Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:55:13 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE MSGFgui PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1137/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
MSGFgui 1.22.0 Thomas Lin Pedersen
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | ERROR | ERROR | skipped | skipped |
Package: MSGFgui |
Version: 1.22.0 |
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MSGFgui.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MSGFgui_1.22.0.tar.gz |
StartedAt: 2020-10-17 03:27:42 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 03:29:10 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 87.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MSGFgui.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MSGFgui.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MSGFgui_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/MSGFgui.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 ‘MSGFgui/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MSGFgui’ 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 ‘MSGFgui’ 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 Package in Depends field not imported from: ‘xlsx’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE getAAtable: no visible global function definition for ‘read.csv’ getAdductTable: no visible global function definition for ‘read.csv’ getIonTrace: no visible global function definition for ‘predict’ getIonTrace: no visible global function definition for ‘loess’ getIonTrace : gauss: no visible global function definition for ‘dnorm’ getIonTrace: no visible global function definition for ‘optimize’ getScoreDistribution: no visible global function definition for ‘density’ renderMzID: no visible global function definition for ‘scans’ renderMzID: no visible global function definition for ‘peptides’ renderMzID: no visible global function definition for ‘modifications’ renderMzID: no visible global function definition for ‘database’ server: no visible global function definition for ‘scans’ server : <anonymous>: no visible global function definition for ‘createWorkbook’ server : <anonymous>: no visible global function definition for ‘createSheet’ server : <anonymous>: no visible global function definition for ‘addDataFrame’ server : <anonymous>: no visible global function definition for ‘saveWorkbook’ server : <anonymous>: no visible global function definition for ‘write.table’ Undefined global functions or variables: addDataFrame createSheet createWorkbook database density dnorm loess modifications optimize peptides predict read.csv saveWorkbook scans write.table Consider adding importFrom("stats", "density", "dnorm", "loess", "optimize", "predict") importFrom("utils", "read.csv", "write.table") to your NAMESPACE file. * 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-all.R’ OK * 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 ‘/home/biocbuild/bbs-3.11-bioc/meat/MSGFgui.Rcheck/00check.log’ for details.
MSGFgui.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL MSGFgui ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘MSGFgui’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** 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 (MSGFgui)
MSGFgui.Rcheck/tests/test-all.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > test_check('MSGFgui') Loading required package: MSGFgui Loading required package: mzR Loading required package: Rcpp Loading required package: xlsx ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 17 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ] > > proc.time() user system elapsed 5.347 0.417 4.985
MSGFgui.Rcheck/MSGFgui-Ex.timings
name | user | system | elapsed | |
MSGFgui | 0 | 0 | 0 | |
currentData | 0.002 | 0.000 | 0.001 | |