Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-04 11:37:09 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
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 158/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
bgx 1.68.3 (landing page) Ernest Turro
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the bgx package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bgx.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: bgx |
Version: 1.68.3 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bgx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bgx_1.68.3.tar.gz |
StartedAt: 2024-03-03 19:08:56 -0500 (Sun, 03 Mar 2024) |
EndedAt: 2024-03-03 19:10:53 -0500 (Sun, 03 Mar 2024) |
EllapsedTime: 116.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: bgx.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bgx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bgx_1.68.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/bgx.Rcheck’ * using R version 4.3.2 Patched (2023-11-01 r85457) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘bgx/DESCRIPTION’ ... OK * this is package ‘bgx’ version ‘1.68.3’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘bgx’ can be installed ... WARNING Found the following significant warnings: clang: warning: argument unused during compilation: '-mcpu=pentium2' [-Wunused-command-line-argument] See ‘/Users/biocbuild/bbs-3.18-bioc/meat/bgx.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * 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 ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 * 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 ... NOTE Namespace in Imports field not imported from: ‘Rcpp’ All declared Imports should be used. Packages in Depends field not imported from: ‘Biobase’ ‘affy’ 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 bgx: no visible global function definition for ‘geneNames’ bgx: no visible global function definition for ‘sampleNames’ bgx: no visible global function definition for ‘new’ bgx: no visible global function definition for ‘annotation’ bgx: no visible global function definition for ‘description’ bgx: no visible global function definition for ‘assayDataElementReplace’ loessNorm: no visible global function definition for ‘loess’ loessNorm: no visible global function definition for ‘predict’ plotDEDensity: no visible global function definition for ‘density’ plotDEDensity: no visible global function definition for ‘abline’ plotDEHistogram: no visible global function definition for ‘hist’ plotDEHistogram: no visible global function definition for ‘glm’ plotDEHistogram: no visible binding for global variable ‘poisson’ plotDEHistogram: no visible global function definition for ‘lines’ plotDEHistogram: no visible global function definition for ‘points’ plotDiffRank: no visible global function definition for ‘quantile’ plotDiffRank: no visible global function definition for ‘sd’ plotDiffRank: no visible global function definition for ‘segments’ plotDiffRank: no visible global function definition for ‘abline’ plotExpressionDensity: no visible global function definition for ‘density’ plotExpressionDensity: no visible global function definition for ‘lines’ plotExpressionDensity: no visible global function definition for ‘legend’ readSingle.bgx: no visible global function definition for ‘read.delim’ saveAffinityPlot.bgx: no visible global function definition for ‘pdf’ saveAffinityPlot.bgx: no visible global function definition for ‘par’ saveAffinityPlot.bgx: no visible global function definition for ‘dev.off’ setupVars.bgx : calcProbeAffCategories: no visible global function definition for ‘cdfName’ setupVars.bgx : calcProbeAffCategories: no visible global function definition for ‘median’ setupVars.bgx: no visible global function definition for ‘pData’ setupVars.bgx: no visible global function definition for ‘indexProbes’ standalone.bgx: no visible global function definition for ‘write.table’ standalone.bgx: no visible global function definition for ‘geneNames’ standalone.bgx: no visible global function definition for ‘sampleNames’ Undefined global functions or variables: abline annotation assayDataElementReplace cdfName density description dev.off geneNames glm hist indexProbes legend lines loess median new pData par pdf points poisson predict quantile read.delim sampleNames sd segments write.table Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "abline", "hist", "legend", "lines", "par", "points", "segments") importFrom("methods", "new") importFrom("stats", "density", "glm", "loess", "median", "poisson", "predict", "quantile", "sd") importFrom("utils", "read.delim", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE prepare_Rd: analysis.bgx.Rd:48-49: Dropping empty section \examples checkRd: (-1) bgx.Rd:9: Escaped LaTeX specials: \_ \_ prepare_Rd: mcmc.bgx.Rd:48-49: Dropping empty section \examples prepare_Rd: readOutput.bgx.Rd:23-24: Dropping empty section \examples prepare_Rd: saveAffinityPlot.bgx.Rd:18-19: Dropping empty section \details prepare_Rd: saveAffinityPlot.bgx.Rd:20-21: Dropping empty section \value prepare_Rd: saveAffinityPlot.bgx.Rd:26-27: Dropping empty section \examples prepare_Rd: setupVars.bgx.Rd:21-22: Dropping empty section \details prepare_Rd: setupVars.bgx.Rd:43-44: Dropping empty section \examples * 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 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 ... NOTE Package has both ‘src/Makevars.in’ and ‘src/Makevars’. Installation with --no-configure' is unlikely to work. If you intended ‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’ otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a ‘cleanup’ script. * 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 ... OK * checking compiled code ... NOTE Note: information on .o files is not available * 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 bgx 21.347 0.527 22.039 * 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, 7 NOTEs See ‘/Users/biocbuild/bbs-3.18-bioc/meat/bgx.Rcheck/00check.log’ for details.
bgx.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL bgx ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘bgx’ ... ** using staged installation checking for gcc... clang -arch x86_64 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether clang -arch x86_64 accepts -g... yes checking for clang -arch x86_64 option to accept ISO C89... none needed checking for C compiler vendor... gnu checking whether C compiler accepts -ffast-math... yes checking whether C compiler accepts -O3... yes checking build system type... x86_64-apple-darwin21.6.0 checking host system type... x86_64-apple-darwin21.6.0 checking for gcc architecture flag... checking for x86 cpuid 0 output... 16:756e6547:6c65746e:49656e69 checking for x86 cpuid 1 output... 50657:37400800:7ffefbff:bfebfbff checking whether C compiler accepts -march=pentium2... no checking whether C compiler accepts -mcpu=pentium2... yes checking for gcc architecture flag... -mcpu=pentium2 checking for clang -arch x86_64 option to accept ISO C99... none needed checking for main in -lm... yes Untarring Boost header files... checking for an ANSI C-conforming const... yes checking for inline... inline 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 C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../boostIncl -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -falign-functions=64 -Wall -g -O2 -ffast-math -O3 -DUSING_R -c bgx.cc -o bgx.o bgx.cc:44:13: warning: 'FLUSH' macro redefined [-Wmacro-redefined] #define FLUSH {R_FlushConsole(); R_ProcessEvents();} ^ ./rand.hh:42:13: note: previous definition is here #define FLUSH R_FlushConsole(); ^ In file included from bgx.cc:36: ./bgx_updates.hh:47:8: warning: private field 'categories' is not used [-Wunused-private-field] int* categories; ^ ./bgx_updates.hh:310:8: warning: private field 'categories' is not used [-Wunused-private-field] int *categories; ^ ./bgx_updates.hh:311:7: warning: private field 'numberCategories' is not used [-Wunused-private-field] int numberCategories; ^ 4 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../boostIncl -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -falign-functions=64 -Wall -g -O2 -ffast-math -O3 -DUSING_R -c bgx_frontend.cc -o bgx_frontend.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../boostIncl -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -falign-functions=64 -Wall -g -O2 -mcpu=pentium2 -ffast-math -O3 -c qnorm.c -o qnorm.o clang: warning: argument unused during compilation: '-mcpu=pentium2' [-Wunused-command-line-argument] clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../boostIncl -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -falign-functions=64 -Wall -g -O2 -ffast-math -O3 -DUSING_R -c rundir.cc -o rundir.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../boostIncl -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -falign-functions=64 -Wall -g -O2 -ffast-math -O3 -DUSING_R -c sokal.cc -o sokal.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o bgx.so bgx.o bgx_frontend.o qnorm.o rundir.o sokal.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation rm -r ../boostIncl installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-bgx/00new/bgx/libs ** R ** 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 (bgx)
bgx.Rcheck/bgx-Ex.timings
name | user | system | elapsed | |
bgx | 21.347 | 0.527 | 22.039 | |