##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:glmGamPoi.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings glmGamPoi_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/glmGamPoi.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘glmGamPoi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘glmGamPoi’ version ‘1.13.0’
* 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 ‘glmGamPoi’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
* 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 R 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 loading without being on the library search path ... 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 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error: Object 'Coef_1' not found. Allowed variables in contrast are:
  conditionctrl, conditiontreated, cont1, cont2
  Backtrace:
      ▆
   1. └─glmGamPoi::test_de(fit2, contrast = Coef_1 - Coef_2) at test-test_de.R:144:2
   2.   └─glmGamPoi:::test_de_q(...)
   3.     └─glmGamPoi:::parse_contrast(...)
   4.       └─base::tryCatch(...)
   5.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   6.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   7.             └─value[[3L]](cond)
  
  [ FAIL 5 | WARN 837 | SKIP 5 | PASS 418 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘glmGamPoi.Rmd’ using ‘UTF-8’... OK
  ‘pseudobulk.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/glmGamPoi.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL glmGamPoi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘glmGamPoi’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I/usr/local/include    -fPIC  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I/usr/local/include    -fPIC  -g -O2  -c beta_estimation.cpp -o beta_estimation.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I/usr/local/include    -fPIC  -g -O2  -c deviance.cpp -o deviance.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I/usr/local/include    -fPIC  -g -O2  -c overdispersion.cpp -o overdispersion.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/site-library/beachmat/include' -I/usr/local/include    -fPIC  -g -O2  -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o glmGamPoi.so RcppExports.o beta_estimation.o deviance.o overdispersion.o utils.o -llapack -lblas -lgfortran -lm -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-glmGamPoi/00new/glmGamPoi/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (glmGamPoi)

R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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(glmGamPoi)
> 
> test_check("glmGamPoi")
[ FAIL 5 | WARN 837 | SKIP 5 | PASS 418 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• Beta estimation is unprecise on Non-MacOS architectures (1)
• Printing tests should be run interactively (1)
• empty test (2)
• isNamespaceLoaded("devtools") is not TRUE (1)

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-glm_gp.R:3:3'): glm_gp works for simple cases ────────────────
`{ ... }` produced warnings.
── Failure ('test-glm_gp.R:242:3'): glm_gp can handle intercept model ──────────
`{ ... }` produced warnings.
── Failure ('test-pseudobulk.R:37:3'): forming pseudobulk works ────────────────
unname(SummarizedExperiment::assay(tmp4, "counts")[, "a"]) not equal to matrixStats::rowMins(...).
names for current but not for target
── Failure ('test-pseudobulk.R:39:3'): forming pseudobulk works ────────────────
unname(SummarizedExperiment::assay(tmp4, "logcounts")[, "b"]) not equal to matrixStats::rowMeans2(...).
names for current but not for target
── Error ('test-test_de.R:144:3'): Pseudo bulk produces same results as making it manually ──
Error: Object 'Coef_1' not found. Allowed variables in contrast are:
conditionctrl, conditiontreated, cont1, cont2
Backtrace:
    ▆
 1. └─glmGamPoi::test_de(fit2, contrast = Coef_1 - Coef_2) at test-test_de.R:144:2
 2.   └─glmGamPoi:::test_de_q(...)
 3.     └─glmGamPoi:::parse_contrast(...)
 4.       └─base::tryCatch(...)
 5.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.             └─value[[3L]](cond)

[ FAIL 5 | WARN 837 | SKIP 5 | PASS 418 ]
Error: Test failures
Execution halted