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This page was generated on 2022-10-19 13:20:11 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 DifferentialRegulation on nebbiolo1


To the developers/maintainers of the DifferentialRegulation package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DifferentialRegulation.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.

raw results

Package 526/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DifferentialRegulation 1.0.7  (landing page)
Simone Tiberi
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/DifferentialRegulation
git_branch: RELEASE_3_15
git_last_commit: 013f193
git_last_commit_date: 2022-07-25 09:46:18 -0400 (Mon, 25 Jul 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DifferentialRegulation
Version: 1.0.7
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:DifferentialRegulation.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings DifferentialRegulation_1.0.7.tar.gz
StartedAt: 2022-10-18 19:27:00 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 19:31:01 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 240.9 seconds
RetCode: 0
Status:   OK  
CheckDir: DifferentialRegulation.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:DifferentialRegulation.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings DifferentialRegulation_1.0.7.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/DifferentialRegulation.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DifferentialRegulation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DifferentialRegulation’ version ‘1.0.7’
* 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 ‘DifferentialRegulation’ 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 ... 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 ... NOTE
MCMC_ECs: no visible binding for global variable ‘cl’
MCMC_USA: no visible binding for global variable ‘cl’
Undefined global functions or variables:
  cl
* 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
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
DifferentialRegulation 2.717  0.232  26.142
plot_pi                1.666  0.070  22.118
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testhat.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/DifferentialRegulation.Rcheck/00check.log’
for details.



Installation output

DifferentialRegulation.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘DifferentialRegulation’ ...
** 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/usr/local/include   -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/usr/local/include   -fpic  -g -O2  -Wall -c Rcpp_MCMC.cpp -o Rcpp_MCMC.o
Rcpp_MCMC.cpp: In function ‘Rcpp::NumericVector Rcpp_MCMC(const unsigned int&, const unsigned int&, const unsigned int&, const unsigned int&, const IntegerVector&, const IntegerVector&, const Rcpp::ListOf<Rcpp::Vector<13> >&, const IntegerVector&, const unsigned int&, const unsigned int&, Rcpp::NumericMatrix&, Rcpp::ListOf<Rcpp::Matrix<14> >&, const Rcpp::ListOf<Rcpp::Matrix<14> >&, const Rcpp::ListOf<Rcpp::ListOf<Rcpp::Vector<13> > >&, const Rcpp::ListOf<Rcpp::ListOf<Rcpp::Vector<14, Rcpp::PreserveStorage> > >&, const Rcpp::ListOf<Rcpp::Vector<13> >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, Rcpp::ListOf<Rcpp::ListOf<Rcpp::Matrix<14> > >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, const bool&, const double&, const double&, const double&)’:
Rcpp_MCMC.cpp:279:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const type’ {aka ‘const int’} [-Wsign-compare]
  279 |         for(sample = 0; sample < n_samples_per_group[ gr ]; sample ++){
Rcpp_MCMC.cpp:144:10: warning: unused variable ‘tmp_1’ [-Wunused-variable]
  144 |   double tmp_1, tmp_2, tmp_3;
      |          ^~~~~
Rcpp_MCMC.cpp:144:17: warning: unused variable ‘tmp_2’ [-Wunused-variable]
  144 |   double tmp_1, tmp_2, tmp_3;
      |                 ^~~~~
Rcpp_MCMC.cpp:144:24: warning: unused variable ‘tmp_3’ [-Wunused-variable]
  144 |   double tmp_1, tmp_2, tmp_3;
      |                        ^~~~~
Rcpp_MCMC.cpp:365:10: warning: ‘ll_original’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  365 |       ll += ll_original;
      |       ~~~^~~~~~~~~~~~~~
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/usr/local/include   -fpic  -g -O2  -Wall -c Rcpp_MCMC_sce.cpp -o Rcpp_MCMC_sce.o
Rcpp_MCMC_sce.cpp: In function ‘Rcpp::NumericVector Rcpp_MCMC_sce(const unsigned int&, const unsigned int&, const unsigned int&, const IntegerVector&, const Rcpp::ListOf<Rcpp::Vector<13> >&, const IntegerVector&, const unsigned int&, const unsigned int&, Rcpp::ListOf<Rcpp::Matrix<14> >&, const Rcpp::ListOf<Rcpp::Matrix<14> >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, Rcpp::ListOf<Rcpp::ListOf<Rcpp::Matrix<14> > >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, const bool&, const double&, const double&, const double&)’:
Rcpp_MCMC_sce.cpp:234:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const type’ {aka ‘const int’} [-Wsign-compare]
  234 |         for(sample = 0; sample < n_samples_per_group[ gr ]; sample ++){
Rcpp_MCMC_sce.cpp:145:10: warning: unused variable ‘tmp_1’ [-Wunused-variable]
  145 |   double tmp_1, tmp_2, tmp_3;
      |          ^~~~~
Rcpp_MCMC_sce.cpp:145:17: warning: unused variable ‘tmp_2’ [-Wunused-variable]
  145 |   double tmp_1, tmp_2, tmp_3;
      |                 ^~~~~
Rcpp_MCMC_sce.cpp:145:24: warning: unused variable ‘tmp_3’ [-Wunused-variable]
  145 |   double tmp_1, tmp_2, tmp_3;
      |                        ^~~~~
Rcpp_MCMC_sce.cpp:320:10: warning: ‘ll_original’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  320 |       ll += ll_original;
      |       ~~~^~~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o DifferentialRegulation.so RcppExports.o Rcpp_MCMC.o Rcpp_MCMC_sce.o -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-DifferentialRegulation/00new/DifferentialRegulation/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 (DifferentialRegulation)

Tests output

DifferentialRegulation.Rcheck/tests/testhat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
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(DifferentialRegulation)
> test_check("DifferentialRegulation")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
 11.098   0.666  38.111 

Example timings

DifferentialRegulation.Rcheck/DifferentialRegulation-Ex.timings

nameusersystemelapsed
DifferentialRegulation 2.717 0.23226.142
compute_PB_counts1.0720.0601.133
load_EC1.7790.1601.942
load_USA0.1800.0040.184
plot_pi 1.666 0.07022.118