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 11:40 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
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 829/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeoDiff 1.13.0 (landing page) Nicole Ortogero
| 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 | OK | ||||||||||
To the developers/maintainers of the GeoDiff package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeoDiff.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: GeoDiff |
Version: 1.13.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GeoDiff.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GeoDiff_1.13.0.tar.gz |
StartedAt: 2024-12-23 22:25:18 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 22:32:20 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 421.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeoDiff.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GeoDiff.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GeoDiff_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GeoDiff.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘GeoDiff/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GeoDiff’ version ‘1.13.0’ * 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 ‘GeoDiff’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... INFO installed size is 9.6Mb sub-directories of 1Mb or more: data 4.3Mb libs 5.1Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 loading without being on the library search path ... 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 fitPoisthNorm-methods 50.721 0.098 50.829 fitNBthmDE-methods 13.708 0.044 13.681 fitNBthDE-methods 12.228 0.107 12.335 fitNBth-methods 8.662 0.148 8.810 QuanRange-methods 6.129 0.211 6.340 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/GeoDiff.Rcheck/00check.log’ for details.
GeoDiff.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL GeoDiff ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘GeoDiff’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/roptim/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -DR_NO_REMAP -c NBthDEOptPara.cpp -o NBthDEOptPara.o NBthDEOptPara.cpp: In member function ‘virtual double NBthDE_paranll::operator()(const arma::vec&)’: NBthDEOptPara.cpp:34:9: warning: unused variable ‘m’ [-Wunused-variable] 34 | int m = y.n_elem; | ^ NBthDEOptPara.cpp: In member function ‘virtual void NBthDE_paranll::Gradient(const arma::vec&, arma::vec&)’: NBthDEOptPara.cpp:85:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 85 | for(int k = 0; k < y.n_elem; k++){ | ~~^~~~~~~~~~ NBthDEOptPara.cpp:58:9: warning: unused variable ‘m’ [-Wunused-variable] 58 | int m = y.n_elem; | ^ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/roptim/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -DR_NO_REMAP -c NBthmDEGrad.cpp -o NBthmDEGrad.o NBthmDEGrad.cpp: In function ‘arma::vec NBthmDE_grad(arma::vec&, arma::mat&, arma::mat&, arma::vec&, arma::vec&, arma::vec&, arma::vec&, arma::mat&, double, double)’: NBthmDEGrad.cpp:34:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 34 | for(int i = 0; i < y.n_elem; i++){ | ~~^~~~~~~~~~ NBthmDEGrad.cpp: In function ‘arma::mat NBthmDE_gradM(arma::vec&, arma::mat&, arma::mat&, arma::vec&, arma::mat&, arma::vec&, arma::vec&, arma::mat&, double, double)’: NBthmDEGrad.cpp:90:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 90 | for(int k = 0; k < y.n_elem; k++){ | ~~^~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/roptim/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -DR_NO_REMAP -c NBthmDEMH.cpp -o NBthmDEMH.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/roptim/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -DR_NO_REMAP -c NBthmDEOptPara.cpp -o NBthmDEOptPara.o NBthmDEOptPara.cpp: In member function ‘virtual void NBthmDE_fparanll::Gradient(const arma::vec&, arma::vec&)’: NBthmDEOptPara.cpp:107:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 107 | for(int k = 0; k < y.n_elem; k++){ | ~~^~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/roptim/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -DR_NO_REMAP -c NBthmDEOptU.cpp -o NBthmDEOptU.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/roptim/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -DR_NO_REMAP -c PoisthNormOptPara.cpp -o PoisthNormOptPara.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/roptim/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/roptim/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fopenmp -fpic -g -O2 -Wall -DR_NO_REMAP -c dnbinom_mu_vec.cpp -o dnbinom_mu_vec.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o GeoDiff.so NBthDEOptPara.o NBthmDEGrad.o NBthmDEMH.o NBthmDEOptPara.o NBthmDEOptU.o PoisthNormOptPara.o RcppExports.o dnbinom_mu_vec.o -fopenmp -llapack -L/home/biocbuild/bbs-3.21-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-GeoDiff/00new/GeoDiff/libs ** R ** data ** 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 (GeoDiff)
GeoDiff.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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. > library(testthat) > library(GeoDiff) Loading required package: Biobase Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > library(Biobase) > > proc.time() user system elapsed 7.104 0.719 7.812
GeoDiff.Rcheck/GeoDiff-Ex.timings
name | user | system | elapsed | |
BGScoreTest-methods | 3.710 | 0.094 | 3.804 | |
DENBth-methods | 0.006 | 0.000 | 0.006 | |
NBthDEmod2 | 0.054 | 0.001 | 0.055 | |
NBthmDEmod2 | 0.003 | 0.001 | 0.004 | |
NBthmDEmod2slope | 0.004 | 0.000 | 0.004 | |
QuanRange-methods | 6.129 | 0.211 | 6.340 | |
aggreprobe-methods | 1.618 | 0.010 | 1.628 | |
coefNBth-methods | 0.026 | 0.000 | 0.026 | |
contrastNBth-methods | 0.005 | 0.000 | 0.005 | |
demoData | 0.25 | 0.01 | 0.26 | |
diagPoisBG-methods | 1.403 | 0.064 | 1.467 | |
fitNBth-methods | 8.662 | 0.148 | 8.810 | |
fitNBthDE-methods | 12.228 | 0.107 | 12.335 | |
fitNBthmDE-methods | 13.708 | 0.044 | 13.681 | |
fitPoisBG-methods | 0.551 | 0.002 | 0.554 | |
fitPoisthNorm-methods | 50.721 | 0.098 | 50.829 | |
kidney | 0.470 | 0.044 | 0.514 | |