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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:sSNAPPY.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings sSNAPPY_1.0.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/sSNAPPY.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sSNAPPY/DESCRIPTION’ ... OK
* this is package ‘sSNAPPY’ version ‘1.0.2’
* 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 ‘sSNAPPY’ can be installed ... OK
* 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 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 ... 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 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/sSNAPPY.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL sSNAPPY
###
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* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘sSNAPPY’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c code.cpp -o code.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c normaliseByPermutation.cpp -o normaliseByPermutation.o
In file included from /home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include/armadillo:22,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:56,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from normaliseByPermutation.cpp:2:
/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include/armadillo_bits/config.hpp:333:86: note: #pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed
  333 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |                                                                                      ^
/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include/armadillo_bits/config.hpp:338:75: note: #pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead
  338 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |                                                                           ^
/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include/armadillo_bits/config.hpp:341:61: note: #pragma message: INFO: see the documentation for details
  341 |   #pragma message ("INFO: see the documentation for details")
      |                                                             ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c ssPertScore.cpp -o ssPertScore.o
In file included from /home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include/armadillo:22,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:56,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from ssPertScore.cpp:2:
/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include/armadillo_bits/config.hpp:333:86: note: #pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed
  333 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |                                                                                      ^
/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include/armadillo_bits/config.hpp:338:75: note: #pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead
  338 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |                                                                           ^
/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include/armadillo_bits/config.hpp:341:61: note: #pragma message: INFO: see the documentation for details
  341 |   #pragma message ("INFO: see the documentation for details")
      |                                                             ^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o sSNAPPY.so RcppExports.o code.o normaliseByPermutation.o ssPertScore.o -fopenmp -L/home/biocbuild/bbs-3.15-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.15-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-sSNAPPY/00new/sSNAPPY/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 (sSNAPPY)

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.154   0.026   0.169 

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(sSNAPPY)

> 
> test_check("sSNAPPY")

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

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

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

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

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

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

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

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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 60 ]
> 
> proc.time()
   user  system elapsed 
 33.690   4.369  28.463