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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ptairMS_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ptairMS.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 ‘ptairMS/DESCRIPTION’ ... OK
* this is package ‘ptairMS’ 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 ‘ptairMS’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’
See ‘/home/biocbuild/bbs-3.20-bioc/meat/ptairMS.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
  ‘htmlwidgets’ ‘plyr’
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘getCalibrationInfo’ ‘getPeakList’ ‘getPeaksInfo’ ‘getTimeInfo’
  ‘processFileTemporalNominalMass’ ‘tofToMz’
* 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 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
detectPeak           130.240  0.447 130.944
alignSamples          26.940  0.252  27.316
imputeMat             26.994  0.164  27.210
writeEset             25.912  0.115  26.079
getPeakList           24.907  0.080  25.037
impute                24.020  0.083  24.153
annotation            23.170  0.112  23.330
plot                  19.508  0.072  19.618
plotTIC               19.449  0.092  19.581
defineKnots           18.329  0.119  18.487
plotRaw               18.159  0.103  18.298
plotFeatures          18.108  0.144  18.288
updatePtrSet          17.887  0.104  18.028
rmPeakList            17.700  0.112  17.846
setSampleMetadata     17.730  0.056  17.822
plotCalib             17.567  0.072  17.674
getSampleMetadata     16.822  0.072  16.928
getDirectory          16.478  0.100  16.612
resetSampleMetadata   16.524  0.048  16.604
importSampleMetadata  16.461  0.076  16.571
exportSampleMetada    16.136  0.076  16.246
getFileNames          15.686  0.052  15.771
convert_to_mzML       15.336  0.304  15.678
changeTimeLimits      15.473  0.043  15.551
createPtrSet          12.514  0.052  12.656
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/ptairMS.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ptairMS
###
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* installing to library ‘/home/biocbuild/R/R-4.4.0/site-library’
* installing *source* package ‘ptairMS’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c align.cpp -o align.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c findEqualGreaterM.cpp -o findEqualGreaterM.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.0/lib -L/usr/local/lib -o ptairMS.so RcppExports.o align.o findEqualGreaterM.o -L/home/biocbuild/R/R-4.4.0/lib -lR
installing to /home/biocbuild/R/R-4.4.0/site-library/00LOCK-ptairMS/00new/ptairMS/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’
** testing if installed package keeps a record of temporary installation path
* DONE (ptairMS)

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
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(ptairMS)
Warning message:
replacing previous import 'Biobase::cache' by 'bit64::cache' when loading 'ptairMS' 
> 
> test_check("ptairMS")
Control1.h5 : 3 peaks detected 
Control2.h5 : 4 peaks detected 
Specie-a1.h5 : 2 peaks detected 
Specie-a2.h5 : 3 peaks detected 
specie-b1.h5 : 4 peaks detected 
specie-b2.h5 : 3 peaks detected 
Control1.h5 : 2 peaks detected 
Control2.h5 : 2 peaks detected 
Specie-a1.h5 : 3 peaks detected 
Specie-a2.h5 : 3 peaks detected 
specie-b1.h5 : 2 peaks detected 
specie-b2.h5 : 3 peaks detected 
Control1.h5 : 4 peaks detected 
Control2.h5 : 6 peaks detected 
Specie-a1.h5 : 3 peaks detected 
Specie-a2.h5 : 4 peaks detected 
specie-b1.h5 : 5 peaks detected 
specie-b2.h5 : 4 peaks detected 
Control1.h5 : 3 peaks detected 
Control2.h5 : 2 peaks detected 
Specie-a1.h5 : 3 peaks detected 
Specie-a2.h5 : 3 peaks detected 
specie-b1.h5 : 3 peaks detected 
specie-b2.h5 : 4 peaks detected 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 59 ]
> 
> proc.time()
   user  system elapsed 
112.593   0.779 113.802