Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:43:42 -0400 (Thu, 12 Apr 2018).
Package 1301/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
SIMLR 1.4.1 Daniele Ramazzotti
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | ![]() |
Package: SIMLR |
Version: 1.4.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SIMLR_1.4.1.tar.gz |
StartedAt: 2018-04-12 09:40:31 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 09:48:47 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 496.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SIMLR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SIMLR_1.4.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/SIMLR.Rcheck’ * using R version 3.4.4 (2018-03-15) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SIMLR/DESCRIPTION’ ... OK * this is package ‘SIMLR’ version ‘1.4.1’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘SIMLR’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.1Mb sub-directories of 1Mb or more: data 4.5Mb * 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 loading without being on the library search path ... 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 ... OK * 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 SIMLR_Feature_Ranking 69.577 1.406 71.999 CIMLR 31.437 0.146 41.766 SIMLR 23.295 7.566 34.402 CIMLR_Estimate_Number_of_Clusters 4.486 0.049 13.639 SIMLR_Estimate_Number_of_Clusters 3.431 0.859 7.592 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.6-bioc/meat/SIMLR.Rcheck/00check.log’ for details.
SIMLR.Rcheck/00install.out
* installing *source* package ‘SIMLR’ ... ** libs clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Rtsne.cpp -o Rtsne.o clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c projsplx_R.c -o projsplx_R.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c sptree.cpp -o sptree.o In file included from sptree.cpp:39: In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/RcppCommon.h:138: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/exceptions.h:106:53: warning: all paths through this function will call itself [-Winfinite-recursion] inline void warning(const std::string& message) { // #nocov start ^ 1 warning generated. clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c tsne.cpp -o tsne.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 SIMLR.so RcppExports.o Rtsne.o projsplx_R.o sptree.o tsne.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.6-bioc/meat/SIMLR.Rcheck/SIMLR/libs ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (SIMLR)
SIMLR.Rcheck/tests/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-apple-darwin15.6.0 (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. > Sys.setenv("R_TESTS" = "") > > library(testthat) > library(SIMLR) > > test_check("SIMLR") Computing the multiple Kernels. Performing network diffiusion. Iteration: 1 Iteration: 2 Iteration: 3 Iteration: 4 Iteration: 5 Iteration: 6 Iteration: 7 Iteration: 8 Iteration: 9 Iteration: 10 Iteration: 11 Performing t-SNE. Epoch: Iteration # 100 error is: 0.1140084 Epoch: Iteration # 200 error is: 0.06181848 Epoch: Iteration # 300 error is: 0.05932105 Epoch: Iteration # 400 error is: 0.05923113 Epoch: Iteration # 500 error is: 0.05914954 Epoch: Iteration # 600 error is: 0.05907505 Epoch: Iteration # 700 error is: 0.05900841 Epoch: Iteration # 800 error is: 0.05894696 Epoch: Iteration # 900 error is: 0.05889082 Epoch: Iteration # 1000 error is: 0.0588387 Performing Kmeans. Performing t-SNE. Epoch: Iteration # 100 error is: 10.90326 Epoch: Iteration # 200 error is: 0.581636 Epoch: Iteration # 300 error is: 0.3507923 Epoch: Iteration # 400 error is: 0.1652774 Epoch: Iteration # 500 error is: 0.1285538 Epoch: Iteration # 600 error is: 0.08857476 Epoch: Iteration # 700 error is: 0.08779421 Epoch: Iteration # 800 error is: 0.0877622 Epoch: Iteration # 900 error is: 0.08774816 Epoch: Iteration # 1000 error is: 0.08773213 Computing the multiple Kernels. Performing network diffiusion. Iteration: 1 Iteration: 2 Iteration: 3 Iteration: 4 Iteration: 5 Iteration: 6 Iteration: 7 Iteration: 8 Iteration: 9 Iteration: 10 Iteration: 11 Iteration: 12 Iteration: 13 Iteration: 14 Iteration: 15 Iteration: 16 Iteration: 17 Performing t-SNE. Epoch: Iteration # 100 error is: 0.08442679 Epoch: Iteration # 200 error is: 0.07563968 Epoch: Iteration # 300 error is: 0.0686836 Epoch: Iteration # 400 error is: 0.06687578 Epoch: Iteration # 500 error is: 0.06663136 Epoch: Iteration # 600 error is: 0.06645222 Epoch: Iteration # 700 error is: 0.06630663 Epoch: Iteration # 800 error is: 0.06618637 Epoch: Iteration # 900 error is: 0.06608476 Epoch: Iteration # 1000 error is: 0.0659978 Performing Kmeans. Performing t-SNE. Epoch: Iteration # 100 error is: 11.85422 Epoch: Iteration # 200 error is: 0.6876375 Epoch: Iteration # 300 error is: 0.3637225 Epoch: Iteration # 400 error is: 0.199312 Epoch: Iteration # 500 error is: 0.1344634 Epoch: Iteration # 600 error is: 0.130829 Epoch: Iteration # 700 error is: 0.1280689 Epoch: Iteration # 800 error is: 0.1244788 Epoch: Iteration # 900 error is: 0.1191421 Epoch: Iteration # 1000 error is: 0.1138787 Computing the multiple Kernels. Performing network diffiusion. Iteration: 1 Iteration: 2 Iteration: 3 Iteration: 4 Iteration: 5 Iteration: 6 Iteration: 7 Iteration: 8 Iteration: 9 Iteration: 10 Iteration: 11 Performing t-SNE. Epoch: Iteration # 100 error is: 0.1302831 Epoch: Iteration # 200 error is: 0.08219885 Epoch: Iteration # 300 error is: 0.0587416 Epoch: Iteration # 400 error is: 0.05864968 Epoch: Iteration # 500 error is: 0.05856638 Epoch: Iteration # 600 error is: 0.05849335 Epoch: Iteration # 700 error is: 0.05842535 Epoch: Iteration # 800 error is: 0.05836222 Epoch: Iteration # 900 error is: 0.05830468 Epoch: Iteration # 1000 error is: 0.05825144 Performing Kmeans. Performing t-SNE. Epoch: Iteration # 100 error is: 10.76985 Epoch: Iteration # 200 error is: 0.7716755 Epoch: Iteration # 300 error is: 0.5344263 Epoch: Iteration # 400 error is: 0.3142703 Epoch: Iteration # 500 error is: 0.2881386 Epoch: Iteration # 600 error is: 0.2656426 Epoch: Iteration # 700 error is: 0.1371832 Epoch: Iteration # 800 error is: 0.109503 Epoch: Iteration # 900 error is: 0.08730035 Epoch: Iteration # 1000 error is: 0.08726732 Computing the multiple Kernels. Performing network diffusion. Iteration: 1 Iteration: 2 Iteration: 3 Iteration: 4 Iteration: 5 Iteration: 6 Iteration: 7 Iteration: 8 Iteration: 9 Iteration: 10 Iteration: 11 Iteration: 12 Iteration: 13 Iteration: 14 Iteration: 15 Performing t-SNE. Epoch: Iteration # 100 error is: 0.3839462 Epoch: Iteration # 200 error is: 0.2236962 Epoch: Iteration # 300 error is: 0.09802584 Epoch: Iteration # 400 error is: 0.09667109 Epoch: Iteration # 500 error is: 0.09599822 Epoch: Iteration # 600 error is: 0.1047978 Epoch: Iteration # 700 error is: 0.0968507 Epoch: Iteration # 800 error is: 0.09639386 Epoch: Iteration # 900 error is: 0.1018992 Epoch: Iteration # 1000 error is: 0.09661557 Performing Kmeans. Performing t-SNE. Epoch: Iteration # 100 error is: 24.90385 Epoch: Iteration # 200 error is: 2.428993 Epoch: Iteration # 300 error is: 1.213393 Epoch: Iteration # 400 error is: 0.480937 Epoch: Iteration # 500 error is: 0.8211609 Epoch: Iteration # 600 error is: 2.956876 Epoch: Iteration # 700 error is: 1.230773 Epoch: Iteration # 800 error is: 0.8430302 Epoch: Iteration # 900 error is: 0.6177196 Epoch: Iteration # 1000 error is: 0.7617236 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 ══ testthat results ═══════════════════════════════════════════════════════════ OK: 8 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 176.787 28.136 228.149
SIMLR.Rcheck/SIMLR-Ex.timings
name | user | system | elapsed | |
CIMLR | 31.437 | 0.146 | 41.766 | |
CIMLR_Estimate_Number_of_Clusters | 4.486 | 0.049 | 13.639 | |
SIMLR | 23.295 | 7.566 | 34.402 | |
SIMLR_Estimate_Number_of_Clusters | 3.431 | 0.859 | 7.592 | |
SIMLR_Feature_Ranking | 69.577 | 1.406 | 71.999 | |
SIMLR_Large_Scale | 0.055 | 0.012 | 0.073 | |