| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:32 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 807/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeoDiff 1.7.1 (landing page) Nicole Ortogero
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: GeoDiff |
| Version: 1.7.1 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:GeoDiff.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings GeoDiff_1.7.1.tar.gz |
| StartedAt: 2023-06-05 23:07:03 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 23:16:49 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 586.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeoDiff.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:GeoDiff.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings GeoDiff_1.7.1.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GeoDiff.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* 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
* checking for file ‘GeoDiff/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeoDiff’ version ‘1.7.1’
* 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 15.8Mb
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 66.316 0.108 66.497
fitNBthmDE-methods 22.498 0.168 22.655
fitNBthDE-methods 19.918 0.153 20.109
fitNBth-methods 14.574 0.148 14.747
QuanRange-methods 8.741 0.251 9.009
BGScoreTest-methods 5.821 0.176 6.007
* 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 ...
‘Workflow_WTA_kidney.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/GeoDiff.Rcheck/00check.log’
for details.
GeoDiff.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL GeoDiff ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/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-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/roptim/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c NBthDEOptPara.cpp -o NBthDEOptPara.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/roptim/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c NBthmDEGrad.cpp -o NBthmDEGrad.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/roptim/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c NBthmDEMH.cpp -o NBthmDEMH.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/roptim/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c NBthmDEOptPara.cpp -o NBthmDEOptPara.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/roptim/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c NBthmDEOptU.cpp -o NBthmDEOptU.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/roptim/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c PoisthNormOptPara.cpp -o PoisthNormOptPara.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/roptim/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/roptim/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c dnbinom_mu_vec.cpp -o dnbinom_mu_vec.o g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.0/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 -lblas -lgfortran -lm -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/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 version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
> 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, sort, 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")'.
The legacy packages maptools, rgdal, and rgeos, underpinning this package
will retire shortly. Please refer to R-spatial evolution reports on
https://r-spatial.org/r/2023/05/15/evolution4.html for details.
This package is now running under evolution status 0
> library(Biobase)
>
> proc.time()
user system elapsed
8.824 0.333 9.162
GeoDiff.Rcheck/GeoDiff-Ex.timings
| name | user | system | elapsed | |
| BGScoreTest-methods | 5.821 | 0.176 | 6.007 | |
| DENBth-methods | 0.005 | 0.002 | 0.007 | |
| NBthDEmod2 | 0.066 | 0.000 | 0.066 | |
| NBthmDEmod2 | 0.005 | 0.000 | 0.005 | |
| NBthmDEmod2slope | 0.005 | 0.000 | 0.005 | |
| QuanRange-methods | 8.741 | 0.251 | 9.009 | |
| aggreprobe-methods | 2.917 | 0.052 | 2.974 | |
| coefNBth-methods | 0.04 | 0.00 | 0.04 | |
| contrastNBth-methods | 0.006 | 0.000 | 0.006 | |
| demoData | 0.295 | 0.000 | 0.296 | |
| diagPoisBG-methods | 1.472 | 0.048 | 1.522 | |
| fitNBth-methods | 14.574 | 0.148 | 14.747 | |
| fitNBthDE-methods | 19.918 | 0.153 | 20.109 | |
| fitNBthmDE-methods | 22.498 | 0.168 | 22.655 | |
| fitPoisBG-methods | 0.667 | 0.004 | 0.671 | |
| fitPoisthNorm-methods | 66.316 | 0.108 | 66.497 | |
| kidney | 0.439 | 0.012 | 0.452 | |