Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1967/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SIMLR 1.32.0 (landing page) Luca De Sano
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the SIMLR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SIMLR.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: SIMLR |
Version: 1.32.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SIMLR_1.32.0.tar.gz |
StartedAt: 2024-11-20 02:44:31 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 02:51:44 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 433.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SIMLR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SIMLR_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SIMLR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SIMLR/DESCRIPTION’ ... OK * this is package ‘SIMLR’ version ‘1.32.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 * 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 ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 ... 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 use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed SIMLR_Feature_Ranking 40.150 1.058 41.322 SIMLR 12.728 2.213 16.842 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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-3.20-bioc/meat/SIMLR.Rcheck/00check.log’ for details.
SIMLR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SIMLR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘SIMLR’ ... ** using staged installation ** 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'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rtsne.cpp -o Rtsne.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c package_init.c -o package_init.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c projsplx_R.c -o projsplx_R.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sptree.cpp -o sptree.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tsne.cpp -o tsne.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 SIMLR.so RcppExports.o Rtsne.o package_init.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/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-SIMLR/00new/SIMLR/libs ** R ** data ** 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 (SIMLR)
SIMLR.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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: 0.1144355 Epoch: Iteration # 200 error is: 0.05998489 Epoch: Iteration # 300 error is: 0.05827469 Epoch: Iteration # 400 error is: 0.05822451 Epoch: Iteration # 500 error is: 0.05817789 Epoch: Iteration # 600 error is: 0.05813481 Epoch: Iteration # 700 error is: 0.05809402 Epoch: Iteration # 800 error is: 0.05805695 Epoch: Iteration # 900 error is: 0.0580205 Epoch: Iteration # 1000 error is: 0.05798613 Performing Kmeans. Performing t-SNE. Epoch: Iteration # 100 error is: 10.43941 Epoch: Iteration # 200 error is: 0.8167422 Epoch: Iteration # 300 error is: 0.5990123 Epoch: Iteration # 400 error is: 0.6280304 Epoch: Iteration # 500 error is: 0.3483288 Epoch: Iteration # 600 error is: 0.3053931 Epoch: Iteration # 700 error is: 0.2874313 Epoch: Iteration # 800 error is: 0.272726 Epoch: Iteration # 900 error is: 0.2554069 Epoch: Iteration # 1000 error is: 0.130218 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: 0.08265127 Epoch: Iteration # 200 error is: 0.07541818 Epoch: Iteration # 300 error is: 0.06890541 Epoch: Iteration # 400 error is: 0.06466017 Epoch: Iteration # 500 error is: 0.06442995 Epoch: Iteration # 600 error is: 0.06427845 Epoch: Iteration # 700 error is: 0.06415696 Epoch: Iteration # 800 error is: 0.06405127 Epoch: Iteration # 900 error is: 0.06396323 Epoch: Iteration # 1000 error is: 0.06388545 Performing Kmeans. Performing t-SNE. Epoch: Iteration # 100 error is: 11.29585 Epoch: Iteration # 200 error is: 1.037793 Epoch: Iteration # 300 error is: 0.8170344 Epoch: Iteration # 400 error is: 0.8806583 Epoch: Iteration # 500 error is: 0.5231122 Epoch: Iteration # 600 error is: 0.3805755 Epoch: Iteration # 700 error is: 0.3324769 Epoch: Iteration # 800 error is: 0.1412275 Epoch: Iteration # 900 error is: 0.1389803 Epoch: Iteration # 1000 error is: 0.138217 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: 0.1206666 Epoch: Iteration # 200 error is: 0.07268618 Epoch: Iteration # 300 error is: 0.05866626 Epoch: Iteration # 400 error is: 0.05862102 Epoch: Iteration # 500 error is: 0.05857784 Epoch: Iteration # 600 error is: 0.05853699 Epoch: Iteration # 700 error is: 0.05849837 Epoch: Iteration # 800 error is: 0.05846287 Epoch: Iteration # 900 error is: 0.05842908 Epoch: Iteration # 1000 error is: 0.05839741 Performing Kmeans. Performing t-SNE. Epoch: Iteration # 100 error is: 11.07836 Epoch: Iteration # 200 error is: 1.133247 Epoch: Iteration # 300 error is: 0.5646751 Epoch: Iteration # 400 error is: 0.3695311 Epoch: Iteration # 500 error is: 0.3263231 Epoch: Iteration # 600 error is: 0.3117919 Epoch: Iteration # 700 error is: 0.2943099 Epoch: Iteration # 800 error is: 0.4149942 Epoch: Iteration # 900 error is: 0.2707365 Epoch: Iteration # 1000 error is: 0.14135 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 [ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ] > > proc.time() user system elapsed 81.898 10.166 98.197
SIMLR.Rcheck/SIMLR-Ex.timings
name | user | system | elapsed | |
SIMLR | 12.728 | 2.213 | 16.842 | |
SIMLR_Estimate_Number_of_Clusters | 1.683 | 0.183 | 3.769 | |
SIMLR_Feature_Ranking | 40.150 | 1.058 | 41.322 | |
SIMLR_Large_Scale | 0.030 | 0.002 | 0.031 | |