Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 13:04:39 -0400 (Wed, 16 Oct 2019).
Package 415/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
DeMixT 1.0.4 Zeya Wang
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK |
Package: DeMixT |
Version: 1.0.4 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DeMixT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DeMixT_1.0.4.tar.gz |
StartedAt: 2019-10-16 02:06:19 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 02:10:15 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 236.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: DeMixT.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DeMixT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DeMixT_1.0.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DeMixT.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DeMixT/DESCRIPTION’ ... OK * this is package ‘DeMixT’ version ‘1.0.4’ * 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 ‘DeMixT’ 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 * 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 DeMixT_S1: no visible binding for global variable ‘sd’ DeMixT_S2: no visible binding for global variable ‘sd’ Undefined global functions or variables: sd Consider adding importFrom("stats", "sd") 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 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 compiled code ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed DeMixT 35.661 1.298 3.489 DeMixT_S1 33.122 1.293 3.079 Optimum_KernelC 18.443 0.411 18.198 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... WARNING Located more than one ‘weave’ output file (by engine ‘knitr::rmarkdown’) for vignette with name ‘demixt’: ‘demixt.html’, ‘demixt.pdf’ Package vignette without corresponding single PDF/HTML: ‘demixt.Rmd’ * 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 ‘/Users/biocbuild/bbs-3.9-bioc/meat/DeMixT.Rcheck/00check.log’ for details.
DeMixT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DeMixT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘DeMixT’ ... ** using staged installation ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c DeMixT.c -o DeMixT.o DeMixT.c:255:26: warning: implicit declaration of function 'Rprintf' is invalid in C99 [-Wimplicit-function-declaration] if (nHavepi != 1) Rprintf("Iteration %d: updating purities\n", i+1); ^ 1 warning generated. clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c init.c -o init.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o DeMixT.so DeMixT.o init.o registerDynamicSymbol.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-DeMixT/00new/DeMixT/libs ** R ** data *** moving datasets to lazyload DB ** 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 (DeMixT)
DeMixT.Rcheck/DeMixT-Ex.timings
name | user | system | elapsed | |
DeMixT | 35.661 | 1.298 | 3.489 | |
DeMixT_S1 | 33.122 | 1.293 | 3.079 | |
DeMixT_S2 | 3.420 | 0.226 | 0.339 | |
Optimum_KernelC | 18.443 | 0.411 | 18.198 | |
test.data1.comp1 | 0.033 | 0.004 | 0.037 | |
test.data1.truth | 0.004 | 0.004 | 0.007 | |
test.data1.y | 0.013 | 0.004 | 0.018 | |
test.data2.comp1 | 0.014 | 0.005 | 0.018 | |
test.data2.comp2 | 0.014 | 0.005 | 0.019 | |
test.data2.truth | 0.004 | 0.004 | 0.008 | |
test.data2.y | 0.009 | 0.005 | 0.014 | |
test.data3.comp1 | 0.016 | 0.006 | 0.022 | |
test.data3.comp2 | 0.017 | 0.006 | 0.024 | |
test.data3.truth | 0.003 | 0.004 | 0.007 | |
test.data3.y | 0.012 | 0.003 | 0.016 | |