Vlad Petyuk
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/MSnID |
| Branch: RELEASE_3_9 |
| Last Commit: d328143 |
| Last Changed Date: 2019-07-03 03:08:09 -0400 (Wed, 03 Jul 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:05:20 -0400 (Wed, 16 Oct 2019).
| Package 1056/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MSnID 1.18.1 Vlad Petyuk
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: MSnID |
| Version: 1.18.1 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MSnID.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MSnID_1.18.1.tar.gz |
| StartedAt: 2019-10-16 03:23:59 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:28:44 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 284.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MSnID.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MSnID.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MSnID_1.18.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MSnID.Rcheck’ * using R version 3.6.1 (2019-07-05) * 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 ‘1.18.1’ * 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 :: 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’ infer_parsimonious_accessions,MSnID: no visible binding for global variable ‘accession’ infer_parsimonious_accessions,MSnID: no visible binding for global variable ‘pepSeq’ infer_parsimonious_accessions,MSnID: no visible global function definition for ‘.’ infer_parsimonious_accessions,MSnID: no visible binding for global variable ‘num’ 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 num 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 or elapsed time > 5s user system elapsed infer_parsimonious_accessions 151.381 0.739 27.507 optimize_filter 33.601 0.339 16.158 * 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-3.9-bioc/meat/MSnID.Rcheck/00check.log’ for details.
MSnID.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL MSnID ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 -- Wed Oct 16 03:28:40 2019
***********************************************
Number of test functions: 19
Number of errors: 0
Number of failures: 0
1 Test Suite :
MSnID RUnit Tests - 19 test functions, 0 errors, 0 failures
Number of test functions: 19
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
378.088 1.938 118.762
MSnID.Rcheck/MSnID-Ex.timings
| name | user | system | elapsed | |
| MSnID-class | 0.000 | 0.000 | 0.001 | |
| MSnIDFilter-class | 1.942 | 0.013 | 0.386 | |
| accessions | 0.497 | 0.004 | 0.500 | |
| apply_filter | 3.606 | 0.012 | 0.757 | |
| assess_missed_cleavages | 0.253 | 0.000 | 0.235 | |
| assess_termini | 0.261 | 0.000 | 0.261 | |
| correct_peak_selection | 0.135 | 0.000 | 0.135 | |
| data | 0.784 | 0.004 | 0.226 | |
| evaluate_filter | 2.476 | 0.012 | 0.605 | |
| id_quality | 1.047 | 0.007 | 0.298 | |
| infer_parsimonious_accessions | 151.381 | 0.739 | 27.507 | |
| mass_measurement_error | 0.140 | 0.017 | 0.143 | |
| optimize_filter | 33.601 | 0.339 | 16.158 | |
| peptides | 0.070 | 0.000 | 0.071 | |
| psms | 0.081 | 0.004 | 0.085 | |
| read_mzIDs | 0.001 | 0.000 | 0.000 | |
| recalibrate | 0.094 | 0.004 | 0.097 | |