Alan O'Callaghan
| Snapshot Date: 2025-01-23 13:40 -0500 (Thu, 23 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/densvis |
| git_branch: devel |
| git_last_commit: af1be7b |
| git_last_commit_date: 2024-10-29 10:52:45 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-24 11:42 -0500 (Fri, 24 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4609 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4393 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 3839 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 3835 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4408 |
| 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 539/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| densvis 1.17.0 (landing page) Alan O'Callaghan
| 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 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the densvis package: - 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 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: densvis |
| Version: 1.17.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data densvis |
| StartedAt: 2025-01-23 15:48:11 -0500 (Thu, 23 Jan 2025) |
| EndedAt: 2025-01-23 15:48:17 -0500 (Thu, 23 Jan 2025) |
| EllapsedTime: 6.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data densvis
###
##############################################################################
##############################################################################
* checking for file ‘densvis/DESCRIPTION’ ... OK
* preparing ‘densvis’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘densvis’ ...
** this is package ‘densvis’ version ‘1.17.0’
** using non-staged installation via StagedInstall field
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
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/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c densvis.cpp -o densvis.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c sptree.cpp -o sptree.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 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/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: search path '/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0' not found
ld: library 'emutls_w' not found
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [densvis.so] Error 1
ERROR: compilation failed for package ‘densvis’
* removing ‘/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpiqg0VM/Rinstdd0a1ade9db1/densvis’
-----------------------------------
ERROR: package installation failed