Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 |
Package 1246/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mgsa 1.54.0 (landing page) Sebastian Bauer
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the mgsa package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mgsa.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: mgsa |
Version: 1.54.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mgsa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mgsa_1.54.0.tar.gz |
StartedAt: 2024-12-20 05:56:23 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 05:57:45 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 81.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: mgsa.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mgsa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mgsa_1.54.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/mgsa.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mgsa/DESCRIPTION’ ... OK * this is package ‘mgsa’ version ‘1.54.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘mgsa’ can be installed ... WARNING Found the following significant warnings: mgsa.c:67:23: warning: more '%' conversions than data arguments [-Wformat-insufficient-args] See ‘/Users/biocbuild/bbs-3.20-bioc/meat/mgsa.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 code 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 ... NOTE Warning: no function found corresponding to methods exports from ‘mgsa’ for: ‘show’ A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE 'library' or 'require' call to ‘gplots’ which was already attached by Depends. Please remove these calls from your code. 'library' or 'require' calls in package code: ‘DBI’ ‘GO.db’ ‘RSQLite’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespaces in Imports field not imported from: ‘stats’ ‘utils’ All declared Imports should be used. Packages in Depends field not imported from: ‘gplots’ ‘methods’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE createMgsaGoSets: no visible global function definition for ‘new’ mcmcSummary: no visible binding for global variable ‘sd’ mgsa.wrapper: no visible global function definition for ‘str’ mgsa.wrapper: no visible global function definition for ‘new’ readGAF: no visible global function definition for ‘read.delim’ readGAF: no visible global function definition for ‘na.omit’ readGAF: no visible global function definition for ‘new’ initialize,MgsaSets: no visible global function definition for ‘callNextMethod’ initialize,MgsaSets: no visible global function definition for ‘relist’ mgsa,character-MgsaSets: no visible global function definition for ‘na.omit’ plot,MgsaResults: no visible global function definition for ‘split.screen’ plot,MgsaResults: no visible global function definition for ‘screen’ plot,MgsaResults: no visible global function definition for ‘par’ plot,MgsaResults: no visible global function definition for ‘barplot2’ plot,MgsaResults: no visible global function definition for ‘close.screen’ Undefined global functions or variables: barplot2 callNextMethod close.screen na.omit new par read.delim relist screen sd split.screen str Consider adding importFrom("graphics", "close.screen", "par", "screen", "split.screen") importFrom("methods", "callNextMethod", "new") importFrom("stats", "na.omit", "sd") importFrom("utils", "read.delim", "relist", "str") 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 line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... NOTE PKG_CXXFLAGS set in ‘src/Makevars.in’ without any corresponding files * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/mgsa/libs/mgsa.so’: Found ‘_printf’, possibly from ‘printf’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed readGAF 9.749 0.845 10.83 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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, 5 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/mgsa.Rcheck/00check.log’ for details.
mgsa.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mgsa ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘mgsa’ ... ** using staged installation configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I. -fPIC -falign-functions=64 -Wall -g -O2 -c mgsa-core.c -o mgsa-core.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I. -fPIC -falign-functions=64 -Wall -g -O2 -c mgsa.c -o mgsa.o mgsa.c:67:23: warning: more '%' conversions than data arguments [-Wformat-insufficient-args] error("Parameter '%s' has been requested to be discrete but no values were specified"); ~^ 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I. -fPIC -falign-functions=64 -Wall -g -O2 -c mt.c -o mt.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o mgsa.so mgsa-core.o mgsa.o mt.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-mgsa/00new/mgsa/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mgsa)
mgsa.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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("mgsa") Loading required package: gplots Attaching package: 'gplots' The following object is masked from 'package:stats': lowess > > > test_check("mgsa") [ FAIL 0 | WARN 6 | SKIP 0 | PASS 19 ] [ FAIL 0 | WARN 6 | SKIP 0 | PASS 19 ] > > proc.time() user system elapsed 13.610 1.082 14.869
mgsa.Rcheck/mgsa-Ex.timings
name | user | system | elapsed | |
MgsaSets-class | 0.014 | 0.001 | 0.015 | |
mgsa-methods | 1.193 | 0.014 | 1.220 | |
readGAF | 9.749 | 0.845 | 10.830 | |