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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings flagme_1.55.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/flagme.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* 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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘flagme/DESCRIPTION’ ... OK
* this is package ‘flagme’ version ‘1.55.1’
* 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 ‘flagme’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘xcms:::rectUnique’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addXCMSPeaks: no visible global function definition for ‘bpparam’
addXCMSPeaks: no visible global function definition for ‘sampnames’
addXCMSPeaks : <anonymous> : <anonymous>: no visible global function
  definition for ‘setNames’
importSpec : <anonymous>: no visible global function definition for
  ‘setNames’
Undefined global functions or variables:
  bpparam sampnames setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'addXCMSPeaks.Rd':
  ‘[xcms]{findPeaks-matchedFilter}’ ‘[xcms]{findPeaks-centWave}’
  ‘[xcms]{peaksDataset}’

Missing link or links in documentation object 'plotAlignment-peaksAlignment-method.Rd':
  ‘plotAlignment’

Missing link or links in documentation object 'plotClustAlignment-clusterAlignment-method.Rd':
  ‘plotAlignment’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘plotAlignment’ ‘plotChrom’ ‘plotClustAlignment’
Undocumented S4 methods:
  generic 'show' and siglist 'betweenAlignment'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
plotAlignedFrags                           98.322 14.857  60.637
dynRT                                      53.154  9.615  44.857
addXCMSPeaks                               54.609  6.872  43.892
peaksAlignment-class                       49.197 11.833  42.277
progressiveAlignment-class                 50.335  9.021  41.738
corPrt                                     51.364  6.737  40.097
plotFrags                                  48.926  8.795  40.696
retFatMatrix                               50.213  7.275  40.241
plotAlignment-peaksAlignment-method        48.480  7.518  38.851
ndpRT                                      48.474  7.123  38.499
imputePeaks                                11.224  0.164  12.220
plotChrom-peaksDataset-method               9.282  0.256   9.538
calcTimeDiffs                               8.752  0.324   9.081
rmaFitUnit                                  8.359  0.112   8.471
gatherInfo                                  7.926  0.183   9.803
clusterAlignment                            7.319  0.268   7.587
multipleAlignment-class                     7.261  0.283   7.546
normDotProduct                              6.549  0.152   6.701
dp                                          6.506  0.175   6.682
peaksDataset                                6.146  0.324   6.470
plotClustAlignment-clusterAlignment-method  6.324  0.124   6.449
addChromaTOFPeaks                           5.640  0.128   5.768
addAMDISPeaks                               5.214  0.233   5.494
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘flagme-knitr.Rnw’ using ‘UTF-8’... OK
  ‘flagme.Rnw’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/flagme.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL flagme
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘flagme’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c dp.c -o dp.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c pearson.c -o pearson.o
gcc -shared -L/usr/local/lib -o flagme.so dp.o init.o pearson.o
installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-flagme/00new/flagme/libs
** R
** 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 (flagme)