Mike Morgan
| Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/miloR |
| git_branch: RELEASE_3_21 |
| git_last_commit: e8685ed |
| git_last_commit_date: 2025-04-15 12:29:21 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-22 13:16 -0400 (Tue, 22 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 | ||||
| Package 1287/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| miloR 2.4.0 (landing page) Mike Morgan
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the miloR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/miloR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: miloR |
| Version: 2.4.0 |
| Command: rm -rf miloR.buildbin-libdir && mkdir miloR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh miloR_2.4.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R miloR.buildbin-libdir |
| StartedAt: 2025-04-22 00:54:53 -0400 (Tue, 22 Apr 2025) |
| EndedAt: 2025-04-22 00:57:25 -0400 (Tue, 22 Apr 2025) |
| EllapsedTime: 152.0 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: miloR_2.4.0.tgz |
| PackageFileSize: 7.371 MiB |
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###
### Running command:
###
### rm -rf miloR.buildbin-libdir && mkdir miloR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh miloR_2.4.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R miloR.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=miloR.buildbin-libdir miloR_2.4.0.tar.gz'
>>>>>>>
* installing *source* package ‘miloR’ ...
** this is package ‘miloR’ version ‘2.4.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c computeMatrices.cpp -o computeMatrices.o
computeMatrices.cpp:246:9: warning: variable 'stot' set but not used [-Wunused-but-set-variable]
int stot = 0;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c fitGeneticPLGlmm.cpp -o fitGeneticPLGlmm.o
fitGeneticPLGlmm.cpp:113:12: warning: variable '_intercept' set but not used [-Wunused-but-set-variable]
double _intercept = constval; // intercept for HE regression
^
fitGeneticPLGlmm.cpp:200:10: warning: unused variable '_phi_est' [-Wunused-variable]
bool _phi_est = true; // control if we re-estimate phi or not
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c fitPLGlmm.cpp -o fitPLGlmm.o
fitPLGlmm.cpp:172:10: warning: unused variable '_phi_est' [-Wunused-variable]
bool _phi_est = true; // control if we re-estimate phi or not
^
fitPLGlmm.cpp:106:12: warning: variable '_intercept' set but not used [-Wunused-but-set-variable]
double _intercept = constval; // intercept for HE regression?? need a better estimate.
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c inference.cpp -o inference.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c invertPseudoVar.cpp -o invertPseudoVar.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c multiP.cpp -o multiP.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c paramEst.cpp -o paramEst.o
paramEst.cpp:36:33: warning: left operand of comma operator has no effect [-Wunused-value]
double rhs = 0.5 * mid1[0, 0];
^
paramEst.cpp:172:12: warning: unused variable 'lambda' [-Wunused-variable]
double lambda = 1e-1;
^
paramEst.cpp:173:12: warning: unused variable 'lambda_step' [-Wunused-variable]
double lambda_step = 10;
^
paramEst.cpp:174:12: warning: unused variable '_illcond_eps' [-Wunused-variable]
double _illcond_eps = 1e-6;
^
paramEst.cpp:175:12: warning: unused variable '_lcond_target' [-Wunused-variable]
double _lcond_target = 1e-5;
^
paramEst.cpp:241:19: warning: unused variable 'nsq' [-Wunused-variable]
unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix, no diag
^
paramEst.cpp:242:18: warning: unused variable 'i' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:242:21: warning: unused variable 'j' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:243:12: warning: unused variable '_ycovij' [-Wunused-variable]
double _ycovij; // Declare temp_value
^
paramEst.cpp:276:19: warning: unused variable 'nsq' [-Wunused-variable]
unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
^
paramEst.cpp:277:18: warning: unused variable 'i' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:277:21: warning: unused variable 'j' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:278:12: warning: unused variable '_ycovij' [-Wunused-variable]
double _ycovij; // Declare temp_value
^
paramEst.cpp:342:19: warning: unused variable 'nsq' [-Wunused-variable]
unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
^
paramEst.cpp:409:19: warning: unused variable 'nsq' [-Wunused-variable]
unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
^
paramEst.cpp:410:18: warning: unused variable 'i' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:410:21: warning: unused variable 'j' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:442:19: warning: unused variable 'nsq' [-Wunused-variable]
unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
^
paramEst.cpp:443:18: warning: unused variable 'i' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:443:21: warning: unused variable 'j' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:774:12: warning: unused variable 'half_logli' [-Wunused-variable]
double half_logli = nbLogLik(mu, disp/2.0, y) - normlihood;
^
paramEst.cpp:779:10: warning: unused variable 'comp_vals' [-Wunused-variable]
bool comp_vals = false;
^
22 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c pseudovarPartial.cpp -o pseudovarPartial.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c solveQP.cpp -o solveQP.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o miloR.so RcppExports.o computeMatrices.o fitGeneticPLGlmm.o fitPLGlmm.o inference.o invertPseudoVar.o multiP.o paramEst.o pseudovarPartial.o solveQP.o utils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.21-bioc/meat/miloR.buildbin-libdir/00LOCK-miloR/00new/miloR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘graph’ in package ‘miloR’
** 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 (miloR)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR miloR.buildbin-libdir/miloR/libs/miloR.so
>>>>>>>
>>>>>>> Paths before fix:
miloR.buildbin-libdir/miloR/libs/miloR.so:
miloR.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.5.0, current version 4.5.0)
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "miloR.buildbin-libdir/miloR/libs/miloR.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "miloR.buildbin-libdir/miloR/libs/miloR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "miloR.buildbin-libdir/miloR/libs/miloR.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "miloR.buildbin-libdir/miloR/libs/miloR.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "miloR.buildbin-libdir/miloR/libs/miloR.so"
>>>>>>> Paths after fix:
miloR.buildbin-libdir/miloR/libs/miloR.so:
miloR.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.5.0, current version 4.5.0)
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)