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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 1238/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miloR 2.1.0  (landing page)
Mike Morgan
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/miloR
git_branch: devel
git_last_commit: 15c14c9
git_last_commit_date: 2024-04-30 11:34:02 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
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  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for miloR on palomino6

To the developers/maintainers of the miloR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/miloR.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: miloR
Version: 2.1.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:miloR.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings miloR_2.1.0.tar.gz
StartedAt: 2024-07-16 01:44:59 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 01:53:20 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 501.8 seconds
RetCode: 0
Status:   OK  
CheckDir: miloR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:miloR.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings miloR_2.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/miloR.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'miloR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'miloR' version '2.1.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... 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 whether package 'miloR' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... NOTE
Unexported object imported by a ':::' call: 'S4Vectors:::disableValidity'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotDAbeeswarm: no visible binding for global variable 'SpatialFDR'
plotDAbeeswarm: no visible binding for global variable 'logFC'
plotDAbeeswarm: no visible binding for global variable 'is_signif'
plotDAbeeswarm: no visible binding for global variable 'Nhood'
plotDAbeeswarm: no visible binding for global variable 'logFC_color'
plotNhoodCounts: no visible binding for global variable 'cond'
plotNhoodCounts: no visible binding for global variable 'values'
plotNhoodCounts: no visible binding for global variable 'y'
plotNhoodExpressionDA: no visible binding for global variable 'Nhood'
plotNhoodExpressionDA: no visible binding for global variable 'logFC'
plotNhoodExpressionDA: no visible binding for global variable
  'SpatialFDR'
plotNhoodExpressionDA: no visible binding for global variable
  'logFC_rank'
plotNhoodExpressionDA: no visible binding for global variable '.'
plotNhoodExpressionDA: no visible binding for global variable
  'is_signif'
plotNhoodExpressionDA: no visible binding for global variable 'feature'
plotNhoodExpressionDA: no visible binding for global variable
  'avg_expr'
plotNhoodExpressionDA: no visible binding for global variable 'label'
plotNhoodExpressionGroups: no visible binding for global variable
  'Nhood'
plotNhoodExpressionGroups: no visible binding for global variable
  'NhoodGroup'
plotNhoodExpressionGroups: no visible binding for global variable
  'logFC'
plotNhoodExpressionGroups: no visible binding for global variable
  'feature'
plotNhoodExpressionGroups: no visible binding for global variable
  'logFC_rank'
plotNhoodExpressionGroups: no visible binding for global variable
  'avg_expr'
plotNhoodExpressionGroups: no visible binding for global variable '.'
plotNhoodExpressionGroups: no visible binding for global variable
  'label'
plotNhoodGraph: no visible binding for global variable 'weight'
plotNhoodGraph: no visible binding for global variable 'size'
plotNhoodGraphDA: no visible binding for global variable 'layout'
plotNhoodGroups: no visible binding for global variable 'layout'
plotNhoodMA: no visible binding for global variable 'logCPM'
plotNhoodMA: no visible binding for global variable 'logFC'
plotNhoodMA: no visible binding for global variable 'Sig'
plotNhoodSizeHist: no visible binding for global variable 'nh_size'
testNhoods: no visible global function definition for 'type'
Undefined global functions or variables:
  . Nhood NhoodGroup Sig SpatialFDR avg_expr cond feature is_signif
  label layout logCPM logFC logFC_color logFC_rank nh_size size type
  values weight y
Consider adding
  importFrom("graphics", "layout")
to your NAMESPACE file.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 for x64 is not available
File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/miloR/libs/x64/miloR.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
* 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
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/miloR.Rcheck/00check.log'
for details.


Installation output

miloR.Rcheck/00install.out

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL miloR
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'miloR' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -std=c++11   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -std=c++11   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c computeMatrices.cpp -o computeMatrices.o
computeMatrices.cpp: In function 'arma::mat initialiseG(Rcpp::List, arma::vec)':
computeMatrices.cpp:135:30: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare]
  135 |     for(unsigned long k=0; k < stot; k++){
      |                            ~~^~~~~~
computeMatrices.cpp:143:28: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
  143 |             for(int l=0; l < q; l++){
      |                          ~~^~~
computeMatrices.cpp: In function 'arma::mat invGmat(Rcpp::List, arma::vec)':
computeMatrices.cpp:327:30: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare]
  327 |     for(unsigned long k=0; k < stot; k++){
      |                            ~~^~~~~~
computeMatrices.cpp:335:28: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
  335 |             for(int l=0; l < q; l++){
      |                          ~~^~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -std=c++11   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fitGeneticPLGlmm.cpp -o fitGeneticPLGlmm.o
fitGeneticPLGlmm.cpp: In function 'Rcpp::List fitGeneticPLGlmm(const arma::mat&, const arma::mat&, const arma::mat&, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::mat, const arma::vec&, Rcpp::List, double, const Rcpp::List&, double, const bool&, const int&, std::string, std::string)':
fitGeneticPLGlmm.cpp:197:10: warning: unused variable '_phi_est' [-Wunused-variable]
  197 |     bool _phi_est = true; // control if we re-estimate phi or not
      |          ^~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -std=c++11   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fitPLGlmm.cpp -o fitPLGlmm.o
fitPLGlmm.cpp: In function 'Rcpp::List fitPLGlmm(const arma::mat&, const arma::mat&, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::mat, const arma::vec&, Rcpp::List, double, const Rcpp::List&, double, const bool&, const int&, std::string, std::string)':
fitPLGlmm.cpp:177:10: warning: unused variable '_phi_est' [-Wunused-variable]
  177 |     bool _phi_est = true; // control if we re-estimate phi or not
      |          ^~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -std=c++11   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c inference.cpp -o inference.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -std=c++11   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c invertPseudoVar.cpp -o invertPseudoVar.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -std=c++11   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c multiP.cpp -o multiP.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -std=c++11   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c paramEst.cpp -o paramEst.o
paramEst.cpp:46: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   46 |     #pragma omp parallel for
      | 
paramEst.cpp:50: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   50 |         #pragma omp parallel for
      | 
paramEst.cpp:257: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  257 |     #pragma omp parallel for private(i, j, _ycovij)
      | 
paramEst.cpp:301: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  301 |     #pragma omp parallel for private(i, j, _ycovij)
      | 
paramEst.cpp:380: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  380 |     #pragma omp parallel for private(i, j, _ycovij)
      | 
paramEst.cpp:489: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  489 |     #pragma omp parallel for private(i, j, _ycovij)
      | 
paramEst.cpp:714: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  714 |             #pragma omp parallel for reduction(+:temp_value)
      | 
paramEst.cpp:729: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  729 |             #pragma omp parallel for reduction(+:temp_value)
      | 
paramEst.cpp: In function 'arma::vec sigmaScoreREML_arma(const Rcpp::List&, const arma::vec&, const arma::mat&, const arma::vec&, const arma::mat&, const arma::mat&)':
paramEst.cpp:29:33: warning: left operand of comma operator has no effect [-Wunused-value]
   29 |         double rhs = 0.5 * mid1[0, 0];
      |                                 ^
paramEst.cpp: In function 'arma::vec estHasemanElstonGenetic(const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&, const arma::mat&)':
paramEst.cpp:258:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  258 |     for (int i = 0; i < n; i++) {
      |                     ~~^~~
paramEst.cpp:259:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  259 |         for (int j = i; j < n; j++) {
      |                         ~~^~~
paramEst.cpp:252:18: warning: unused variable 'i' [-Wunused-variable]
  252 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:252:21: warning: unused variable 'j' [-Wunused-variable]
  252 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp:253:12: warning: unused variable '_ycovij' [-Wunused-variable]
  253 |     double _ycovij; // Declare temp_value
      |            ^~~~~~~
paramEst.cpp: In function 'arma::vec estHasemanElston(const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&)':
paramEst.cpp:302:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  302 |     for (int i = 0; i < n; i++) {
      |                     ~~^~~
paramEst.cpp:303:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  303 |         for (int j = i; j < n; j++) {
      |                         ~~^~~
paramEst.cpp:294:18: warning: unused variable 'i' [-Wunused-variable]
  294 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:294:21: warning: unused variable 'j' [-Wunused-variable]
  294 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp:295:12: warning: unused variable '_ycovij' [-Wunused-variable]
  295 |     double _ycovij; // Declare temp_value
      |            ^~~~~~~
paramEst.cpp: In function 'arma::vec estHasemanElstonConstrained(const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&, arma::vec, const int&)':
paramEst.cpp:381:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  381 |     for (int i = 0; i < n; i++) {
      |                     ~~^~~
paramEst.cpp:382:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  382 |         for (int j = i; j < n; j++) {
      |                         ~~^~~
paramEst.cpp:373:18: warning: unused variable 'i' [-Wunused-variable]
  373 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:373:21: warning: unused variable 'j' [-Wunused-variable]
  373 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp:374:12: warning: unused variable '_ycovij' [-Wunused-variable]
  374 |     double _ycovij; // Declare temp_value
      |            ^~~~~~~
paramEst.cpp: In function 'arma::vec estHasemanElstonConstrainedGenetic(const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&, const arma::mat&, arma::vec, const int&)':
paramEst.cpp:490:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  490 |     for (int i = 0; i < n; i++) {
      |                     ~~^~~
paramEst.cpp:491:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  491 |         for (int j = i; j < n; j++) {
      |                         ~~^~~
paramEst.cpp:484:18: warning: unused variable 'i' [-Wunused-variable]
  484 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:484:21: warning: unused variable 'j' [-Wunused-variable]
  484 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp:485:12: warning: unused variable '_ycovij' [-Wunused-variable]
  485 |     double _ycovij; // Declare temp_value
      |            ^~~~~~~
paramEst.cpp: In function 'arma::vec nnlsSolve(const arma::mat&, const arma::vec&, arma::vec, const int&)':
paramEst.cpp:549:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  549 |     for(int i=0; i < m; i++){
      |                  ~~^~~
paramEst.cpp:559:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  559 |     for(int i=0; i < m; i++){
      |                  ~~^~~
paramEst.cpp:587:24: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  587 |         for(int i=0; i < m; i++){
      |                      ~~^~~
paramEst.cpp:623:28: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  623 |             for(int i=0; i < m; i++){
      |                          ~~^~~
paramEst.cpp:543:18: warning: variable 'inner_count' set but not used [-Wunused-but-set-variable]
  543 |     unsigned int inner_count = 0;
      |                  ^~~~~~~~~~~
paramEst.cpp:544:18: warning: unused variable 'outer_count' [-Wunused-variable]
  544 |     unsigned int outer_count = 0;
      |                  ^~~~~~~~~~~
paramEst.cpp: In function 'arma::mat vectoriseZ(const arma::mat&, const Rcpp::List&, const arma::mat&)':
paramEst.cpp:688:9: warning: unused variable 'j' [-Wunused-variable]
  688 |     int j, k, l, a;
      |         ^
paramEst.cpp:688:12: warning: unused variable 'k' [-Wunused-variable]
  688 |     int j, k, l, a;
      |            ^
paramEst.cpp:688:15: warning: unused variable 'l' [-Wunused-variable]
  688 |     int j, k, l, a;
      |               ^
paramEst.cpp:688:18: warning: unused variable 'a' [-Wunused-variable]
  688 |     int j, k, l, a;
      |                  ^
paramEst.cpp: In function 'double phiLineSearch(double, double, double, const int&, const arma::vec&, const arma::mat&, double, const arma::vec&, const arma::vec&, const arma::vec&)':
paramEst.cpp:866:12: warning: unused variable 'half_logli' [-Wunused-variable]
  866 |     double half_logli = nbLogLik(mu, disp/2.0, y) - normlihood;
      |            ^~~~~~~~~~
paramEst.cpp:871:10: warning: unused variable 'comp_vals' [-Wunused-variable]
  871 |     bool comp_vals = false;
      |          ^~~~~~~~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -std=c++11   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pseudovarPartial.cpp -o pseudovarPartial.o
pseudovarPartial.cpp:60: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   60 |             #pragma omp parallel for reduction(+:temp_value)
      | 
pseudovarPartial.cpp: In function 'Rcpp::List pseudovarPartial_P(Rcpp::List, const arma::mat&)':
pseudovarPartial.cpp:58:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   58 |         for (int j = 0; j < n; j++) {
      |                         ~~^~~
pseudovarPartial.cpp:61:31: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   61 |             for (int k = 0; k < n; k++) {
      |                             ~~^~~
pseudovarPartial.cpp:64:32: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   64 |                 for(int a=0; a < n; a++){
      |                              ~~^~~
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -std=c++11   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.cpp -o utils.o
g++ -std=gnu++17 -shared -s -static-libgcc -o miloR.dll tmp.def RcppExports.o computeMatrices.o fitGeneticPLGlmm.o fitPLGlmm.o inference.o invertPseudoVar.o multiP.o paramEst.o pseudovarPartial.o utils.o -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRlapack -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRblas -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-miloR/00new/miloR/libs/x64
** R
** data
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'graph' in package 'miloR'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (miloR)

Tests output

miloR.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(miloR)
Loading required package: edgeR
Loading required package: limma
> require(mvtnorm)
Loading required package: mvtnorm
> require(scran)
Loading required package: scran
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following object is masked from 'package:limma':

    plotMA

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'SingleCellExperiment'

The following object is masked from 'package:edgeR':

    cpm

Loading required package: scuttle
> require(scater)
Loading required package: scater
Loading required package: ggplot2

Attaching package: 'scater'

The following object is masked from 'package:limma':

    plotMDS

> require(MASS)
Loading required package: MASS
> 
> test_check("miloR")
A patchwork composed of 2 patches
- Autotagging is turned off
- Guides are collected

Layout:
2 patch areas, spanning 2 columns and 1 rows

    t l b r
1:  1 1 1 1
2:  1 2 1 2
A patchwork composed of 2 patches
- Autotagging is turned off
- Guides are collected

Layout:
2 patch areas, spanning 2 columns and 1 rows

    t l b r
1:  1 1 1 1
2:  1 2 1 2
Coefficients not estimable: ConditionA 

warning: solve(): system is singular; attempting approx solution

warning: solve(): system is singular; attempting approx solution

warning: solve(): system is singular; attempting approx solution
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 213 ]
> 
> proc.time()
   user  system elapsed 
 253.09   12.50  266.84 

Example timings

miloR.Rcheck/miloR-Ex.timings

nameusersystemelapsed
Milo1.500.031.53
Satterthwaite_df000
annotateNhoods000
buildFromAdjacency1.100.051.13
buildGraph0.530.050.57
buildNhoodGraph000
calcNhoodDistance1.170.041.22
calcNhoodExpression0.800.020.81
checkSeparation2.780.052.84
computePvalue000
countCells0.690.030.72
findNhoodGroupMarkers000
findNhoodMarkers3.500.073.56
fitGLMM0.340.150.50
fitGeneticPLGlmm000
fitPLGlmm000
glmmControl.defaults000
graphSpatialFDR000
initialiseG0.000.020.02
initializeFullZ000
makeNhoods0.490.030.52
matrix.trace000
methods0.370.020.40
plotDAbeeswarm000
plotNhoodCounts2.600.062.66
plotNhoodExpressionDA000
plotNhoodGraph000
plotNhoodGraphDA000
plotNhoodGroups000
plotNhoodMA000
plotNhoodSizeHist0.560.080.64
sim_discrete000
sim_family000
sim_nbglmm0.020.000.02
sim_trajectory000
testDiffExp3.390.033.42
testNhoods2.980.083.06