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This page was generated on 2022-01-27 11:05:46 -0500 (Thu, 27 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
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

CHECK results for GeoDiff on nebbiolo1


To the developers/maintainers of the GeoDiff package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 761/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeoDiff 1.1.2  (landing page)
Nicole Ortogero
Snapshot Date: 2022-01-26 13:55:18 -0500 (Wed, 26 Jan 2022)
git_url: https://git.bioconductor.org/packages/GeoDiff
git_branch: master
git_last_commit: 696da1e
git_last_commit_date: 2021-11-08 14:10:32 -0500 (Mon, 08 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'Biobase' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GeoDiff
Version: 1.1.2
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:GeoDiff.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings GeoDiff_1.1.2.tar.gz
StartedAt: 2022-01-26 19:26:13 -0500 (Wed, 26 Jan 2022)
EndedAt: 2022-01-26 19:30:22 -0500 (Wed, 26 Jan 2022)
EllapsedTime: 249.1 seconds
RetCode: 0
Status:   OK  
CheckDir: GeoDiff.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:GeoDiff.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings GeoDiff_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/GeoDiff.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeoDiff/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeoDiff’ version ‘1.1.2’
* 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
* checking installed package size ... NOTE
  installed size is 10.4Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   5.9Mb
* 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 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 50.065  0.176  50.250
fitNBthmDE-methods    14.841  0.161  14.922
fitNBthDE-methods     13.200  0.196  13.396
fitNBth-methods        9.544  0.124   9.668
QuanRange-methods      6.499  0.228   6.727
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/GeoDiff.Rcheck/00check.log’
for details.



Installation output

GeoDiff.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL GeoDiff
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘GeoDiff’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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/bbs-3.15-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 -L/home/biocbuild/bbs-3.15-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.15-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/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)

Tests output

GeoDiff.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
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.

> 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, 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")'.

> library(Biobase)
> 
> proc.time()
   user  system elapsed 
  6.012   0.381   6.380 

Example timings

GeoDiff.Rcheck/GeoDiff-Ex.timings

nameusersystemelapsed
BGScoreTest-methods3.9170.1404.057
DENBth-methods0.0080.0000.008
NBthDEmod20.060.000.06
NBthmDEmod20.0050.0000.005
NBthmDEmod2slope0.0040.0000.004
QuanRange-methods6.4990.2286.727
aggreprobe-methods1.8180.0201.838
coefNBth-methods0.030.000.03
contrastNBth-methods0.0040.0010.005
demoData0.2770.0060.283
diagPoisBG-methods1.6020.1121.714
fitNBth-methods9.5440.1249.668
fitNBthDE-methods13.200 0.19613.396
fitNBthmDE-methods14.841 0.16114.922
fitPoisBG-methods0.6400.0040.645
fitPoisthNorm-methods50.065 0.17650.250
kidney0.4960.0480.544