Nicole Ortogero
| Snapshot Date: 2023-12-05 14:00:18 -0500 (Tue, 05 Dec 2023) |
| git_url: https://git.bioconductor.org/packages/GeoDiff |
| git_branch: devel |
| git_last_commit: 5846afa |
| git_last_commit_date: 2023-10-24 11:37:56 -0500 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2023-12-06 11:39:24 -0500 (Wed, 06 Dec 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences" | 4609 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-11-14 r85524 ucrt) -- "Unsuffered Consequences" | 4350 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences" | 4375 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2023-11-01 r85459) -- "Unsuffered Consequences" | 4262 |
| 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 825/2229 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeoDiff 1.9.0 (landing page) Nicole Ortogero
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: GeoDiff |
| Version: 1.9.0 |
| Command: /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:GeoDiff.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings GeoDiff_1.9.0.tar.gz |
| StartedAt: 2023-12-06 04:47:34 -0000 (Wed, 06 Dec 2023) |
| EndedAt: 2023-12-06 04:53:34 -0000 (Wed, 06 Dec 2023) |
| EllapsedTime: 360.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeoDiff.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:GeoDiff.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings GeoDiff_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GeoDiff.Rcheck’
* using R Under development (unstable) (2023-11-01 r85459)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeoDiff/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeoDiff’ version ‘1.9.0’
* 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++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 15.9Mb
sub-directories of 1Mb or more:
data 4.2Mb
libs 11.3Mb
* 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 ... 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 48.016 0.139 48.278
fitNBthmDE-methods 22.549 0.176 22.731
fitNBthDE-methods 19.925 0.143 20.118
fitNBth-methods 14.199 0.175 14.406
QuanRange-methods 8.829 0.511 9.365
BGScoreTest-methods 5.720 0.255 5.992
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/GeoDiff.Rcheck/00check.log’
for details.
GeoDiff.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD INSTALL GeoDiff
###
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library’
* installing *source* package ‘GeoDiff’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/roptim/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c NBthDEOptPara.cpp -o NBthDEOptPara.o
NBthDEOptPara.cpp: In member function ‘virtual double NBthDE_paranll::operator()(const 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 vec&, arma::vec&)’:
NBthDEOptPara.cpp:85:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const 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/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/roptim/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -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 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 uword’ {aka ‘const unsigned int’} [-Wsign-compare]
90 | for(int k = 0; k < y.n_elem; k++){
| ~~^~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/roptim/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c NBthmDEMH.cpp -o NBthmDEMH.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/roptim/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c NBthmDEOptPara.cpp -o NBthmDEOptPara.o
NBthmDEOptPara.cpp: In member function ‘virtual void NBthmDE_fparanll::Gradient(const vec&, arma::vec&)’:
NBthmDEOptPara.cpp:107:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const unsigned int’} [-Wsign-compare]
107 | for(int k = 0; k < y.n_elem; k++){
| ~~^~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/roptim/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c NBthmDEOptU.cpp -o NBthmDEOptU.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/roptim/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c PoisthNormOptPara.cpp -o PoisthNormOptPara.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/roptim/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/roptim/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c dnbinom_mu_vec.cpp -o dnbinom_mu_vec.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-devel/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 -lopenblas -lgfortran -lm -L/home/biocbuild/R/R-devel/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2023.11.02/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) (2023-11-01 r85459) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
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, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, 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
9.661 0.478 10.147
GeoDiff.Rcheck/GeoDiff-Ex.timings
| name | user | system | elapsed | |
| BGScoreTest-methods | 5.720 | 0.255 | 5.992 | |
| DENBth-methods | 0.008 | 0.000 | 0.008 | |
| NBthDEmod2 | 0.055 | 0.000 | 0.055 | |
| NBthmDEmod2 | 0.005 | 0.000 | 0.005 | |
| NBthmDEmod2slope | 0.005 | 0.000 | 0.005 | |
| QuanRange-methods | 8.829 | 0.511 | 9.365 | |
| aggreprobe-methods | 2.894 | 0.028 | 2.929 | |
| coefNBth-methods | 0.043 | 0.000 | 0.044 | |
| contrastNBth-methods | 0.006 | 0.000 | 0.006 | |
| demoData | 0.401 | 0.004 | 0.405 | |
| diagPoisBG-methods | 1.593 | 0.064 | 1.661 | |
| fitNBth-methods | 14.199 | 0.175 | 14.406 | |
| fitNBthDE-methods | 19.925 | 0.143 | 20.118 | |
| fitNBthmDE-methods | 22.549 | 0.176 | 22.731 | |
| fitPoisBG-methods | 0.917 | 0.000 | 0.919 | |
| fitPoisthNorm-methods | 48.016 | 0.139 | 48.278 | |
| kidney | 0.468 | 0.016 | 0.485 | |