| Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:03 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 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. |
| Package 534/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DifferentialRegulation 1.2.2 (landing page) Simone Tiberi
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: DifferentialRegulation |
| Version: 1.2.2 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:DifferentialRegulation.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings DifferentialRegulation_1.2.2.tar.gz |
| StartedAt: 2023-04-10 20:19:03 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 20:24:25 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 321.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DifferentialRegulation.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:DifferentialRegulation.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings DifferentialRegulation_1.2.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/DifferentialRegulation.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
libs 4.2Mb
* 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 ... 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 2.895 0.180 25.587
plot_pi 1.736 0.029 24.989
* 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 ...
‘DifferentialRegulation.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-3.16-bioc/meat/DifferentialRegulation.Rcheck/00check.log’
for details.
DifferentialRegulation.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL DifferentialRegulation
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘DifferentialRegulation’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/lib -L/usr/local/lib -o DifferentialRegulation.so RcppExports.o Rcpp_MCMC.o Rcpp_MCMC_sce.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.16-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-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)
DifferentialRegulation.Rcheck/tests/testhat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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
12.156 1.190 35.877
DifferentialRegulation.Rcheck/DifferentialRegulation-Ex.timings
| name | user | system | elapsed | |
| DifferentialRegulation | 2.895 | 0.180 | 25.587 | |
| compute_PB_counts | 1.094 | 0.060 | 1.153 | |
| load_EC | 1.674 | 0.057 | 1.732 | |
| load_USA | 0.18 | 0.00 | 0.18 | |
| plot_pi | 1.736 | 0.029 | 24.989 | |