Alan O'Callaghan
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/densvis |
| git_branch: RELEASE_3_16 |
| git_last_commit: 463637d |
| git_last_commit_date: 2023-01-25 08:08:52 -0400 (Wed, 25 Jan 2023) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:05 -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 densvis package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/densvis.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 513/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| densvis 1.8.3 (landing page) Alan O'Callaghan
| 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: densvis |
| Version: 1.8.3 |
| Command: rm -rf densvis.buildbin-libdir && mkdir densvis.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh densvis_1.8.3.tar.gz /Library/Frameworks/R.framework/Resources/bin/R densvis.buildbin-libdir |
| StartedAt: 2023-04-10 23:40:24 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 23:40:56 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 32.6 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: densvis_1.8.3.tgz |
| PackageFileSize: 1.689 MiB |
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### Running command:
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### rm -rf densvis.buildbin-libdir && mkdir densvis.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh densvis_1.8.3.tar.gz /Library/Frameworks/R.framework/Resources/bin/R densvis.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=densvis.buildbin-libdir densvis_1.8.3.tar.gz'
>>>>>>>
* installing *source* package ‘densvis’ ...
** using non-staged installation via StagedInstall field
** 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/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.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/usr/local/include -fPIC -Wall -g -O2 -c densne.cpp -o densne.o
densne.cpp:181:24: warning: variable 'row_P' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
for(int i = 0; i < N * N; i++) P[i] /= sum_P;
^~~~~~~~~
densne.cpp:201:33: note: uninitialized use occurs here
computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift);
^~~~~
densne.cpp:181:24: note: remove the condition if it is always true
for(int i = 0; i < N * N; i++) P[i] /= sum_P;
^~~~~~~~~
densne.cpp:154:35: note: initialize the variable 'row_P' to silence this warning
double* P; unsigned int* row_P; unsigned int* col_P; double* val_P; double* val_D;
^
= nullptr
densne.cpp:181:24: warning: variable 'col_P' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
for(int i = 0; i < N * N; i++) P[i] /= sum_P;
^~~~~~~~~
densne.cpp:201:40: note: uninitialized use occurs here
computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift);
^~~~~
densne.cpp:181:24: note: remove the condition if it is always true
for(int i = 0; i < N * N; i++) P[i] /= sum_P;
^~~~~~~~~
densne.cpp:154:56: note: initialize the variable 'col_P' to silence this warning
double* P; unsigned int* row_P; unsigned int* col_P; double* val_P; double* val_D;
^
= nullptr
densne.cpp:181:24: warning: variable 'val_P' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
for(int i = 0; i < N * N; i++) P[i] /= sum_P;
^~~~~~~~~
densne.cpp:201:47: note: uninitialized use occurs here
computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift);
^~~~~
densne.cpp:181:24: note: remove the condition if it is always true
for(int i = 0; i < N * N; i++) P[i] /= sum_P;
^~~~~~~~~
densne.cpp:154:71: note: initialize the variable 'val_P' to silence this warning
double* P; unsigned int* row_P; unsigned int* col_P; double* val_P; double* val_D;
^
= nullptr
densne.cpp:181:24: warning: variable 'val_D' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
for(int i = 0; i < N * N; i++) P[i] /= sum_P;
^~~~~~~~~
densne.cpp:201:54: note: uninitialized use occurs here
computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift);
^~~~~
densne.cpp:181:24: note: remove the condition if it is always true
for(int i = 0; i < N * N; i++) P[i] /= sum_P;
^~~~~~~~~
densne.cpp:154:86: note: initialize the variable 'val_D' to silence this warning
double* P; unsigned int* row_P; unsigned int* col_P; double* val_P; double* val_D;
^
= nullptr
4 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/usr/local/include -fPIC -Wall -g -O2 -c densvis.cpp -o densvis.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/usr/local/include -fPIC -Wall -g -O2 -c sptree.cpp -o sptree.o
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 densvis.so RcppExports.o densne.o densvis.o sptree.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/densvis.buildbin-libdir/densvis/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
* DONE (densvis)
>>>>>>>
>>>>>>> FIXING LINKS FOR densvis.buildbin-libdir/densvis/libs/densvis.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" "densvis.buildbin-libdir/densvis/libs/densvis.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "densvis.buildbin-libdir/densvis/libs/densvis.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "densvis.buildbin-libdir/densvis/libs/densvis.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "densvis.buildbin-libdir/densvis/libs/densvis.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "densvis.buildbin-libdir/densvis/libs/densvis.so"