Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:26:39 -0400 (Thu, 12 Apr 2018).
Package 358/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
destiny 2.6.2 Philipp Angerer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | ![]() |
Package: destiny |
Version: 2.6.2 |
Command: rm -rf destiny.buildbin-libdir destiny.Rcheck && mkdir destiny.buildbin-libdir destiny.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=destiny.buildbin-libdir destiny_2.6.2.tar.gz >destiny.Rcheck\00install.out 2>&1 && cp destiny.Rcheck\00install.out destiny-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=destiny.buildbin-libdir --install="check:destiny-install.out" --force-multiarch --no-vignettes --timings destiny_2.6.2.tar.gz |
StartedAt: 2018-04-11 23:28:39 -0400 (Wed, 11 Apr 2018) |
EndedAt: 2018-04-11 23:34:18 -0400 (Wed, 11 Apr 2018) |
EllapsedTime: 338.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: destiny.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf destiny.buildbin-libdir destiny.Rcheck && mkdir destiny.buildbin-libdir destiny.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=destiny.buildbin-libdir destiny_2.6.2.tar.gz >destiny.Rcheck\00install.out 2>&1 && cp destiny.Rcheck\00install.out destiny-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=destiny.buildbin-libdir --install="check:destiny-install.out" --force-multiarch --no-vignettes --timings destiny_2.6.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/destiny.Rcheck' * using R version 3.4.4 (2018-03-15) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'destiny/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'destiny' version '2.6.2' * package encoding: UTF-8 * 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 'destiny' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/DiffusionMap-class.Rd:56: missing file link 'ExpressionSet' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/ExpressionSet-helpers.Rd:10: missing file link 'ExpressionSet' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/ExpressionSet-helpers.Rd:34: missing file link 'ExpressionSet' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/ExpressionSet-helpers.Rd:20: missing file link 'ExpressionSet' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/ExpressionSet-helpers.Rd:31: missing file link 'ExpressionSet' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/ExpressionSet-helpers.Rd:50: missing file link 'ExpressionSet' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/dm_predict.Rd:13: missing file link 'ExpressionSet' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/find_sigmas.Rd:13: missing file link 'ExpressionSet' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/guo.Rd:10: missing file link 'ExpressionSet' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/guo.Rd:16: missing file link 'ExpressionSet' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/projection_dist.Rd:17: missing file link 'ExpressionSet' See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/destiny.Rcheck/00install.out' for details. * checking installed package size ... NOTE installed size is 5.5Mb sub-directories of 1Mb or more: doc 3.1Mb libs 1.7Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE 'LinkingTo' for 'grDevices' is unused as it has no 'include' directory * 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 ... NOTE Namespace in Imports field not imported from: 'scatterplot3d' All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE plot_gradient_map_impl : <anonymous>: no visible binding for global variable 'Gene' scatterplot3d : <anonymous>: no visible global function definition for 'formula' scatterplot3d : <anonymous>: no visible global function definition for 'predict' Undefined global functions or variables: Gene formula predict Consider adding importFrom("stats", "formula", "predict") 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 ... NOTE S3 methods shown with full name in documentation object 'plot.DPT': 'plot.DPT' S3 methods shown with full name in documentation object 'plot.DiffusionMap': 'plot.DiffusionMap' The \usage entries for S3 methods should use the \method markup and not their full name. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * 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 ... 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-3.6-bioc/meat/destiny.buildbin-libdir/destiny/libs/i386/destiny.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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed destiny 28.93 0.20 29.17 Gene-Relevance-plotting 7.08 0.19 7.27 DiffusionMap-class 5.14 0.30 5.43 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed destiny 13.20 0.10 13.31 Gene-Relevance-plotting 7.14 0.15 7.29 * 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 ... NOTE '::' or ':::' import not declared from: 'viridis' 'library' or 'require' calls not declared from: 'IRdisplay' 'IRkernel' 'base64enc' 'repr' 'xlsx' * 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 'C:/Users/biocbuild/bbs-3.6-bioc/meat/destiny.Rcheck/00check.log' for details.
destiny.Rcheck/00install.out
install for i386 * installing *source* package 'destiny' ... ** libs C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/grDevices/include" -I"C:/local323/include" -ggdb -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/grDevices/include" -I"C:/local323/include" -ggdb -O2 -Wall -mtune=generic -c censoring.cpp -o censoring.o C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/grDevices/include" -I"C:/local323/include" -ggdb -O2 -Wall -mtune=generic -c knn.cpp -o knn.o C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/grDevices/include" -I"C:/local323/include" -ggdb -O2 -Wall -mtune=generic -c utils.cpp -o utils.o C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o destiny.dll tmp.def RcppExports.o censoring.o knn.o utils.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/destiny.buildbin-libdir/destiny/libs/i386 ** R ** data ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices converting help for package 'destiny' finding HTML links ... done DPT-matrix-methods html DPT-methods html DPT html DiffusionMap-accessors html DiffusionMap-class html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/DiffusionMap-class.Rd:56: missing file link 'ExpressionSet' DiffusionMap-methods html ExpressionSet-helpers html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/ExpressionSet-helpers.Rd:10: missing file link 'ExpressionSet' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/ExpressionSet-helpers.Rd:34: missing file link 'ExpressionSet' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/ExpressionSet-helpers.Rd:20: missing file link 'ExpressionSet' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/ExpressionSet-helpers.Rd:31: missing file link 'ExpressionSet' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/ExpressionSet-helpers.Rd:50: missing file link 'ExpressionSet' Gene-Relevance-methods html Gene-Relevance-plotting html Gene-Relevance html Sigmas-class html coercions html colorlegend html cube_helix html destiny-deprecated html destiny-generics html destiny html dm_predict html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/dm_predict.Rd:13: missing file link 'ExpressionSet' eig_decomp html extractions html find_dm_k html find_sigmas html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/find_sigmas.Rd:13: missing file link 'ExpressionSet' find_tips html guo html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/guo.Rd:10: missing file link 'ExpressionSet' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/guo.Rd:16: missing file link 'ExpressionSet' knn html l_which html plot.DPT html plot.DiffusionMap html plot.Sigmas html projection_dist html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/projection_dist.Rd:17: missing file link 'ExpressionSet' random_root html updateObject-method html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'destiny' ... ** libs C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/grDevices/include" -I"C:/local323/include" -ggdb -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/grDevices/include" -I"C:/local323/include" -ggdb -O2 -Wall -mtune=generic -c censoring.cpp -o censoring.o C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/grDevices/include" -I"C:/local323/include" -ggdb -O2 -Wall -mtune=generic -c knn.cpp -o knn.o C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/grDevices/include" -I"C:/local323/include" -ggdb -O2 -Wall -mtune=generic -c utils.cpp -o utils.o C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o destiny.dll tmp.def RcppExports.o censoring.o knn.o utils.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/destiny.buildbin-libdir/destiny/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'destiny' as destiny_2.6.2.zip * DONE (destiny) In R CMD INSTALL In R CMD INSTALL
destiny.Rcheck/tests_i386/testthat.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 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(destiny) > > test_check('destiny') == testthat results =========================================================== OK: 10 SKIPPED: 1 FAILED: 0 > > proc.time() user system elapsed 6.68 0.31 7.10 |
destiny.Rcheck/tests_x64/testthat.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 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(destiny) > > test_check('destiny') == testthat results =========================================================== OK: 10 SKIPPED: 1 FAILED: 0 > > proc.time() user system elapsed 8.17 0.35 8.56 |
destiny.Rcheck/examples_i386/destiny-Ex.timings
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destiny.Rcheck/examples_x64/destiny-Ex.timings
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