Tim Daniel Rose
| Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/mosbi |
| git_branch: RELEASE_3_18 |
| git_last_commit: adf6bad |
| git_last_commit_date: 2023-10-24 11:37:53 -0400 (Tue, 24 Oct 2023) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:14 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 1307/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mosbi 1.8.0 (landing page) Tim Daniel Rose
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the mosbi package: - 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: mosbi |
| Version: 1.8.0 |
| Command: rm -rf mosbi.buildbin-libdir && mkdir mosbi.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh mosbi_1.8.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R mosbi.buildbin-libdir |
| StartedAt: 2024-04-18 10:12:38 -0400 (Thu, 18 Apr 2024) |
| EndedAt: 2024-04-18 10:14:24 -0400 (Thu, 18 Apr 2024) |
| EllapsedTime: 105.4 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: mosbi_1.8.0.tgz |
| PackageFileSize: 3.06 MiB |
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### Running command:
###
### rm -rf mosbi.buildbin-libdir && mkdir mosbi.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh mosbi_1.8.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R mosbi.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=mosbi.buildbin-libdir mosbi_1.8.0.tar.gz'
>>>>>>>
* installing *source* package ‘mosbi’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++17
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c attr_graph.cpp -o attr_graph.o
attr_graph.cpp:123:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if((rownames(m)!=R_NilValue)&(colnames(m)!=R_NilValue)){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
attr_graph.cpp:123:6: note: cast one or both operands to int to silence this warning
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c attributeConnector.cpp -o attributeConnector.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c attribute_overlap.cpp -o attribute_overlap.o
attribute_overlap.cpp:175:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if((rownames(occurance_m)!=R_NilValue)&(colnames(occurance_m)!=R_NilValue)){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
attribute_overlap.cpp:175:6: note: cast one or both operands to int to silence this warning
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bicluster_methods.cpp -o bicluster_methods.o
bicluster_methods.cpp:125:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
if((row1.length()>row2.length())|(col1.length()>col2.length())){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
bicluster_methods.cpp:125:6: note: cast one or both operands to int to silence this warning
bicluster_methods.cpp:130:18: warning: loop variable 'i' of type 'const int &' binds to a temporary constructed from type 'typename storage_type<14>::type &' (aka 'double &') [-Wrange-loop-construct]
for(const int& i : row1){
^
bicluster_methods.cpp:130:7: note: use non-reference type 'int' to make construction explicit or type 'const typename storage_type<14>::type &' (aka 'const double &') to prevent copying
for(const int& i : row1){
^~~~~~~~~~~~~~
bicluster_methods.cpp:137:18: warning: loop variable 'j' of type 'const int &' binds to a temporary constructed from type 'typename storage_type<14>::type &' (aka 'double &') [-Wrange-loop-construct]
for(const int& j : col1){
^
bicluster_methods.cpp:137:7: note: use non-reference type 'int' to make construction explicit or type 'const typename storage_type<14>::type &' (aka 'const double &') to prevent copying
for(const int& j : col1){
^~~~~~~~~~~~~~
bicluster_methods.cpp:144:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if((irow==row1.length())&(irow==row2.length())&
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bicluster_methods.cpp:144:6: note: cast one or both operands to int to silence this warning
bicluster_methods.cpp:144:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if((irow==row1.length())&(irow==row2.length())&
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
bicluster_methods.cpp:144:6: note: cast one or both operands to int to silence this warning
bicluster_methods.cpp:144:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if((irow==row1.length())&(irow==row2.length())&
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
bicluster_methods.cpp:144:6: note: cast one or both operands to int to silence this warning
bicluster_methods.cpp:150:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if((irow==row1.length())&(icol==col1.length())){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
bicluster_methods.cpp:150:6: note: cast one or both operands to int to silence this warning
bicluster_methods.cpp:214:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if((!iinv(b, ereaseV))&(!iinv(b, identicalV))){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
bicluster_methods.cpp:214:8: note: cast one or both operands to int to silence this warning
8 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost_graph.cpp -o boost_graph.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost_write.cpp -o boost_write.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c distance_matrix.cpp -o distance_matrix.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c extractBF.cpp -o extractBF.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c extractQUBIC2.cpp -o extractQUBIC2.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c full_graph.cpp -o full_graph.o
full_graph.cpp:111:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if((rownames(m)!=R_NilValue)&(colnames(m)!=R_NilValue)){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
full_graph.cpp:111:6: note: cast one or both operands to int to silence this warning
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c misc.cpp -o misc.o
misc.cpp:20:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
return(!((colnames(m)==R_NilValue)|(rownames(m)==R_NilValue)));
~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
misc.cpp:20:12: note: cast one or both operands to int to silence this warning
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c network_edge_strength.cpp -o network_edge_strength.o
network_edge_strength.cpp:86:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if((rownames(mat)!=R_NilValue)&(colnames(mat)!=R_NilValue)){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
network_edge_strength.cpp:86:6: note: cast one or both operands to int to silence this warning
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sample_biclusters.cpp -o sample_biclusters.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c write_matrix.cpp -o write_matrix.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o mosbi.so RcppExports.o attr_graph.o attributeConnector.o attribute_overlap.o bicluster_methods.o boost_graph.o boost_write.o distance_matrix.o extractBF.o extractQUBIC2.o full_graph.o misc.o network_edge_strength.o sample_biclusters.o write_matrix.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/mosbi.buildbin-libdir/00LOCK-mosbi/00new/mosbi/libs
** R
** data
** 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 (mosbi)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR mosbi.buildbin-libdir/mosbi/libs/mosbi.so
>>>>>>>
>>>>>>> Paths before fix:
mosbi.buildbin-libdir/mosbi/libs/mosbi.so:
mosbi.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/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/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "mosbi.buildbin-libdir/mosbi/libs/mosbi.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "mosbi.buildbin-libdir/mosbi/libs/mosbi.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "mosbi.buildbin-libdir/mosbi/libs/mosbi.so"
>>>>>>> Paths after fix:
mosbi.buildbin-libdir/mosbi/libs/mosbi.so:
mosbi.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/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)