_proteingroups 5.90 0.14 5.87 explore_transformations 5.69 0.07 5.77 subtract_baseline 5.58 0.10 7.38 analyze 5.43 0.20 7.41 * 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: 1 WARNING, 1 NOTE See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/autonomics.Rcheck/00check.log' for details.
autonomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/autonomics_1.2.0.tar.gz && rm -rf autonomics.buildbin-libdir && mkdir autonomics.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=autonomics.buildbin-libdir autonomics_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL autonomics_1.2.0.zip && rm autonomics_1.2.0.tar.gz autonomics_1.2.0.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 9413k 2 194k 0 0 399k 0 0:00:23 --:--:-- 0:00:23 399k 13 9413k 13 1272k 0 0 855k 0 0:00:11 0:00:01 0:00:10 855k 34 9413k 34 3253k 0 0 1309k 0 0:00:07 0:00:02 0:00:05 1309k 57 9413k 57 5390k 0 0 1545k 0 0:00:06 0:00:03 0:00:03 1545k 82 9413k 82 7725k 0 0 1721k 0 0:00:05 0:00:04 0:00:01 1721k 100 9413k 100 9413k 0 0 1870k 0 0:00:05 0:00:05 --:--:-- 2028k 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_1.2.0.zip * DONE (autonomics) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'autonomics' successfully unpacked and MD5 sums checked
autonomics.Rcheck/tests_i386/testthat.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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 111.73 4.48 115.28 |
autonomics.Rcheck/tests_x64/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-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 131.23 3.26 132.78 |
autonomics.Rcheck/examples_i386/autonomics-Ex.timings
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autonomics.Rcheck/examples_x64/autonomics-Ex.timings
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