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CHECK report for isobar on malbec2

This page was generated on 2020-10-17 11:54:59 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE isobar PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 898/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
isobar 1.34.0
Florian P Breitwieser
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/isobar
Branch: RELEASE_3_11
Last Commit: b9a3005
Last Changed Date: 2020-04-27 14:27:35 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: isobar
Version: 1.34.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:isobar.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings isobar_1.34.0.tar.gz
StartedAt: 2020-10-17 02:29:20 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:33:38 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 257.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: isobar.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:isobar.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings isobar_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/isobar.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘isobar/DESCRIPTION’ ... OK
* this is package ‘isobar’ version ‘1.34.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘isobar’ 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
* 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.as.matrix’ ‘.as.vect’ ‘.convertPeptideModif’
  ‘.proteinGroupAsConciseDataFrame’ ‘.read.idfile’ ‘.sum.bool’
* checking S3 generic/method consistency ... WARNING
sequence:
  function(nvec, ...)
sequence.coverage:
  function(protein.group, protein.g, specificity, simplify, ...)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  as.data.frame.IBSpectra as.data.frame.ProteinGroup plot.NoiseModel
  sequence.coverage summary.ProteinGroup
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.calcProbXGreaterThanY.orig: no visible global function definition for
  ‘d’
.read.peaklist: no visible binding for global variable ‘type’
.round.distr: no visible global function definition for ‘param’
.write.summarized.table: no visible binding for global variable ‘name’
distrprint: no visible global function definition for ‘param’
distrprint : <anonymous>: no visible global function definition for
  ‘param’
shared.ratios.sign: no visible binding for global variable ‘ratio’
shared.ratios.sign: no visible binding for global variable ‘g’
spectra.count2: no visible binding for global variable ‘peptide’
twodistr.plot: no visible global function definition for ‘d’
ProteinGroup,data.frame-missing: no visible binding for global variable
  ‘peptide’
coerce,IBSpectra-MSnSet: no visible global function definition for ‘mz’
coerce,IBSpectra-MSnSet: no visible binding for global variable ‘o’
coerce,MSnSet-IBSpectra: no visible global function definition for
  ‘qual’
df,Tlsd: no visible global function definition for ‘param’
estimateRatio,IBSpectra-ANY-missing-missing-character-missing: no
  visible binding for global variable ‘i’
estimateRatio,IBSpectra-ANY-missing-missing-missing-character: no
  visible binding for global variable ‘i’
estimateRatioNumeric,numeric-numeric-NoiseModel: no visible binding for
  global variable ‘center.var’
location,Tlsd: no visible global function definition for ‘param’
plotRatio,IBSpectra-character-character-character: no visible binding
  for global variable ‘pch’
plotRatio,IBSpectra-character-character-character: no visible binding
  for global variable ‘noise.model.col’
plotRatio,IBSpectra-character-character-character: no visible binding
  for global variable ‘pch.p’
scale,Tlsd: no visible global function definition for ‘param’
Undefined global functions or variables:
  center.var d g i mz name noise.model.col o param pch pch.p peptide
  qual ratio type
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'IBSpectra-class.Rd':
  ‘[MSnbase]{MSnbase}’

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

* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'peptide.count':
  ‘sequence.coverage’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
NoiseModel-class 10.839  0.052  10.891
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/isobar.Rcheck/00check.log’
for details.



Installation output

isobar.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL isobar
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘isobar’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘coerce’ with signature ‘"MSnSet","IBSpectra"’: no definition for class “MSnSet”
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “MSnSet”
** help
*** installing help indices
** 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
* DONE (isobar)

Tests output


Example timings

isobar.Rcheck/isobar-Ex.timings

nameusersystemelapsed
IBSpectra-class0.5230.0120.535
NoiseModel-class10.839 0.05210.891
ProteinGroup-class0.2840.0000.284
TlsParameter-class0.0010.0000.001
Tlsd-class0.0010.0000.001
calculate-pvalues0.0250.0000.026
calculate.dNSAF2.1250.0082.133
calculate.emPAI0.2490.0080.269
distr-methods0.0680.0000.096
fit-distr3.7050.0163.722
getPtmInfo000
groupMemberPeptides0.3950.0160.411
isobar-analysis0.3590.0120.371
isobar-data0.3240.0080.333
isobar-import1.3250.0121.337
isobar-log1.6490.0161.665
isobar-plots1.7630.0401.803
isobar-preprocessing1.2340.0201.254
number.ranges000
observedKnownSites0.2960.0000.296
peptide.count3.3640.0083.372
proteinInfo-methods0.2730.0000.274
proteinNameAndDescription0.2640.0000.264
ratio-summ0.3230.0120.335
sanitize0.0000.0000.001
spectra.count20.2540.0000.254
subsetIBSpectra2.1170.0072.166
utils000