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 MSnID PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1142/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
MSnID 1.22.0 Vlad Petyuk
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK |
Package: MSnID |
Version: 1.22.0 |
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MSnID.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MSnID_1.22.0.tar.gz |
StartedAt: 2020-10-17 03:28:44 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 03:32:43 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 239.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MSnID.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MSnID.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MSnID_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/MSnID.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 ‘MSnID/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MSnID’ 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 ‘MSnID’ 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .construct_optimization_grid : <anonymous>: no visible global function definition for ‘quantile’ .get_num_pep_for_fdr: no visible global function definition for ‘rnorm’ .optimize_filter: no visible global function definition for ‘optim’ .read_mzIDs.mzR: no visible binding for global variable ‘i’ .read_mzIDs.mzR.engine.single.file: no visible binding for global variable ‘spectrumID’ .read_mzIDs.mzR.engine.single.file: no visible binding for global variable ‘name’ .read_mzIDs.mzR.engine.single.file: no visible binding for global variable ‘mass’ .read_mzIDs.mzR.engine.single.file: no visible binding for global variable ‘location’ .read_mzIDs.mzR.engine.single.file: no visible binding for global variable ‘modification’ .read_mzIDs.mzR.engine.single.file: no visible binding for global variable ‘DatabaseAccess’ .read_mzIDs.mzR.engine.single.file: no visible binding for global variable ‘DatabaseDescription’ .read_mzIDs.mzR.engine.single.file: no visible binding for global variable ‘DBseqLength’ infer_parsimonious_accessions,MSnID : infer_acc: no visible binding for global variable ‘accession’ infer_parsimonious_accessions,MSnID : infer_acc: no visible binding for global variable ‘N’ infer_parsimonious_accessions,MSnID : infer_acc: no visible binding for global variable ‘pepSeq’ recalibrate,MSnID: no visible global function definition for ‘median’ recalibrate,MSnID: no visible global function definition for ‘density’ Undefined global functions or variables: DBseqLength DatabaseAccess DatabaseDescription N accession density i location mass median modification name optim pepSeq quantile rnorm spectrumID Consider adding importFrom("stats", "density", "median", "optim", "quantile", "rnorm") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in documentation object 'read_mzIDs.Rd': ‘[mzR]{mzR-package}’ 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 (user + system) or elapsed time > 5s user system elapsed infer_parsimonious_accessions 36.926 0.799 7.640 optimize_filter 25.435 0.225 14.673 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.11-bioc/meat/MSnID.Rcheck/00check.log’ for details.
MSnID.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL MSnID ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘MSnID’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** demo ** 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 (MSnID)
MSnID.Rcheck/tests/runTests.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. > BiocGenerics:::testPackage("MSnID") Note, the anticipated/suggested columns in the peptide-to-spectrum matching results are: ----------------------------------------------- accession calculatedMassToCharge chargeState experimentalMassToCharge isDecoy peptide spectrumFile spectrumID Reading from mzIdentMLs ... reading c_elegans.mzid.gz... DONE! Reading from mzIdentMLs ... RUNIT TEST PROTOCOL -- Sat Oct 17 03:32:40 2020 *********************************************** Number of test functions: 17 Number of errors: 0 Number of failures: 0 1 Test Suite : MSnID RUnit Tests - 17 test functions, 0 errors, 0 failures Number of test functions: 17 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 167.468 1.737 77.671
MSnID.Rcheck/MSnID-Ex.timings
name | user | system | elapsed | |
MSnID-class | 0.001 | 0.000 | 0.000 | |
MSnIDFilter-class | 0.914 | 0.017 | 0.284 | |
accessions | 0.116 | 0.008 | 0.124 | |
apply_filter | 2.145 | 0.017 | 0.556 | |
assess_missed_cleavages | 0.290 | 0.007 | 0.278 | |
assess_termini | 0.280 | 0.000 | 0.281 | |
correct_peak_selection | 0.530 | 0.004 | 0.533 | |
data | 0.853 | 0.024 | 0.223 | |
evaluate_filter | 1.407 | 0.021 | 0.358 | |
id_quality | 0.995 | 0.000 | 0.197 | |
infer_parsimonious_accessions | 36.926 | 0.799 | 7.640 | |
mass_measurement_error | 0.143 | 0.012 | 0.153 | |
optimize_filter | 25.435 | 0.225 | 14.673 | |
peptides | 0.121 | 0.000 | 0.121 | |
psms | 0.123 | 0.000 | 0.124 | |
read_mzIDs | 0 | 0 | 0 | |
recalibrate | 0.473 | 0.007 | 0.480 | |