Mike Morgan
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/miloR |
| git_branch: RELEASE_3_20 |
| git_last_commit: 5e1d958 |
| git_last_commit_date: 2024-10-29 10:59:29 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 1261/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| miloR 2.2.0 (landing page) Mike Morgan
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: miloR |
| Version: 2.2.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:miloR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings miloR_2.2.0.tar.gz |
| StartedAt: 2024-12-20 06:01:59 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 06:18:40 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 1000.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: miloR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:miloR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings miloR_2.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/miloR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘miloR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miloR’ version ‘2.2.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘miloR’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
findNhoodMarkers 6.411 0.094 6.636
testNhoods 6.032 0.115 6.167
checkSeparation 5.868 0.138 6.055
plotNhoodCounts 5.845 0.059 5.959
fitGLMM 1.727 3.772 5.564
* 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/miloR.Rcheck/00check.log’
for details.
miloR.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL miloR
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘miloR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c computeMatrices.cpp -o computeMatrices.o
computeMatrices.cpp:246:9: warning: variable 'stot' set but not used [-Wunused-but-set-variable]
int stot = 0;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c fitGeneticPLGlmm.cpp -o fitGeneticPLGlmm.o
fitGeneticPLGlmm.cpp:113:12: warning: variable '_intercept' set but not used [-Wunused-but-set-variable]
double _intercept = constval; // intercept for HE regression
^
fitGeneticPLGlmm.cpp:200:10: warning: unused variable '_phi_est' [-Wunused-variable]
bool _phi_est = true; // control if we re-estimate phi or not
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c fitPLGlmm.cpp -o fitPLGlmm.o
fitPLGlmm.cpp:106:12: warning: variable '_intercept' set but not used [-Wunused-but-set-variable]
double _intercept = constval; // intercept for HE regression?? need a better estimate.
^
fitPLGlmm.cpp:172:10: warning: unused variable '_phi_est' [-Wunused-variable]
bool _phi_est = true; // control if we re-estimate phi or not
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c inference.cpp -o inference.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c invertPseudoVar.cpp -o invertPseudoVar.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c multiP.cpp -o multiP.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c paramEst.cpp -o paramEst.o
paramEst.cpp:36:33: warning: left operand of comma operator has no effect [-Wunused-value]
double rhs = 0.5 * mid1[0, 0];
^
paramEst.cpp:172:12: warning: unused variable 'lambda' [-Wunused-variable]
double lambda = 1e-1;
^
paramEst.cpp:173:12: warning: unused variable 'lambda_step' [-Wunused-variable]
double lambda_step = 10;
^
paramEst.cpp:174:12: warning: unused variable '_illcond_eps' [-Wunused-variable]
double _illcond_eps = 1e-6;
^
paramEst.cpp:175:12: warning: unused variable '_lcond_target' [-Wunused-variable]
double _lcond_target = 1e-5;
^
paramEst.cpp:241:19: warning: unused variable 'nsq' [-Wunused-variable]
unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix, no diag
^
paramEst.cpp:242:18: warning: unused variable 'i' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:242:21: warning: unused variable 'j' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:243:12: warning: unused variable '_ycovij' [-Wunused-variable]
double _ycovij; // Declare temp_value
^
paramEst.cpp:276:19: warning: unused variable 'nsq' [-Wunused-variable]
unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
^
paramEst.cpp:277:18: warning: unused variable 'i' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:277:21: warning: unused variable 'j' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:278:12: warning: unused variable '_ycovij' [-Wunused-variable]
double _ycovij; // Declare temp_value
^
paramEst.cpp:342:19: warning: unused variable 'nsq' [-Wunused-variable]
unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
^
paramEst.cpp:409:19: warning: unused variable 'nsq' [-Wunused-variable]
unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
^
paramEst.cpp:410:18: warning: unused variable 'i' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:410:21: warning: unused variable 'j' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:442:19: warning: unused variable 'nsq' [-Wunused-variable]
unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
^
paramEst.cpp:443:18: warning: unused variable 'i' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:443:21: warning: unused variable 'j' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:774:12: warning: unused variable 'half_logli' [-Wunused-variable]
double half_logli = nbLogLik(mu, disp/2.0, y) - normlihood;
^
paramEst.cpp:779:10: warning: unused variable 'comp_vals' [-Wunused-variable]
bool comp_vals = false;
^
22 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c pseudovarPartial.cpp -o pseudovarPartial.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c solveQP.cpp -o solveQP.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o miloR.so RcppExports.o computeMatrices.o fitGeneticPLGlmm.o fitPLGlmm.o inference.o invertPseudoVar.o multiP.o paramEst.o pseudovarPartial.o solveQP.o utils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-miloR/00new/miloR/libs
** 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
** 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 (miloR)
miloR.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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(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, saveRDS, 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
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
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 214 ]
>
> proc.time()
user system elapsed
471.196 9.061 500.601
miloR.Rcheck/miloR-Ex.timings
| name | user | system | elapsed | |
| Milo | 1.144 | 0.032 | 1.239 | |
| Satterthwaite_df | 0.001 | 0.000 | 0.000 | |
| annotateNhoods | 0.000 | 0.000 | 0.001 | |
| buildFromAdjacency | 0.918 | 0.039 | 1.011 | |
| buildGraph | 1.652 | 0.036 | 1.761 | |
| buildNhoodGraph | 0.000 | 0.001 | 0.001 | |
| calcNhoodDistance | 2.344 | 0.202 | 2.572 | |
| calcNhoodExpression | 1.408 | 0.097 | 1.510 | |
| checkSeparation | 5.868 | 0.138 | 6.055 | |
| computePvalue | 0.000 | 0.000 | 0.001 | |
| countCells | 1.368 | 0.018 | 1.393 | |
| findNhoodGroupMarkers | 0.001 | 0.000 | 0.000 | |
| findNhoodMarkers | 6.411 | 0.094 | 6.636 | |
| fitGLMM | 1.727 | 3.772 | 5.564 | |
| fitGeneticPLGlmm | 0.000 | 0.001 | 0.001 | |
| fitPLGlmm | 0.001 | 0.001 | 0.000 | |
| glmmControl.defaults | 0.000 | 0.000 | 0.001 | |
| graphSpatialFDR | 0.000 | 0.001 | 0.001 | |
| initialiseG | 0.012 | 0.003 | 0.015 | |
| initializeFullZ | 0.008 | 0.003 | 0.011 | |
| makeNhoods | 0.890 | 0.018 | 0.917 | |
| matrix.trace | 0.001 | 0.001 | 0.001 | |
| methods | 0.611 | 0.025 | 0.687 | |
| plotDAbeeswarm | 0.000 | 0.000 | 0.001 | |
| plotNhoodCounts | 5.845 | 0.059 | 5.959 | |
| plotNhoodExpressionDA | 0.001 | 0.000 | 0.001 | |
| plotNhoodGraph | 0 | 0 | 0 | |
| plotNhoodGraphDA | 0.000 | 0.000 | 0.001 | |
| plotNhoodGroups | 0.000 | 0.000 | 0.001 | |
| plotNhoodMA | 0.000 | 0.001 | 0.001 | |
| plotNhoodSizeHist | 1.253 | 0.034 | 1.296 | |
| sim_discrete | 0.000 | 0.000 | 0.001 | |
| sim_family | 0 | 0 | 0 | |
| sim_nbglmm | 0.007 | 0.004 | 0.010 | |
| sim_trajectory | 0.000 | 0.001 | 0.000 | |
| testDiffExp | 3.822 | 0.073 | 3.909 | |
| testNhoods | 6.032 | 0.115 | 6.167 | |