Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:24:00 -0400 (Wed, 17 Oct 2018).
Package 754/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
isobar 1.26.0 Florian P Breitwieser
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: isobar |
Version: 1.26.0 |
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:isobar.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings isobar_1.26.0.tar.gz |
StartedAt: 2018-10-16 01:23:38 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 01:25:46 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 127.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: isobar.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:isobar.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings isobar_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/isobar.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * 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 ‘1.26.0’ * 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 ... 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed NoiseModel-class 8.524 0.056 8.588 * 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, 2 NOTEs See ‘/home/biocbuild/bbs-3.7-bioc/meat/isobar.Rcheck/00check.log’ for details.
isobar.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL isobar ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘isobar’ ... ** 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 * DONE (isobar)
isobar.Rcheck/isobar-Ex.timings
name | user | system | elapsed | |
IBSpectra-class | 0.316 | 0.004 | 0.338 | |
NoiseModel-class | 8.524 | 0.056 | 8.588 | |
ProteinGroup-class | 0.236 | 0.004 | 0.238 | |
TlsParameter-class | 0.004 | 0.000 | 0.001 | |
Tlsd-class | 0.000 | 0.000 | 0.001 | |
calculate-pvalues | 0.024 | 0.000 | 0.024 | |
calculate.dNSAF | 2.292 | 0.000 | 2.290 | |
calculate.emPAI | 0.276 | 0.000 | 0.306 | |
distr-methods | 0.044 | 0.000 | 0.069 | |
fit-distr | 2.684 | 0.024 | 2.720 | |
getPtmInfo | 0.000 | 0.000 | 0.001 | |
groupMemberPeptides | 0.364 | 0.000 | 0.362 | |
isobar-analysis | 0.240 | 0.004 | 0.244 | |
isobar-data | 0.216 | 0.000 | 0.215 | |
isobar-import | 1.084 | 0.004 | 1.089 | |
isobar-log | 0.888 | 0.008 | 0.895 | |
isobar-plots | 0.984 | 0.024 | 1.006 | |
isobar-preprocessing | 1.028 | 0.012 | 1.040 | |
number.ranges | 0.000 | 0.000 | 0.001 | |
observedKnownSites | 0.252 | 0.000 | 0.258 | |
peptide.count | 2.196 | 0.008 | 2.205 | |
proteinInfo-methods | 0.184 | 0.004 | 0.189 | |
proteinNameAndDescription | 0.224 | 0.004 | 0.226 | |
ratio-summ | 0.280 | 0.004 | 0.284 | |
sanitize | 0 | 0 | 0 | |
spectra.count2 | 0.288 | 0.000 | 0.292 | |
subsetIBSpectra | 1.604 | 0.012 | 1.617 | |
utils | 0 | 0 | 0 | |