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This page was generated on 2024-11-09 21:30 -0500 (Sat, 09 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4505
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4538
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4486
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 544/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
densvis 1.16.0  (landing page)
Alan O'Callaghan
Snapshot Date: 2024-11-08 13:40 -0500 (Fri, 08 Nov 2024)
git_url: https://git.bioconductor.org/packages/densvis
git_branch: RELEASE_3_20
git_last_commit: c6a55af
git_last_commit_date: 2024-10-29 10:52:45 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for densvis on kjohnson3

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.

raw results


Summary

Package: densvis
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:densvis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings densvis_1.16.0.tar.gz
StartedAt: 2024-11-09 00:43:08 -0500 (Sat, 09 Nov 2024)
EndedAt: 2024-11-09 00:47:29 -0500 (Sat, 09 Nov 2024)
EllapsedTime: 261.5 seconds
RetCode: 0
Status:   OK  
CheckDir: densvis.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:densvis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings densvis_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/densvis.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘densvis/DESCRIPTION’ ... OK
* this is package ‘densvis’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘densvis’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/densvis.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
densmap 7.531  1.555    8.82
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/densvis.Rcheck/00check.log’
for details.


Installation output

densvis.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL densvis
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘densvis’ ...
** 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/4.4-arm64/Resources/library/Rcpp/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/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -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++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -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/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -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-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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)

Tests output

densvis.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(densvis)
> 
> test_check("densvis")
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/densvis/1.16.0/densvis/lib/python3.11/site-packages/umap/distances.py:1063: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/densvis/1.16.0/densvis/lib/python3.11/site-packages/umap/distances.py:1071: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/densvis/1.16.0/densvis/lib/python3.11/site-packages/umap/distances.py:1086: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/densvis/1.16.0/densvis/lib/python3.11/site-packages/umap/umap_.py:660: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 20 ]
> 
> proc.time()
   user  system elapsed 
 20.665   4.694  12.436 

Example timings

densvis.Rcheck/densvis-Ex.timings

nameusersystemelapsed
densmap7.5311.5558.820
densne0.1210.0010.123