isobar 1.22.0
Florian P Breitwieser
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/isobar | | Branch: RELEASE_3_5 | | Last Commit: 66e054d | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings isobar_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/isobar.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.22.0’
* 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 loading without being on the library search path ... 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 ... OK
* 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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
NoiseModel-class 8.045 0.216 8.54
* 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 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/isobar.Rcheck/00check.log’
for details.
* installing *source* package ‘isobar’ ...
** R
** data
** inst
** preparing 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
* DONE (isobar)