Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:35:51 -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: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:isobar.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings isobar_1.26.0.tar.gz |
StartedAt: 2018-10-17 02:50:35 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 02:54:40 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 244.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: isobar.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:isobar.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings isobar_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/isobar.Rcheck' * using R version 3.5.1 Patched (2018-07-24 r75005) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * 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 whether package 'isobar' can be installed ... WARNING Found the following significant warnings: Note: possible error in 'png(sprintf("pairwise_correlation_%s.png", ': unused argument (title = "Pairwise Correlation plot") Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/IBSpectra-class.Rd:175: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/IBSpectra-class.Rd:176: missing file link 'MSnbase' Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/IBSpectra-class.Rd:178: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/IBSpectra-class.Rd:232: file link 'ProteinGroup' in package 'isobar' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/ProteinGroup-class.Rd:177: file link 'IBSpectra' in package 'isobar' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/fit-distr.Rd:28: file link 'Cauchy' in package 'distr' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/fit-distr.Rd:28: file link 'Norm' in package 'distr' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/isobar.Rcheck/00install.out' for details. Information on the location(s) of code generating the 'Note's can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to 'yes'. * 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 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' .plot.pairs: possible error in png(sprintf("pairwise_correlation_%s.png", name), title = "Pairwise Correlation plot", width = 1000, height = 1000, pointsize = 14): unused argument (title = "Pairwise Correlation plot") .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 ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed NoiseModel-class 10.53 0.24 10.77 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed NoiseModel-class 13.96 0.06 14.02 * 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, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/isobar.Rcheck/00check.log' for details.
isobar.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/isobar_1.26.0.tar.gz && rm -rf isobar.buildbin-libdir && mkdir isobar.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=isobar.buildbin-libdir isobar_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL isobar_1.26.0.zip && rm isobar_1.26.0.tar.gz isobar_1.26.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 2189k 100 2189k 0 0 21.6M 0 --:--:-- --:--:-- --:--:-- 23.2M install for i386 * 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" Note: possible error in 'png(sprintf("pairwise_correlation_%s.png", ': unused argument (title = "Pairwise Correlation plot") ** help *** installing help indices converting help for package 'isobar' finding HTML links ... done IBSpectra-class html finding level-2 HTML links ... done Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/IBSpectra-class.Rd:175: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/IBSpectra-class.Rd:176: missing file link 'MSnbase' Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/IBSpectra-class.Rd:178: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/IBSpectra-class.Rd:232: file link 'ProteinGroup' in package 'isobar' does not exist and so has been treated as a topic NoiseModel-class html ProteinGroup-class html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/ProteinGroup-class.Rd:177: file link 'IBSpectra' in package 'isobar' does not exist and so has been treated as a topic TlsParameter-class html Tlsd-class html calc.delta.score html calc.startpos html calculate-pvalues html calculate.dNSAF html calculate.emPAI html correct.peptide.ratios html distr-methods html fit-distr html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/fit-distr.Rd:28: file link 'Cauchy' in package 'distr' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuIF7gp/R.INSTALL14744c9f58db/isobar/man/fit-distr.Rd:28: file link 'Norm' in package 'distr' does not exist and so has been treated as a topic getPeptideModifContext html getPhosphoRSProbabilities html getPtmInfo html groupMemberPeptides html human.protein.names html isobar-analysis html isobar-data html isobar-import html isobar-log html isobar-package html isobar-plots html isobar-preprocessing html isobar-reports html maplot.protein html number.ranges html observedKnownSites html peptide.count html proteinInfo-methods html proteinNameAndDescription html ratio-summ html ratiosReshapeWide html reporter.protein-methods html sanitize html shared.ratios html shared.ratios.sign html specificities html spectra.count2 html subsetIBSpectra html utils html writeHscoreData html writeIBSpectra html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'isobar' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'isobar' as isobar_1.26.0.zip * DONE (isobar) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library' package 'isobar' successfully unpacked and MD5 sums checked In R CMD INSTALL
isobar.Rcheck/examples_i386/isobar-Ex.timings
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isobar.Rcheck/examples_x64/isobar-Ex.timings
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