Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SIMLR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SIMLR_1.32.0.tar.gz |
StartedAt: 2024-12-20 06:03:43 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 06:10:06 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 383.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SIMLR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SIMLR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SIMLR_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/SIMLR.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * 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 ... 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 'SIMLR' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.3.0' * used C++ compiler: 'G__~1.EXE (GCC) 13.3.0' * 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/SIMLR/libs/x64/SIMLR.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) 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 nor [v]sprintf. 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed SIMLR_Feature_Ranking 74.52 5.95 80.49 SIMLR 21.51 4.73 29.29 SIMLR_Estimate_Number_of_Clusters 2.60 0.38 5.60 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/SIMLR.Rcheck/00check.log' for details.
SIMLR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL SIMLR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'SIMLR' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.3.0' using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Rtsne.cpp -o Rtsne.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c package_init.c -o package_init.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c projsplx_R.c -o projsplx_R.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sptree.cpp -o sptree.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tsne.cpp -o tsne.o tsne.cpp: In member function 'bool TSNE::load_data(double**, int*, int*, int*, double*, double*, int*)': tsne.cpp:979:48: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 979 | if (fread(*data, sizeof(double), *n * *d, h) != *n * *d) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from tsne.cpp:43: vptree.h: In instantiation of 'void VpTree<T, distance>::search(Node*, const T&, int, std::priority_queue<HeapItem>&) [with T = DataPoint; double (* distance)(const T&, const T&) = precomputed_distance; typename std::vector<HeapItem, std::allocator<HeapItem> >::value_type = VpTree<DataPoint, precomputed_distance>::HeapItem]': vptree.h:131:15: required from 'void VpTree<T, distance>::search(const T&, int, std::vector<T>*, std::vector<double>*) [with T = DataPoint; double (* distance)(const T&, const T&) = precomputed_distance]' tsne.cpp:484:21: required from here vptree.h:237:28: warning: comparison of integer expressions of different signedness: 'std::priority_queue<VpTree<DataPoint, precomputed_distance>::HeapItem, std::vector<VpTree<DataPoint, precomputed_distance>::HeapItem, std::allocator<VpTree<DataPoint, precomputed_distance>::HeapItem> >, std::less<VpTree<DataPoint, precomputed_distance>::HeapItem> >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 237 | if(heap.size() == k) heap.pop(); // remove furthest node from result list (if we already have k results) | ~~~~~~~~~~~~^~~~ vptree.h:239:28: warning: comparison of integer expressions of different signedness: 'std::priority_queue<VpTree<DataPoint, precomputed_distance>::HeapItem, std::vector<VpTree<DataPoint, precomputed_distance>::HeapItem, std::allocator<VpTree<DataPoint, precomputed_distance>::HeapItem> >, std::less<VpTree<DataPoint, precomputed_distance>::HeapItem> >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 239 | if(heap.size() == k) _tau = heap.top().dist; // update value of tau (farthest point in result list) | ~~~~~~~~~~~~^~~~ vptree.h: In instantiation of 'void VpTree<T, distance>::search(Node*, const T&, int, std::priority_queue<HeapItem>&) [with T = DataPoint; double (* distance)(const T&, const T&) = euclidean_distance; typename std::vector<HeapItem, std::allocator<HeapItem> >::value_type = VpTree<DataPoint, euclidean_distance>::HeapItem]': vptree.h:131:15: required from 'void VpTree<T, distance>::search(const T&, int, std::vector<T>*, std::vector<double>*) [with T = DataPoint; double (* distance)(const T&, const T&) = euclidean_distance]' tsne.cpp:562:21: required from here vptree.h:237:28: warning: comparison of integer expressions of different signedness: 'std::priority_queue<VpTree<DataPoint, euclidean_distance>::HeapItem, std::vector<VpTree<DataPoint, euclidean_distance>::HeapItem, std::allocator<VpTree<DataPoint, euclidean_distance>::HeapItem> >, std::less<VpTree<DataPoint, euclidean_distance>::HeapItem> >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 237 | if(heap.size() == k) heap.pop(); // remove furthest node from result list (if we already have k results) | ~~~~~~~~~~~~^~~~ vptree.h:239:28: warning: comparison of integer expressions of different signedness: 'std::priority_queue<VpTree<DataPoint, euclidean_distance>::HeapItem, std::vector<VpTree<DataPoint, euclidean_distance>::HeapItem, std::allocator<VpTree<DataPoint, euclidean_distance>::HeapItem> >, std::less<VpTree<DataPoint, euclidean_distance>::HeapItem> >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 239 | if(heap.size() == k) _tau = heap.top().dist; // update value of tau (farthest point in result list) | ~~~~~~~~~~~~^~~~ g++ -std=gnu++17 -shared -s -static-libgcc -o SIMLR.dll tmp.def RcppExports.o Rtsne.o package_init.o projsplx_R.o sptree.o tsne.o -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-SIMLR/00new/SIMLR/libs/x64 ** 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 ** 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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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: 0.1113014 Epoch: Iteration # 200 error is: 0.05998534 Epoch: Iteration # 300 error is: 0.05920885 Epoch: Iteration # 400 error is: 0.05904812 Epoch: Iteration # 500 error is: 0.05890865 Epoch: Iteration # 600 error is: 0.05879012 Epoch: Iteration # 700 error is: 0.05868304 Epoch: Iteration # 800 error is: 0.05858721 Epoch: Iteration # 900 error is: 0.05850376 Epoch: Iteration # 1000 error is: 0.05842733 Performing Kmeans. Performing t-SNE. Epoch: Iteration # 100 error is: 10.76228 Epoch: Iteration # 200 error is: 0.3550057 Epoch: Iteration # 300 error is: 0.1223934 Epoch: Iteration # 400 error is: 0.08884149 Epoch: Iteration # 500 error is: 0.08870909 Epoch: Iteration # 600 error is: 0.08870176 Epoch: Iteration # 700 error is: 0.08866902 Epoch: Iteration # 800 error is: 0.08865011 Epoch: Iteration # 900 error is: 0.08863152 Epoch: Iteration # 1000 error is: 0.08861347 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: 0.08108063 Epoch: Iteration # 200 error is: 0.07477886 Epoch: Iteration # 300 error is: 0.0681391 Epoch: Iteration # 400 error is: 0.06595909 Epoch: Iteration # 500 error is: 0.06572884 Epoch: Iteration # 600 error is: 0.06554725 Epoch: Iteration # 700 error is: 0.06539913 Epoch: Iteration # 800 error is: 0.06527713 Epoch: Iteration # 900 error is: 0.06517343 Epoch: Iteration # 1000 error is: 0.06508542 Performing Kmeans. Performing t-SNE. Epoch: Iteration # 100 error is: 15.03799 Epoch: Iteration # 200 error is: 1.801181 Epoch: Iteration # 300 error is: 1.407701 Epoch: Iteration # 400 error is: 0.7484857 Epoch: Iteration # 500 error is: 0.7412707 Epoch: Iteration # 600 error is: 0.603197 Epoch: Iteration # 700 error is: 0.4566149 Epoch: Iteration # 800 error is: 0.3677818 Epoch: Iteration # 900 error is: 0.2385245 Epoch: Iteration # 1000 error is: 0.1560309 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: 0.1207343 Epoch: Iteration # 200 error is: 0.07172118 Epoch: Iteration # 300 error is: 0.06071198 Epoch: Iteration # 400 error is: 0.06057342 Epoch: Iteration # 500 error is: 0.06044155 Epoch: Iteration # 600 error is: 0.06033219 Epoch: Iteration # 700 error is: 0.06023583 Epoch: Iteration # 800 error is: 0.06014798 Epoch: Iteration # 900 error is: 0.06006964 Epoch: Iteration # 1000 error is: 0.05999928 Performing Kmeans. Performing t-SNE. Epoch: Iteration # 100 error is: 10.56104 Epoch: Iteration # 200 error is: 0.5644992 Epoch: Iteration # 300 error is: 0.5210766 Epoch: Iteration # 400 error is: 0.6935122 Epoch: Iteration # 500 error is: 0.4817172 Epoch: Iteration # 600 error is: 0.4095505 Epoch: Iteration # 700 error is: 0.3311105 Epoch: Iteration # 800 error is: 0.3036321 Epoch: Iteration # 900 error is: 0.2922064 Epoch: Iteration # 1000 error is: 0.2815575 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 143.93 23.17 175.51
SIMLR.Rcheck/SIMLR-Ex.timings
name | user | system | elapsed | |
SIMLR | 21.51 | 4.73 | 29.29 | |
SIMLR_Estimate_Number_of_Clusters | 2.60 | 0.38 | 5.60 | |
SIMLR_Feature_Ranking | 74.52 | 5.95 | 80.49 | |
SIMLR_Large_Scale | 0.04 | 0.00 | 0.04 | |