Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:05:27 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
To the developers/maintainers of the Harman package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/Harman.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 852/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Harman 1.22.0 (landing page) Jason Ross
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: Harman |
Version: 1.22.0 |
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:Harman.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings Harman_1.22.0.tar.gz |
StartedAt: 2022-04-12 07:45:26 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 07:46:37 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 70.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: Harman.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:Harman.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings Harman_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/Harman.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Harman/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Harman’ version ‘1.22.0’ * 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 * 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 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 ... WARNING Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘Harman’ * 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 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 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.14-bioc/meat/Harman.Rcheck/00check.log’ for details.
Harman.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL Harman ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’ * installing *source* package ‘Harman’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_ARRAYALIGNEMT=4 -D_USE_RCPP=1 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include `/home/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -I. -fpic -g -O2 -Wall -c Harman.cpp -o Harman.o Harman.cpp: In function ‘SEXPREC* HarmanMain(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: Harman.cpp:3008:3: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 3008 | else | ^~~~ Harman.cpp:3022:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 3022 | std::vector<unsigned int> tr_std_tmp = Rcpp::as<std::vector<unsigned int> >(tr) ; | ^~~ In file included from Harman.cpp:182: CSelectRandom.h: In instantiation of ‘std::vector<unsigned int>* CSelectRandom<T>::ReturnVectOf32bitIntegersInRange_CSTDLIB(size_t, size_t, size_t, size_t) [with T = double; size_t = long unsigned int]’: Harman.cpp:1764:117: required from here CSelectRandom.h:943:20: warning: comparison of integer expressions of different signedness: ‘long long int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 943 | while (currval < howManyIN) | ~~~~~~~~^~~~~~~~~~~ g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o Harman.so Harman.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.14-bioc/R/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 version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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. > BiocGenerics:::testPackage("Harman") RUNIT TEST PROTOCOL -- Tue Apr 12 07:46:34 2022 *********************************************** Number of test functions: 10 Number of errors: 0 Number of failures: 0 1 Test Suite : Harman RUnit Tests - 10 test functions, 0 errors, 0 failures Number of test functions: 10 Number of errors: 0 Number of failures: 0 There were 12 warnings (use warnings() to see them) > > proc.time() user system elapsed 31.419 0.543 33.360
Harman.Rcheck/Harman-Ex.timings
name | user | system | elapsed | |
arrowPlot | 0.691 | 0.037 | 0.736 | |
harman | 1.057 | 0.096 | 1.153 | |
harmanresults | 1.025 | 0.036 | 1.063 | |
pcaPlot | 0.975 | 0.020 | 0.995 | |
plot.harmanresults | 0.869 | 0.008 | 0.879 | |
prcompPlot | 0.390 | 0.015 | 0.408 | |
reconstructData | 1.177 | 0.024 | 1.203 | |
shiftBetas | 0.000 | 0.003 | 0.002 | |
summary.harmanresults | 0.687 | 0.000 | 0.687 | |