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CHECK report for BRAIN on tokay1

This page was generated on 2020-08-07 12:00:49 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BRAIN PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 191/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BRAIN 1.35.0
Piotr Dittwald
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/BRAIN
Branch: master
Last Commit: cf2d9e9
Last Changed Date: 2020-04-27 14:28:46 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: BRAIN
Version: 1.35.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BRAIN.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BRAIN_1.35.0.tar.gz
StartedAt: 2020-08-07 00:39:30 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 00:41:00 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 89.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BRAIN.Rcheck
Warnings: 2

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:BRAIN.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BRAIN_1.35.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BRAIN.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BRAIN/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BRAIN' version '1.35.0'
* 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 'BRAIN' 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 ... NOTE
Package in Depends field not imported from: 'Biostrings'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 ... WARNING
Codoc mismatches from documentation object 'calculateIsotopicProbabilities':
calculateIsotopicProbabilities
  Code: function(aC, stopOption = "nrPeaks", nrPeaks = NULL, coverage =
                 NULL, abundantEstim = NULL, approx = FALSE,
                 approxStart = 1, approxParam = NULL)
  Docs: function(aC, stopOption = "nrPeaks", nrPeaks, coverage,
                 abundantEstim)
  Argument names in code not in docs:
    approx approxStart approxParam
  Mismatches in argument default values:
    Name: 'nrPeaks' Code: NULL Docs: 
    Name: 'coverage' Code: NULL Docs: 
    Name: 'abundantEstim' Code: NULL Docs: 

* checking Rd \usage sections ... WARNING
Bad \usage lines found in documentation object 'useBRAIN2':
  useBRAIN2(aC, stopOption = "nrPeaks", nrPeaks, approxStart = 1, approxParam = NULL))

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
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/BRAIN.Rcheck/00check.log'
for details.



Installation output

BRAIN.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BRAIN_1.35.0.tar.gz && rm -rf BRAIN.buildbin-libdir && mkdir BRAIN.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BRAIN.buildbin-libdir BRAIN_1.35.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BRAIN_1.35.0.zip && rm BRAIN_1.35.0.tar.gz BRAIN_1.35.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  5 1756k    5 98304    0     0   982k      0  0:00:01 --:--:--  0:00:01 1021k
100 1756k  100 1756k    0     0  9110k      0 --:--:-- --:--:-- --:--:-- 9294k

install for i386

* installing *source* package 'BRAIN' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BRAIN'
    finding HTML links ... done
    BRAIN-package                           html  
    calculateAverageMass                    html  
    calculateIsotopicProbabilities          html  
    calculateMonoisotopicMass               html  
    calculateNrPeaks                        html  
    getAtomsFromSeq                         html  
    useBRAIN                                html  
    useBRAIN2                               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 'BRAIN' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BRAIN' as BRAIN_1.35.0.zip
* DONE (BRAIN)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BRAIN' successfully unpacked and MD5 sums checked

Tests output


Example timings

BRAIN.Rcheck/examples_i386/BRAIN-Ex.timings

nameusersystemelapsed
BRAIN-package0.180.040.25
calculateAverageMass000
calculateIsotopicProbabilities0.030.000.03
calculateMonoisotopicMass000
calculateNrPeaks000
getAtomsFromSeq0.020.000.01
useBRAIN0.120.000.13
useBRAIN20.140.000.14

BRAIN.Rcheck/examples_x64/BRAIN-Ex.timings

nameusersystemelapsed
BRAIN-package0.130.000.13
calculateAverageMass000
calculateIsotopicProbabilities0.020.000.02
calculateMonoisotopicMass000
calculateNrPeaks000
getAtomsFromSeq0.010.000.01
useBRAIN0.350.000.35
useBRAIN20.130.000.13