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This page was generated on 2023-04-20 12:50:31 -0400 (Thu, 20 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-04-19 r84288) -- "Unsuffered Consequences" | 3941 |
| 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 | ||||
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To the developers/maintainers of the MIMOSA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MIMOSA.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 1229/2223 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Greg Finak
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| Package: MIMOSA |
| Version: 1.37.1 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL MIMOSA |
| StartedAt: 2023-04-20 03:52:17 -0400 (Thu, 20 Apr 2023) |
| EndedAt: 2023-04-20 03:52:57 -0400 (Thu, 20 Apr 2023) |
| EllapsedTime: 39.7 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL MIMOSA
###
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘MIMOSA’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include `/home/biocbuild/bbs-3.18-bioc/R/bin/Rscript -e "RcppArmadillo:::CxxFlags()"` -fpic -g -O2 -Wall -c BetaMix.cpp -o BetaMix.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include `/home/biocbuild/bbs-3.18-bioc/R/bin/Rscript -e "RcppArmadillo:::CxxFlags()"` -fpic -g -O2 -Wall -c MCMC.cpp -o MCMC.o
MCMC.cpp: In function ‘SEXPREC* fitMCMC(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
MCMC.cpp:73:16: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
73 | if(file==NULL|fileP==NULL){
| ^
MCMC.cpp:88:25: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
88 | if(alphas.size()!=stim.ncol()){
| ~~~~~~~~~~~~~^~~~~~~~~~~~~
MCMC.cpp:189:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
189 | for(int i=0;i<alphas.size();i++){
| ~^~~~~~~~~~~~~~
MCMC.cpp:192:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
192 | for(int i=0;i<alphau.size();i++){
| ~^~~~~~~~~~~~~~
MCMC.cpp:524:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
524 | for(int j=0;j<p.size();j++){
| ~^~~~~~~~~
MCMC.cpp:544:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
544 | for(int obs=0;obs<alphas.size();obs++){
| ~~~^~~~~~~~~~~~~~
MCMC.cpp:547:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
547 | for(int obs=0;obs<alphau.size();obs++){
| ~~~^~~~~~~~~~~~~~
MCMC.cpp: In function ‘double lkbeta(const std::vector<double>&)’:
MCMC.cpp:631:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
631 | for(int i=0;i<alpha.size();i++){
| ~^~~~~~~~~~~~~
MCMC.cpp: In function ‘void simZ(double&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<bool>&, int, int)’:
MCMC.cpp:681:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
681 | for(i=0;i < lnull.size(); i++){
| ~~^~~~~~~~~~~~~~
MCMC.cpp: In function ‘double normconstIBeta(double, double, double, double)’:
MCMC.cpp:815:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
815 | for(int i=0;i<upper.size();i++){
| ~^~~~~~~~~~~~~
MCMC.cpp: In function ‘double nc(double, double, double, double, double)’:
MCMC.cpp:888:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
888 | for(int i=0;i<(s.size()-1);i++){
| ~^~~~~~~~~~~~~
MCMC.cpp:893:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
893 | for(int i=0;i<s.size();i++){
| ~^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c MIMOSA_init.c -o MIMOSA_init.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c betaintegral.c -o betaintegral.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include `/home/biocbuild/bbs-3.18-bioc/R/bin/Rscript -e "RcppArmadillo:::CxxFlags()"` -fpic -g -O2 -Wall -c betaintegralRcpp.cpp -o betaintegralRcpp.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o MIMOSA.so BetaMix.o MCMC.o MIMOSA_init.o betaintegral.o betaintegralRcpp.o -O3 -lm -lstdc++ -I"/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppArmadillo/include" -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-MIMOSA/00new/MIMOSA/libs
** R
** data
*** moving datasets to lazyload DB
** 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
Warning: Package 'MIMOSA' is deprecated and will be removed from Bioconductor
version 3.18
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'MIMOSA' is deprecated and will be removed from Bioconductor
version 3.18
** testing if installed package keeps a record of temporary installation path
* DONE (MIMOSA)