Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:47 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
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 Linnorm package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Linnorm.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 1001/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Linnorm 2.18.0 (landing page) Ken Shun Hang Yip
| 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: Linnorm |
Version: 2.18.0 |
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Linnorm.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Linnorm_2.18.0.tar.gz |
StartedAt: 2022-04-12 22:00:58 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 22:14:19 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 800.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Linnorm.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Linnorm.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Linnorm_2.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Linnorm.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 'Linnorm/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'Linnorm' version '2.18.0' * 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 'Linnorm' 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 ... NOTE Linnorm.HClust: no visible binding for global variable 'x' Linnorm.HClust: no visible binding for global variable 'y' Linnorm.HClust: no visible binding for global variable 'xend' Linnorm.HClust: no visible binding for global variable 'yend' Linnorm.HClust: no visible binding for global variable 'cluster' Linnorm.HClust: no visible binding for global variable 'X1' Linnorm.HClust: no visible binding for global variable 'X2' Linnorm.HVar: no visible binding for global variable 'SD' Linnorm.HVar: no visible binding for global variable 'group' Undefined global functions or variables: SD X1 X2 cluster group x xend y yend * 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 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 ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Linnorm/libs/i386/Linnorm.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Linnorm/libs/x64/Linnorm.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) 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. 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed RnaXSim 79.62 0.24 79.86 Linnorm.Cor 56.43 0.31 56.74 Linnorm.limma 47.07 0.01 47.08 Linnorm.Norm 46.87 0.05 46.94 Linnorm 46.53 0.03 46.56 Linnorm.tSNE 6.17 0.11 6.41 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed RnaXSim 94.83 0.06 94.90 Linnorm.Cor 52.31 0.19 52.54 Linnorm.Norm 47.28 0.04 47.31 Linnorm 46.35 0.03 46.37 Linnorm.limma 46.19 0.02 46.20 Linnorm.PCA 5.44 0.39 5.96 Linnorm.tSNE 4.95 0.09 5.07 * 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 NOTEs See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Linnorm.Rcheck/00check.log' for details.
Linnorm.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Linnorm_2.18.0.tar.gz && rm -rf Linnorm.buildbin-libdir && mkdir Linnorm.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Linnorm.buildbin-libdir Linnorm_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Linnorm_2.18.0.zip && rm Linnorm_2.18.0.tar.gz Linnorm_2.18.0.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 83 2420k 83 2018k 0 0 2556k 0 --:--:-- --:--:-- --:--:-- 2557k 100 2420k 100 2420k 0 0 2686k 0 --:--:-- --:--:-- --:--:-- 2686k install for i386 * installing *source* package 'Linnorm' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Misc.cpp -o Misc.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Linnorm.dll tmp.def Misc.o -std=c++11 -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -DARMA_64BIT_WORD=1 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/Linnorm.buildbin-libdir/00LOCK-Linnorm/00new/Linnorm/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'Linnorm' finding HTML links ... done Islam2011 html LIHC html LinearRegression html LinearRegressionFP html Linnorm.Cor html Linnorm.DataImput html Linnorm.HClust html Linnorm.HVar html Linnorm.Norm html Linnorm.PCA html Linnorm html Linnorm.SGenes html Linnorm.limma html Linnorm.tSNE html RnaXSim html SEQC 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 'Linnorm' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Misc.cpp -o Misc.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Linnorm.dll tmp.def Misc.o -std=c++11 -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -DARMA_64BIT_WORD=1 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/Linnorm.buildbin-libdir/Linnorm/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'Linnorm' as Linnorm_2.18.0.zip * DONE (Linnorm) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'Linnorm' successfully unpacked and MD5 sums checked
Linnorm.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(Linnorm) > > test_check("Linnorm") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 26 ] > > proc.time() user system elapsed 25.12 0.53 25.62 |
Linnorm.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(Linnorm) > > test_check("Linnorm") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 26 ] > > proc.time() user system elapsed 26.84 0.32 27.15 |
Linnorm.Rcheck/examples_i386/Linnorm-Ex.timings
|
Linnorm.Rcheck/examples_x64/Linnorm-Ex.timings
|