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This page was generated on 2023-04-12 11:06:25 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (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

BUILD BIN results for scde on lconway


To the developers/maintainers of the scde package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scde.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 1795/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scde 2.26.2  (landing page)
Jean Fan
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/scde
git_branch: RELEASE_3_16
git_last_commit: 42cdc08
git_last_commit_date: 2023-01-19 11:18:19 -0400 (Thu, 19 Jan 2023)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: scde
Version: 2.26.2
Command: rm -rf scde.buildbin-libdir && mkdir scde.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh scde_2.26.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R scde.buildbin-libdir
StartedAt: 2023-04-11 00:03:33 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 00:04:48 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 75.2 seconds
RetCode: 0
Status:   OK  
PackageFile: scde_2.26.2.tgz
PackageFileSize: 2.203 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf scde.buildbin-libdir && mkdir scde.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh scde_2.26.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R scde.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=scde.buildbin-libdir scde_2.26.2.tar.gz'
>>>>>>> 

* installing *source* package ‘scde’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 bwpca.cpp -o bwpca.o
bwpca.cpp:28:14: warning: 'random_shuffle<std::__wrap_iter<int *>>' is deprecated [-Wdeprecated-declarations]
        std::random_shuffle(ind.begin(), ind.end());
             ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/shuffle.h:60:1: note: 'random_shuffle<std::__wrap_iter<int *>>' has been explicitly marked deprecated here
_LIBCPP_DEPRECATED_IN_CXX14 void
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1060:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX14'
#  define _LIBCPP_DEPRECATED_IN_CXX14 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
bwpca.cpp:45:14: warning: 'random_shuffle<std::__wrap_iter<int *>>' is deprecated [-Wdeprecated-declarations]
        std::random_shuffle(ind.begin(), ind.end());
             ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/shuffle.h:60:1: note: 'random_shuffle<std::__wrap_iter<int *>>' has been explicitly marked deprecated here
_LIBCPP_DEPRECATED_IN_CXX14 void
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1060:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX14'
#  define _LIBCPP_DEPRECATED_IN_CXX14 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
bwpca.cpp:105:11: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
    totvm %=totvm;
    ~~~~~ ^ ~~~~~
bwpca.cpp:122:15: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
        delta %=delta;
        ~~~~~ ^ ~~~~~
bwpca.cpp:147:19: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
            delta %=delta;
            ~~~~~ ^ ~~~~~
bwpca.cpp:271:19: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
            delta %=delta;
            ~~~~~ ^ ~~~~~
6 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 jpmatLogBoot.cpp -o jpmatLogBoot.o
jpmatLogBoot.cpp:200:24: warning: unused variable 'maxv' [-Wunused-variable]
                double maxv=nbp.max(maxij);
                       ^
jpmatLogBoot.cpp:443:10: warning: unused variable 'maxv' [-Wunused-variable]
                double maxv=nbp.max(maxij);
                       ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 matSlideMult.cpp -o matSlideMult.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 pagoda.cpp -o pagoda.o
pagoda.cpp:56:15: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
            ic%=ic; jc%=jc;
            ~~^ ~~
pagoda.cpp:56:23: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
            ic%=ic; jc%=jc;
                    ~~^ ~~
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 scde.so bwpca.o jpmatLogBoot.o matSlideMult.o pagoda.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 /Users/biocbuild/bbs-3.16-bioc/meat/scde.buildbin-libdir/00LOCK-scde/00new/scde/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (scde)


>>>>>>> 
>>>>>>> FIXING LINKS FOR scde.buildbin-libdir/scde/libs/scde.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "scde.buildbin-libdir/scde/libs/scde.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "scde.buildbin-libdir/scde/libs/scde.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "scde.buildbin-libdir/scde/libs/scde.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "scde.buildbin-libdir/scde/libs/scde.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "scde.buildbin-libdir/scde/libs/scde.so"