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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:Linnorm.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Linnorm_2.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Linnorm.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Linnorm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Linnorm’ version ‘2.30.0’
* 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 ‘Linnorm’ can be installed ... OK
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 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 ... NOTE
Linnorm.HClust: no visible binding for global variable ‘y’
Linnorm.HClust: no visible binding for global variable ‘xend’
Linnorm.HClust: no visible binding for global variable ‘yend’
Linnorm.HClust: no visible binding for global variable ‘cluster’
Linnorm.HClust: no visible binding for global variable ‘X1’
Linnorm.HClust: no visible binding for global variable ‘X2’
Linnorm.HVar: no visible binding for global variable ‘SD’
Linnorm.HVar: no visible binding for global variable ‘group’
Undefined global functions or variables:
  SD X1 X2 cluster group xend y yend
* checking Rd files ... NOTE
checkRd: (-1) Linnorm.Cor.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Cor.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Cor.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Cor.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Cor.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Cor.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Cor.Rd:81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Cor.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Cor.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Cor.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Cor.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HClust.Rd:37: Lost braces; missing escapes or markup?
    37 | \item{method_hclust}{Charcter. Method to be used in hierarchical clustering. (From hclust {fastcluster}: the agglomeration method to be used. This should be (an unambiguous abbreviation of) one of "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median" or "centroid".) Defaults to "ward.D".}
       |                                                                                           ^
checkRd: (-1) Linnorm.HClust.Rd:39: Lost braces; missing escapes or markup?
    39 | \item{method_dist}{Charcter. Method to be used in hierarchical clustering. (From Dist {amap}: the distance measure to be used. This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary", "pearson", "correlation", "spearman" or "kendall". Any unambiguous substring can be given.) Defaults to "pearson".}
       |                                                                                       ^
checkRd: (-1) Linnorm.HClust.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HClust.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HClust.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HVar.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HVar.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HVar.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HVar.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HVar.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HVar.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HVar.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.HVar.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.PCA.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.PCA.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.PCA.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.PCA.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.limma.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.limma.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.limma.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.limma.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.limma.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.limma.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.limma.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.limma.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.tSNE.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.tSNE.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.tSNE.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Linnorm.tSNE.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
* 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
RnaXSim        109.606  0.104 110.000
Linnorm.Cor     60.159  0.184  60.412
Linnorm.Norm    48.069  0.044  48.230
Linnorm.limma   47.989  0.060  48.150
Linnorm         47.654  0.032  47.854
Linnorm.HClust   6.892  0.008   4.381
Linnorm.tSNE     5.852  0.040   5.749
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/Linnorm.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL Linnorm
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘Linnorm’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Misc.cpp -o Misc.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o Linnorm.so Misc.o -std=c++11 -lopenblas -L/usr/lib/gcc/aarch64-linux-gnu/10.3.1 -lgfortran -lm -DARMA_64BIT_WORD=1 -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-Linnorm/00new/Linnorm/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 (Linnorm)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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(Linnorm)
> 
> test_check("Linnorm")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 26 ]
> 
> proc.time()
   user  system elapsed 
 32.262   0.424  32.698