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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings flagme_1.65.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/flagme.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flagme/DESCRIPTION’ ... OK
* this is package ‘flagme’ version ‘1.65.0’
* 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 ‘flagme’ can be installed ... OK
* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* 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 whether 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(s) in Rd file 'addXCMSPeaks.Rd':
  ‘[xcms]{findPeaks-matchedFilter}’ ‘[xcms]{findPeaks-centWave}’
  ‘[xcms]{peaksDataset}’

Missing link(s) in Rd file 'plotAlignment-peaksAlignment-method.Rd':
  ‘plotAlignment’

Missing link(s) in Rd file 'plotClustAlignment-clusterAlignment-method.Rd':
  ‘plotAlignment’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotAlignment-peaksAlignment-method.Rd: plotAlignment
  plotClustAlignment-clusterAlignment-method.Rd: plotAlignment
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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                           102.296 18.785  66.934
addXCMSPeaks                                55.885  9.932  49.317
peaksAlignment-class                        50.450 10.137  44.153
corPrt                                      49.714  9.707  43.683
dynRT                                       48.287 10.865  42.980
retFatMatrix                                49.081  9.636  42.769
plotFrags                                   49.268  9.053  41.953
progressiveAlignment-class                  49.148  8.427  41.549
ndpRT                                       48.248  8.009  40.367
plotAlignment-peaksAlignment-method         48.789  7.240  40.393
imputePeaks                                 12.375  0.275  12.715
plotChrom-peaksDataset-method               10.796  0.235  11.064
rmaFitUnit                                   9.474  0.291   9.799
calcTimeDiffs                                9.048  0.453   9.531
gatherInfo                                   8.687  0.354   9.074
multipleAlignment-class                      8.733  0.147   8.908
dp                                           7.810  0.335   8.178
clusterAlignment                             7.703  0.251   7.979
plotClustAlignment-clusterAlignment-method   7.580  0.064   7.666
normDotProduct                               6.808  0.248   7.073
peaksDataset                                 6.459  0.275   6.753
addAMDISPeaks                                6.242  0.231   6.560
plotImage                                    5.157  0.402   5.580
addChromaTOFPeaks                            5.272  0.175   5.463
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/flagme.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL flagme
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘flagme’ ...
** this is package ‘flagme’ version ‘1.65.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c dp.c -o dp.o
dp.c: In function ‘dp’:
dp.c:264:35: warning: ‘tb’ may be used uninitialized [-Wmaybe-uninitialized]
  264 |           phi[(i+1)+(j+1)*(nr+1)] = tb;
      |           ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
dp.c:217:30: note: ‘tb’ was declared here
  217 |   int i,j, nr=*nr_, nc=*nc_, tb, count=0, done=0;
      |                              ^~
dp.c:263:33: warning: ‘cur_min’ may be used uninitialized [-Wmaybe-uninitialized]
  263 |           D[(i+1)+(j+1)*(nr+1)] = cur_min;
      |           ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
dp.c:218:21: note: ‘cur_min’ was declared here
  218 |   double gap=*gap_, cur_min, a, b, c;
      |                     ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c init.c -o init.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c pearson.c -o pearson.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/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)