Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 1947/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
slalom 1.27.0 (landing page) Davis McCarthy
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
To the developers/maintainers of the slalom package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/slalom.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: slalom |
Version: 1.27.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:slalom.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings slalom_1.27.0.tar.gz |
StartedAt: 2024-06-10 10:00:31 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 10:11:27 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 655.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: slalom.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:slalom.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings slalom_1.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/slalom.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'slalom/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'slalom' version '1.27.0' * 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 'slalom' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * checking installed package size ... NOTE installed size is 21.4Mb sub-directories of 1Mb or more: data 1.7Mb extdata 18.3Mb libs 1.1Mb * 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 LazyData ... 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/slalom/libs/x64/slalom.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 * 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: 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/slalom.Rcheck/00check.log' for details.
slalom.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL slalom ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'slalom' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' 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'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/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'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c slalom-classes.cpp -o slalom-classes.o slalom-classes.cpp: In member function 'void SlalomModel::train()': slalom-classes.cpp:223:20: warning: unused variable 'meanerr' [-Wunused-variable] 223 | double meanerr = arma::mean(error); | ^~~~~~~ slalom-classes.cpp:202:12: warning: unused variable 'meanerr' [-Wunused-variable] 202 | double meanerr = arma::mean(error); | ^~~~~~~ slalom-classes.cpp: In member function 'void SlalomModel::updateEpsilon()': slalom-classes.cpp:431:23: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 431 | for (int i = 0; i < this->epsilon_E1.n_elem; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -shared -s -static-libgcc -o slalom.dll tmp.def RcppExports.o slalom-classes.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-slalom/00new/slalom/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (slalom)
slalom.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 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. > # test package > library(testthat) > library(slalom) > > test_check("slalom") 14 annotated factors retained; 16 annotated factors dropped. 196 genes retained for analysis. 14 annotated factors retained; 16 annotated factors dropped. 196 genes retained for analysis. 14 annotated factors retained; 16 annotated factors dropped. 196 genes retained for analysis. 14 annotated factors retained; 16 annotated factors dropped. 196 genes retained for analysis. 20 annotated factors retained; 3 annotated factors dropped. 500 genes retained for analysis. iteration 0 Switched off factor 20 Switched off factor 17 Switched off factor 15 iteration 100 Switched off factor 10 Switched off factor 11 iteration 200 iteration 300 iteration 400 iteration 500 Model not converged after 500 iterations. 20 annotated factors retained; 3 annotated factors dropped. 500 genes retained for analysis. pre-training model for faster convergence iteration 0 Model not converged after 50 iterations. iteration 0 Model not converged after 50 iterations. iteration 0 Switched off factor 17 Switched off factor 20 Switched off factor 15 iteration 100 Switched off factor 11 Switched off factor 10 iteration 200 iteration 300 iteration 400 iteration 500 Model not converged after 500 iterations. 20 annotated factors retained; 3 annotated factors dropped. 500 genes retained for analysis. pre-training model for faster convergence iteration 0 Model not converged after 50 iterations. iteration 0 Model not converged after 50 iterations. iteration 0 Switched off factor 17 Switched off factor 20 Switched off factor 15 iteration 100 Switched off factor 11 Switched off factor 10 iteration 200 iteration 300 iteration 400 iteration 500 iteration 600 iteration 700 iteration 800 Switched off factor 16 iteration 900 iteration 1000 iteration 1100 iteration 1200 iteration 1300 iteration 1400 iteration 1500 iteration 1600 iteration 1700 iteration 1800 iteration 1900 iteration 2000 iteration 2100 iteration 2200 iteration 2300 iteration 2400 iteration 2500 iteration 2600 iteration 2700 Model converged after 2750 iterations. 20 annotated factors retained; 3 annotated factors dropped. 500 genes retained for analysis. pre-training model for faster convergence iteration 0 Model not converged after 50 iterations. iteration 0 Model not converged after 50 iterations. iteration 0 Switched off factor 20 Switched off factor 17 Switched off factor 10 Switched off factor 15 Switched off factor 16 iteration 100 iteration 200 iteration 300 Switched off factor 11 iteration 400 iteration 500 iteration 600 iteration 700 iteration 800 iteration 900 iteration 1000 Switched off factor 5 iteration 1100 iteration 1200 iteration 1300 iteration 1400 iteration 1500 iteration 1600 iteration 1700 iteration 1800 iteration 1900 iteration 2000 iteration 2100 iteration 2200 iteration 2300 iteration 2400 iteration 2500 iteration 2600 iteration 2700 iteration 2800 iteration 2900 iteration 3000 iteration 3100 iteration 3200 iteration 3300 iteration 3400 iteration 3500 iteration 3600 iteration 3700 iteration 3800 iteration 3900 iteration 4000 iteration 4100 iteration 4200 iteration 4300 iteration 4400 iteration 4500 Model converged after 4550 iterations. 25 annotated factors retained; 75 annotated factors dropped. 355 genes retained for analysis. pre-training model for faster convergence iteration 0 Model not converged after 50 iterations. iteration 0 Model not converged after 50 iterations. iteration 0 Switched off factor 15 Switched off factor 11 Switched off factor 18 Switched off factor 29 Switched off factor 12 Switched off factor 24 Switched off factor 26 Switched off factor 7 Switched off factor 28 Switched off factor 17 Switched off factor 23 Switched off factor 25 Switched off factor 27 Switched off factor 13 Switched off factor 22 Switched off factor 14 Switched off factor 20 Switched off factor 9 Switched off factor 21 Switched off factor 16 Switched off factor 5 Switched off factor 8 Switched off factor 6 Switched off factor 10 Switched off factor 19 iteration 100 Switched off factor 4 iteration 200 iteration 300 iteration 400 iteration 500 iteration 600 iteration 700 iteration 800 iteration 900 iteration 1000 Model converged after 1000 iterations. [ FAIL 0 | WARN 4 | SKIP 1 | PASS 38 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-SlalomModel-methods.R:262:1' [ FAIL 0 | WARN 4 | SKIP 1 | PASS 38 ] > > proc.time() user system elapsed 60.48 14.76 75.21
slalom.Rcheck/slalom-Ex.timings
name | user | system | elapsed | |
addResultsToSingleCellExperiment | 3.00 | 0.03 | 3.03 | |
initSlalom | 0.15 | 0.00 | 0.15 | |
newSlalomModel | 0.39 | 0.00 | 0.39 | |
plotLoadings | 1.80 | 0.08 | 1.87 | |
plotRelevance | 2.75 | 0.05 | 2.83 | |
plotTerms | 1.67 | 0.02 | 1.69 | |
topTerms | 2.61 | 0.01 | 2.62 | |
trainSlalom | 2.47 | 0.06 | 2.53 | |
updateSlalom | 0.12 | 0.02 | 0.15 | |