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CHECK report for adductomicsR on tokay1

This page was generated on 2021-05-06 12:29:49 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the adductomicsR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 19/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
adductomicsR 1.6.0  (landing page)
Josie Hayes
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/adductomicsR
Branch: RELEASE_3_12
Last Commit: 4f15169
Last Changed Date: 2020-10-27 11:42:01 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: adductomicsR
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:adductomicsR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings adductomicsR_1.6.0.tar.gz
StartedAt: 2021-05-06 00:18:32 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 00:25:30 -0400 (Thu, 06 May 2021)
EllapsedTime: 418.6 seconds
RetCode: 0
Status:   WARNINGS   
CheckDir: adductomicsR.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:adductomicsR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings adductomicsR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/adductomicsR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'adductomicsR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'adductomicsR' version '1.6.0'
* 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 whether package 'adductomicsR' can be installed ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Documented arguments not in \usage in documentation object 'probPeaks':
  '...'

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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
rtDevModelling  16.86   0.91   63.02
outputPeakTable  6.92   0.61    8.43
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
rtDevModelling  15.12   1.17   56.17
outputPeakTable  7.80   0.91    9.31
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/adductomicsR.Rcheck/00check.log'
for details.



Installation output

adductomicsR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/adductomicsR_1.6.0.tar.gz && rm -rf adductomicsR.buildbin-libdir && mkdir adductomicsR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=adductomicsR.buildbin-libdir adductomicsR_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL adductomicsR_1.6.0.zip && rm adductomicsR_1.6.0.tar.gz adductomicsR_1.6.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  741k  100  741k    0     0  22.4M      0 --:--:-- --:--:-- --:--:-- 23.3M

install for i386

* installing *source* package 'adductomicsR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'adductomicsR'
    finding HTML links ... done
    IsotopicDistributionMod                 html  
    adductQuant                             html  
    adductQuantif-class                     html  
    adductSpec-class                        html  
    adductSpecGen                           html  
    digestMod                               html  
    finding level-2 HTML links ... done

    dotProdMatrix                           html  
    dotProdSpectra                          html  
    dynamicNoiseFilter                      html  
    filterAdductTable                       html  
    findPeaks                               html  
    generateTargTable                       html  
    loessWrapperMod                         html  
    ms2Group                                html  
    nAdjPeaks                               html  
    outputPeakTable                         html  
    peakIdQuant_newMethod                   html  
    peakIntegrate                           html  
    peakListId                              html  
    peakRangeSum                            html  
    probPeaks                               html  
    retentionCorr                           html  
    rtDevModelSave                          html  
    rtDevModelling                          html  
    signalGrouping                          html  
    specSimPepId                            html  
    spectraCreate                           html  
    truePeakTrough                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'adductomicsR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'adductomicsR' as adductomicsR_1.6.0.zip
* DONE (adductomicsR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'adductomicsR' successfully unpacked and MD5 sums checked

Tests output

adductomicsR.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.

> library(adductomicsR)
Loading required package: adductData
Loading required package: ExperimentHub
Loading required package: BiocGenerics
Loading required package: parallel

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

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
> library(adductData)
> library(testthat)
> 
> test_check("adductomicsR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
   9.92    1.20   11.89 

adductomicsR.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> library(adductomicsR)
Loading required package: adductData
Loading required package: ExperimentHub
Loading required package: BiocGenerics
Loading required package: parallel

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

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
> library(adductData)
> library(testthat)
> 
> test_check("adductomicsR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
  15.92    1.35   17.96 

Example timings

adductomicsR.Rcheck/examples_i386/adductomicsR-Ex.timings

nameusersystemelapsed
IsotopicDistributionMod0.560.050.61
adductQuant000
digestMod0.020.000.02
filterAdductTable000
findPeaks000
generateTargTable0.030.010.04
loessWrapperMod0.230.000.43
outputPeakTable6.920.618.43
rtDevModelling16.86 0.9163.02
specSimPepId000

adductomicsR.Rcheck/examples_x64/adductomicsR-Ex.timings

nameusersystemelapsed
IsotopicDistributionMod0.870.000.88
adductQuant000
digestMod000
filterAdductTable0.010.000.02
findPeaks000
generateTargTable0.030.000.03
loessWrapperMod0.270.000.27
outputPeakTable7.800.919.31
rtDevModelling15.12 1.1756.17
specSimPepId000