##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:proFIA.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings proFIA_1.16.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/proFIA.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘proFIA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘proFIA’ version ‘1.16.3’
* 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 ‘proFIA’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'proFIA' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.12-bioc/meat/proFIA.Rcheck/00install.out’ for details.
* 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 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 ... 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 ... WARNING
Undocumented arguments in documentation object 'proFIAset'
  ‘f’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
proFIAset                            100.220  0.600 101.031
findFIASignal                         17.116  0.064  17.215
impute.FIA-proFIAset-method           16.656  0.036  16.714
impute.randomForest-proFIAset-method  15.240  0.000  15.261
estimateNoiseMS                        6.764  0.072   6.898
plotFlowgrams-proFIAset-method         5.532  0.036   5.668
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.12-bioc/meat/proFIA.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL proFIA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘proFIA’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c FIABandsExtractionCentroid.c -o FIABandsExtractionCentroid.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c UtilFunc.c -o UtilFunc.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fastMatchPpm.c -o fastMatchPpm.o
gcc -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o proFIA.so FIABandsExtractionCentroid.o UtilFunc.o fastMatchPpm.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-proFIA/00new/proFIA/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
Warning: Package 'proFIA' is deprecated and will be removed from Bioconductor
  version 3.14
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'proFIA' is deprecated and will be removed from Bioconductor
  version 3.14
** testing if installed package keeps a record of temporary installation path
* DONE (proFIA)

R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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.

> BiocGenerics:::testPackage("proFIA")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'ProtGenerics'

The following object is masked from 'package:stats':

    smooth


This is MSnbase version 2.16.1 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:base':

    trimws


This is xcms version 3.12.0 


Attaching package: 'xcms'

The following object is masked from 'package:stats':

    sigma

Loading required package: plasFIA
A mass interval of 0.0153m/z will be used for the density estimation.
0 :0 10 :29 20 :54 30 :78 30 :105 40 :141 50 :174 60 :196 70 :208 80 :215 90 :219 
 219  groups have been done .


RUNIT TEST PROTOCOL -- Thu May  6 04:49:48 2021 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
proFIA RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
Warning message:
Package 'proFIA' is deprecated and will be removed from Bioconductor
  version 3.14 
> 
> proc.time()
   user  system elapsed 
 16.252   0.348  16.831