Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:06:51 -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 metagene package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metagene.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 1097/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
metagene 2.26.0 (landing page) Charles Joly Beauparlant
| 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: metagene |
Version: 2.26.0 |
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagene.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings metagene_2.26.0.tar.gz |
StartedAt: 2022-04-12 22:30:01 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 22:38:52 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 530.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: metagene.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagene.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings metagene_2.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/metagene.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 'metagene/DESCRIPTION' ... OK * this is package 'metagene' version '2.26.0' * 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 'metagene' can be installed ... OK * checking installed package size ... NOTE installed size is 7.2Mb sub-directories of 1Mb or more: extdata 5.4Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: 'similaRpeak' A package should be listed in only one of these fields. * 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 ... NOTE NCIS.internal: no visible global function definition for 'est.norm.med.search' avoid_gaps_update: no visible binding for global variable 'value' avoid_gaps_update: no visible binding for global variable 'bam' avoid_gaps_update: no visible binding for global variable 'tab' avoid_gaps_update: no visible binding for global variable 'nuc' bin.data: no visible global function definition for 'hist' permutation_test: no visible global function definition for '.' permutation_test: no visible binding for global variable 'value' plot_metagene: no visible binding for global variable 'bin' plot_metagene: no visible binding for global variable 'value' plot_metagene: no visible binding for global variable 'qinf' plot_metagene: no visible binding for global variable 'qsup' plot_metagene: no visible binding for global variable 'group' plot_metagene: no visible binding for global variable 'nuc' plot_metagene: no visible binding for global variable 'design' plot_metagene: no visible binding for global variable 'nuctot' Undefined global functions or variables: . bam bin design est.norm.med.search group hist nuc nuctot qinf qsup tab value Consider adding importFrom("graphics", "hist") to your NAMESPACE file. * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... Running 'runTests.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: 3 NOTEs See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/metagene.Rcheck/00check.log' for details.
metagene.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/metagene_2.26.0.tar.gz && rm -rf metagene.buildbin-libdir && mkdir metagene.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metagene.buildbin-libdir metagene_2.26.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL metagene_2.26.0.zip && rm metagene_2.26.0.tar.gz metagene_2.26.0.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 22 4875k 22 1116k 0 0 1360k 0 0:00:03 --:--:-- 0:00:03 1359k 70 4875k 70 3431k 0 0 1875k 0 0:00:02 0:00:01 0:00:01 1875k 100 4875k 100 4875k 0 0 2097k 0 0:00:02 0:00:02 --:--:-- 2098k install for i386 * installing *source* package 'metagene' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'metagene' finding HTML links ... done Bam_Handler html avoid_gaps_update html bed_file_filter html exon_by_gene_with_observed_transcripts html get_demo_bam_files html get_demo_design html get_demo_metagene html get_demo_regions html get_promoters_txdb html metagene html permutation_test html plot_metagene html promoters_hg18 html promoters_hg19 html promoters_mm10 html promoters_mm9 html write_bed_file_filter_result 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 'metagene' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'metagene' as metagene_2.26.0.zip * DONE (metagene) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'metagene' successfully unpacked and MD5 sums checked
metagene.Rcheck/tests_i386/runTests.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. > ## Run all tests in the metagene package > BiocGenerics:::testPackage("metagene") Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq [1] TRUE produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq ChIP-Seq flip/unflip Normalization done produce data table : ChIP-Seq [1] TRUE produce data table : ChIP-Seq [1] TRUE produce data table : ChIP-Seq [1] TRUE produce data table : ChIP-Seq [1] TRUE produce data table : ChIP-Seq [1] TRUE produce data table : ChIP-Seq produce data table : ChIP-Seq ChIP-Seq flip/unflip ChIP-Seq flip/unflip produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq [1] TRUE RUNIT TEST PROTOCOL -- Tue Apr 12 22:37:13 2022 *********************************************** Number of test functions: 204 Number of errors: 0 Number of failures: 0 1 Test Suite : metagene RUnit Tests - 204 test functions, 0 errors, 0 failures Number of test functions: 204 Number of errors: 0 Number of failures: 0 There were 13 warnings (use warnings() to see them) > > proc.time() user system elapsed 77.68 2.92 80.84 |
metagene.Rcheck/tests_x64/runTests.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. > ## Run all tests in the metagene package > BiocGenerics:::testPackage("metagene") Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data frame : ChIP-Seq [1] TRUE produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq ChIP-Seq flip/unflip Normalization done produce data table : ChIP-Seq [1] TRUE produce data table : ChIP-Seq [1] TRUE produce data table : ChIP-Seq [1] TRUE produce data table : ChIP-Seq [1] TRUE produce data table : ChIP-Seq [1] TRUE produce data table : ChIP-Seq produce data table : ChIP-Seq ChIP-Seq flip/unflip ChIP-Seq flip/unflip produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq produce data table : ChIP-Seq [1] TRUE RUNIT TEST PROTOCOL -- Tue Apr 12 22:38:45 2022 *********************************************** Number of test functions: 204 Number of errors: 0 Number of failures: 0 1 Test Suite : metagene RUnit Tests - 204 test functions, 0 errors, 0 failures Number of test functions: 204 Number of errors: 0 Number of failures: 0 There were 13 warnings (use warnings() to see them) > > proc.time() user system elapsed 89.89 1.68 91.53 |
metagene.Rcheck/examples_i386/metagene-Ex.timings
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metagene.Rcheck/examples_x64/metagene-Ex.timings
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