Package: isobar

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:isobar.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings isobar_1.30.0.tar.gz

StartedAt: 2019-10-16 03:56:06 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:00:24 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 258.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: isobar.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:isobar.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings isobar_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/isobar.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘isobar/DESCRIPTION’ ... OK
* this is package ‘isobar’ version ‘1.30.0’
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  as.data.frame.IBSpectra as.data.frame.ProteinGroup plot.NoiseModel
  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 : : 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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
NoiseModel-class 11.444  0.747  12.195
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/isobar.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL isobar
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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)

name	user	system	elapsed
IBSpectra-class	0.474	0.043	0.517
NoiseModel-class	11.444	0.747	12.195
ProteinGroup-class	0.252	0.019	0.270
TlsParameter-class	0.002	0.000	0.002
Tlsd-class	0.002	0.001	0.003
calculate-pvalues	0.039	0.001	0.040
calculate.dNSAF	3.924	0.184	4.110
calculate.emPAI	0.376	0.048	0.426
distr-methods	0.074	0.004	0.083
fit-distr	4.519	0.103	4.626
getPtmInfo	0.001	0.000	0.001
groupMemberPeptides	0.612	0.037	0.650
isobar-analysis	0.359	0.023	0.382
isobar-data	0.297	0.018	0.316
isobar-import	1.777	0.099	1.877
isobar-log	1.955	0.085	2.041
isobar-plots	1.332	0.161	1.496
isobar-preprocessing	1.598	0.258	1.878
number.ranges	0.000	0.000	0.001
observedKnownSites	0.458	0.028	0.485
peptide.count	3.179	0.222	3.406
proteinInfo-methods	0.245	0.024	0.268
proteinNameAndDescription	0.313	0.016	0.328
ratio-summ	0.401	0.024	0.425
sanitize	0.000	0.000	0.001
spectra.count2	0.337	0.022	0.359
subsetIBSpectra	3.108	0.099	3.210
utils	0	0	0