Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:45 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 928/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Harman 1.35.0 (landing page) Jason Ross
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the Harman package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Harman.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: Harman |
Version: 1.35.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Harman.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Harman_1.35.0.tar.gz |
StartedAt: 2024-12-23 19:39:53 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 19:40:20 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 27.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Harman.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Harman.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Harman_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Harman.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Harman/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Harman’ version ‘1.35.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘Harman’ can be installed ... OK * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * 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 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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-3.21-bioc/meat/Harman.Rcheck/00check.log’ for details.
Harman.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Harman ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘Harman’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_ARRAYALIGNEMT=4 -D_USE_RCPP=1 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -I. -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c Harman.cpp -o Harman.o In file included from Harman.cpp:182: ./CSelectRandom.h:283:11: warning: variable 'seed' set but not used [-Wunused-but-set-variable] size_t seed ; ^ ./CSelectRandom.h:372:11: warning: variable 'seed' set but not used [-Wunused-but-set-variable] size_t seed ; ^ ./CSelectRandom.h:392:11: warning: unused variable 'currindex' [-Wunused-variable] size_t currindex ; ^ ./CSelectRandom.h:394:35: warning: unused variable 'it1' [-Wunused-variable] std::vector<double>::iterator it1, it2 ; ^ ./CSelectRandom.h:394:40: warning: unused variable 'it2' [-Wunused-variable] std::vector<double>::iterator it1, it2 ; ^ ./CSelectRandom.h:638:20: warning: unused variable 'ts1' [-Wunused-variable] struct timespec ts1, ts2 ; ^ ./CSelectRandom.h:638:25: warning: unused variable 'ts2' [-Wunused-variable] struct timespec ts1, ts2 ; ^ ./CSelectRandom.h:639:11: warning: unused variable 'time1' [-Wunused-variable] double time1, time2 ; ^ ./CSelectRandom.h:639:18: warning: unused variable 'time2' [-Wunused-variable] double time1, time2 ; ^ ./CSelectRandom.h:932:18: warning: variable 'reject' set but not used [-Wunused-but-set-variable] long long int reject ; ^ ./CSelectRandom.h:1019:23: warning: unused variable 'randData2' [-Wunused-variable] size_t randData1, randData2 ; ^ ./CSelectRandom.h:1021:12: warning: variable 'reject' set but not used [-Wunused-but-set-variable] size_t reject ; ^ Harman.cpp:2480:12: warning: variable 'count' set but not used [-Wunused-but-set-variable] size_t count ; ^ 13 warnings generated. clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o Harman.so Harman.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-Harman/00new/Harman/libs ** R ** 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 (Harman)
Harman.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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. > BiocGenerics:::testPackage("Harman") First clustering, now find top two k, done. Reclustering, done. RUNIT TEST PROTOCOL -- Mon Dec 23 19:40:16 2024 *********************************************** Number of test functions: 14 Number of errors: 0 Number of failures: 0 1 Test Suite : Harman RUnit Tests - 14 test functions, 0 errors, 0 failures Number of test functions: 14 Number of errors: 0 Number of failures: 0 Warning message: In kClusterMethylation(betas[1, , drop = FALSE], row_ks = ks[1]) : All rows have a cluster size of 1 > > proc.time() user system elapsed 8.671 0.830 10.683
Harman.Rcheck/Harman-Ex.timings
name | user | system | elapsed | |
arrowPlot | 0.144 | 0.013 | 0.159 | |
clusterStats | 0.027 | 0.010 | 0.590 | |
discoverClusteredMethylation | 0.022 | 0.011 | 0.578 | |
harman | 0.252 | 0.025 | 0.285 | |
harmanresults | 0.181 | 0.021 | 0.204 | |
kClusterMethylation | 0.021 | 0.009 | 0.564 | |
pcaPlot | 0.145 | 0.020 | 0.190 | |
plot.harmanresults | 0.141 | 0.024 | 0.165 | |
prcompPlot | 0.080 | 0.008 | 0.090 | |
reconstructData | 0.162 | 0.022 | 0.183 | |
shiftBetas | 0.001 | 0.000 | 0.001 | |
summary.harmanresults | 0.152 | 0.023 | 0.180 | |