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This page was generated on 2023-02-04 11:05:45 -0500 (Sat, 04 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4511
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4289
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4318
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 lconway


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 534/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DifferentialRegulation 1.2.2  (landing page)
Simone Tiberi
Snapshot Date: 2023-02-03 14:00:04 -0500 (Fri, 03 Feb 2023)
git_url: https://git.bioconductor.org/packages/DifferentialRegulation
git_branch: RELEASE_3_16
git_last_commit: 0ae1b53
git_last_commit_date: 2023-01-19 11:16:11 -0500 (Thu, 19 Jan 2023)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DifferentialRegulation
Version: 1.2.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DifferentialRegulation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DifferentialRegulation_1.2.2.tar.gz
StartedAt: 2023-02-03 20:08:23 -0500 (Fri, 03 Feb 2023)
EndedAt: 2023-02-03 20:12:33 -0500 (Fri, 03 Feb 2023)
EllapsedTime: 249.4 seconds
RetCode: 0
Status:   OK  
CheckDir: DifferentialRegulation.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DifferentialRegulation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DifferentialRegulation_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/DifferentialRegulation.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.2.2’
* 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 2.556  0.137  25.029
plot_pi                1.602  0.048  22.929
* 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
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/DifferentialRegulation.Rcheck/00check.log’
for details.



Installation output

DifferentialRegulation.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DifferentialRegulation
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘DifferentialRegulation’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rcpp_MCMC.cpp -o Rcpp_MCMC.o
Rcpp_MCMC.cpp:144:17: warning: unused variable 'tmp_2' [-Wunused-variable]
  double tmp_1, tmp_2, tmp_3;
                ^
Rcpp_MCMC.cpp:144:10: warning: unused variable 'tmp_1' [-Wunused-variable]
  double tmp_1, tmp_2, tmp_3;
         ^
Rcpp_MCMC.cpp:144:24: warning: unused variable 'tmp_3' [-Wunused-variable]
  double tmp_1, tmp_2, tmp_3;
                       ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rcpp_MCMC_sce.cpp -o Rcpp_MCMC_sce.o
Rcpp_MCMC_sce.cpp:145:24: warning: unused variable 'tmp_3' [-Wunused-variable]
  double tmp_1, tmp_2, tmp_3;
                       ^
Rcpp_MCMC_sce.cpp:145:10: warning: unused variable 'tmp_1' [-Wunused-variable]
  double tmp_1, tmp_2, tmp_3;
         ^
Rcpp_MCMC_sce.cpp:145:17: warning: unused variable 'tmp_2' [-Wunused-variable]
  double tmp_1, tmp_2, tmp_3;
                ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o DifferentialRegulation.so RcppExports.o Rcpp_MCMC.o Rcpp_MCMC_sce.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: dylib (/usr/local/gfortran/lib/libgfortran.dylib) was built for newer macOS version (10.14) than being linked (10.13)
ld: warning: dylib (/usr/local/gfortran/lib/libquadmath.dylib) was built for newer macOS version (10.14) than being linked (10.13)
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/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 4.2.2 (2022-10-31) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
 11.415   0.741  34.351 

Example timings

DifferentialRegulation.Rcheck/DifferentialRegulation-Ex.timings

nameusersystemelapsed
DifferentialRegulation 2.556 0.13725.029
compute_PB_counts1.0390.0171.067
load_EC1.5590.0691.696
load_USA0.1490.0040.154
plot_pi 1.602 0.04822.929