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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:distinct.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings distinct_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/distinct.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘distinct/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘distinct’ version ‘1.11.0’
* 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 ‘distinct’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
  installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   7.0Mb
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘Rfast’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
perm_test_parallel_R: no visible binding for global variable ‘cl_id’
perm_test_parallel_covariates_R: no visible binding for global variable
  ‘cl_id’
plot_cdfs: no visible binding for global variable ‘group’
plot_densities: no visible binding for global variable ‘group’
Undefined global functions or variables:
  cl_id group
* 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 ... ERROR
Running examples in ‘distinct-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: distinct_test
> ### Title: Test for differential state between two groups of samples, based
> ###   on scRNA-seq data.
> ### Aliases: distinct_test
> 
> ### ** Examples
> 
> # load the input data:
> data("Kang_subset", package = "distinct")
> Kang_subset
class: SingleCellExperiment 
dim: 100 9517 
metadata(1): experiment_info
assays(2): logcounts cpm
rownames(100): ISG15 SYF2 ... MX2 PDXK
rowData names(0):
colnames: NULL
colData names(3): stim cell sample_id
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
> 
> # create the design of the study:
> samples = Kang_subset@metadata$experiment_info$sample_id
> group = Kang_subset@metadata$experiment_info$stim
> design = model.matrix(~group)
> # rownames of the design must indicate sample ids:
> rownames(design) = samples
> design
          (Intercept) groupstim
ctrl_107            1         0
ctrl_1015           1         0
ctrl_101            1         0
stim_101            1         1
stim_1015           1         1
stim_107            1         1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"

> 
> # Note that the sample names in `colData(x)$name_sample` have to be the same ones as those in `rownames(design)`.
> rownames(design)
[1] "ctrl_107"  "ctrl_1015" "ctrl_101"  "stim_101"  "stim_1015" "stim_107" 
> unique(SingleCellExperiment::colData(Kang_subset)$sample_id)
[1] ctrl_107  ctrl_1015 ctrl_101  stim_101  stim_1015 stim_107 
Levels: ctrl_101 ctrl_1015 ctrl_107 stim_101 stim_1015 stim_107
> 
> # In order to obtain a finer ranking for the most significant genes, if computational resources are available, we encourage users to increase P_4 (i.e., the number of permutations when a raw p-value is < 0.001) and set P_4 = 20,000 (by default P_4 = 10,000).
> 
> # The group we would like to test for is in the second column of the design, therefore we will specify: column_to_test = 2
> 
> set.seed(61217)
> res = distinct_test(
+   x = Kang_subset, 
+   name_assays_expression = "logcounts",
+   name_cluster = "cell",
+   design = design,
+   column_to_test = 2,
+   min_non_zero_cells = 20,
+   n_cores = 2)
2 groups of samples provided
Data loaded, starting differential testing
Error in unserialize(socklist[[n]]) : error reading from connection
Calls: distinct_test ... recvOneData -> recvOneData.SOCKcluster -> unserialize
Execution halted
* 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:
    2.   └─distinct:::perm_test_parallel_R(...)
    3.     ├─... %dorng% ...
    4.     │ └─base::do.call(`%dopar%`, list(obj, ex), envir = parent.frame())
    5.     └─foreach (local) `<fn>`(...)
    6.       └─e$fun(obj, substitute(ex), parent.frame(), e$data)
    7.         └─parallel::clusterApplyLB(cl, argsList, evalWrapper)
    8.           └─parallel:::dynamicClusterApply(cl, fun, length(x), argfun)
    9.             └─parallel:::recvOneResult(cl)
   10.               ├─parallel:::recvOneData(cl)
   11.               └─parallel:::recvOneData.SOCKcluster(cl)
   12.                 └─base::unserialize(socklist[[n]])
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 7 ]
  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 ...
  ‘distinct.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/distinct.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL distinct
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘distinct’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c Perm.cpp -o Perm.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c Perm_covariates.cpp -o Perm_covariates.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast.h:5,
                 from Perm_covariates.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:553: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  553 |                                 #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:604: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  604 |                                 #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:621: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  621 |                     #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:639: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  639 |                         #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:654: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  654 |                     #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:669: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  669 |                         #pragma omp parallel for
      | 
Perm_covariates.cpp: In function ‘arma::vec my_rint_reg(const mat&, const vec&, Rcpp::IntegerVector, const unsigned int&, const unsigned int&, const double&, const unsigned int&)’:
Perm_covariates.cpp:189:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  189 |   for(int i=0;i<p;i++)
      |               ~^~
Perm_covariates.cpp:210:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  210 |   while(i++<maxiters && sum(abs(b2-b1.col(0))) > tol) {
      |         ~~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c Perm_covariates_parallel.cpp -o Perm_covariates_parallel.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast.h:5,
                 from Perm_covariates_parallel.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:553: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  553 |                                 #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:604: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  604 |                                 #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:621: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  621 |                     #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:639: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  639 |                         #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:654: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  654 |                     #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:669: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  669 |                         #pragma omp parallel for
      | 
Perm_covariates_parallel.cpp: In function ‘arma::vec my_rint_reg_parallel(const mat&, const vec&, Rcpp::IntegerVector, const unsigned int&, const unsigned int&, const double&, const unsigned int&)’:
Perm_covariates_parallel.cpp:189:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  189 |   for(int i=0;i<p;i++)
      |               ~^~
Perm_covariates_parallel.cpp:210:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  210 |   while(i++<maxiters && sum(abs(b2-b1.col(0))) > tol) {
      |         ~~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c Perm_parallel.cpp -o Perm_parallel.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rfast/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o distinct.so Perm.o Perm_covariates.o Perm_covariates_parallel.o Perm_parallel.o RcppExports.o -llapack -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRblas -lgfortran -lm -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-distinct/00new/distinct/libs
** R
** data
** 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 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 (distinct)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
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(distinct)
> test_check("distinct")
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 7 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_distinct_test.R:12'): distinct_test() works faultlessly. ───────
Error in `unserialize(socklist[[n]])`: error reading from connection
Backtrace:
     ▆
  1. └─distinct::distinct_test(...) at test_distinct_test.R:12:2
  2.   └─distinct:::perm_test_parallel_R(...)
  3.     ├─... %dorng% ...
  4.     │ └─base::do.call(`%dopar%`, list(obj, ex), envir = parent.frame())
  5.     └─foreach (local) `<fn>`(...)
  6.       └─e$fun(obj, substitute(ex), parent.frame(), e$data)
  7.         └─parallel::clusterApplyLB(cl, argsList, evalWrapper)
  8.           └─parallel:::dynamicClusterApply(cl, fun, length(x), argfun)
  9.             └─parallel:::recvOneResult(cl)
 10.               ├─parallel:::recvOneData(cl)
 11.               └─parallel:::recvOneData.SOCKcluster(cl)
 12.                 └─base::unserialize(socklist[[n]])

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 7 ]
Error: Test failures
Execution halted