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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ptairMS_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ptairMS.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ptairMS/DESCRIPTION’ ... OK
* this is package ‘ptairMS’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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-3.21-bioc/meat/ptairMS.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'detectPeak.Rd':
  ‘[ptairMS]{ptrSet}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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           83.648  0.975  84.632
writeEset            17.875  0.035  17.911
imputeMat            16.965  0.220  17.185
alignSamples         14.537  0.303  14.850
impute               14.458  0.155  14.612
getPeakList          13.670  0.366  14.037
annotation           12.704  0.246  12.952
plotTIC              11.782  0.060  11.844
convert_to_mzML      11.386  0.419  11.804
rmPeakList           11.345  0.040  11.385
updatePtrSet         11.366  0.017  11.385
plot                 11.159  0.093  11.252
plotCalib            10.886  0.094  10.989
setSampleMetadata    10.730  0.087  10.820
plotFeatures         10.650  0.099  10.749
resetSampleMetadata  10.708  0.026  10.735
defineKnots          10.520  0.210  10.752
plotRaw              10.317  0.058  10.376
importSampleMetadata  9.551  0.119   9.669
exportSampleMetada    8.931  0.466   9.398
getFileNames          9.050  0.273   9.323
getSampleMetadata     9.074  0.116   9.190
createPtrSet          8.530  0.112   8.652
getDirectory          8.280  0.086   8.367
changeTimeLimits      8.103  0.054   8.162
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/ptairMS.Rcheck/00check.log’
for details.