Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 13:30:46 -0400 (Tue, 09 Apr 2019).
Package 1531/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
specL 1.17.3 Christian Panse
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: specL |
Version: 1.17.3 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:specL.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings specL_1.17.3.tar.gz |
StartedAt: 2019-04-09 03:54:02 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 03:55:02 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 60.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: specL.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:specL.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings specL_1.17.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/specL.Rcheck’ * using R Under development (unstable) (2018-11-27 r75683) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘specL/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘specL’ version ‘1.17.3’ * 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 ‘specL’ 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 ... NOTE Found the following apparent S3 methods exported but not registered: merge.specLSet plot.psm plot.psmSet summary.psmSet See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE summary,specLSet : <anonymous>: no visible binding for global variable ‘iRTpeptides’ Undefined global functions or variables: iRTpeptides * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.9-bioc/meat/specL.Rcheck/00check.log’ for details.
specL.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL specL ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘specL’ ... ** R ** data *** moving datasets to lazyload DB ** 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 * DONE (specL)
specL.Rcheck/tests/runTests.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (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("specL") Attaching package: 'specL' The following objects are masked from 'package:protViz': plot.psm, plot.psmSet, summary.psmSet start protein annotation ... time taken: 0.000500102837880453 minutes start protein annotation ... time taken: 0.000482165813446045 minutes normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 137 length of genSwathIonLibSpecL 137 time taken: 0.391197919845581 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 137 length of genSwathIonLibSpecL 137 time taken: 0.364825010299683 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 137 length of genSwathIonLibSpecL 137 time taken: 0.329714059829712 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 normalizing RT ... no iRT peptides found for building the model. => no iRT regression applied, using orgiginal rt instead! generating ion library ... start generating specLSet object ... length of findNN idx 137 length of genSwathIonLibSpecL 137 time taken: 0.337484836578369 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... model with only one file. generating ion library ... start generating specLSet object ... length of findNN idx 1 length of genSwathIonLibSpecL 1 time taken: 0.0160567760467529 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 1 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... model with only one file. generating ion library ... start generating specLSet object ... length of findNN idx 1 length of genSwathIonLibSpecL 1 time taken: 0.0161919593811035 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 1 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 137 length of genSwathIonLibSpecL 137 time taken: 0.34621787071228 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 normalizing RT ... no iRT peptides found for building the model. => no iRT regression applied, using orgiginal rt instead! generating ion library ... start generating specLSet object ... length of findNN idx 137 length of genSwathIonLibSpecL 137 time taken: 0.39314603805542 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... model with only one file. generating ion library ... start generating specLSet object ... length of findNN idx 1 length of genSwathIonLibSpecL 1 time taken: 0.0161588191986084 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 1 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... model with only one file. generating ion library ... start generating specLSet object ... length of findNN idx 1 length of genSwathIonLibSpecL 1 time taken: 0.0146138668060303 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 1 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 69 length of genSwathIonLibSpecL 69 time taken: 0.204054117202759 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 69 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 68 length of genSwathIonLibSpecL 68 time taken: 0.182168006896973 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 68 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 137 length of genSwathIonLibSpecL 137 time taken: 0.417817831039429 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 69 length of genSwathIonLibSpecL 69 time taken: 0.182615041732788 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 69 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 68 length of genSwathIonLibSpecL 68 time taken: 0.194901943206787 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 68 normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 137 length of genSwathIonLibSpecL 137 time taken: 0.418854951858521 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 fetched 137 rows. assigning 28 modifications ... fetched 184 rows. assigning 37 modifications ... normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 137 length of genSwathIonLibSpecL 137 time taken: 0.259363174438477 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 fetched 137 rows. assigning 28 modifications ... fetched 184 rows. assigning 37 modifications ... normalizing RT ... found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw building model ... generating ion library ... start generating specLSet object ... length of findNN idx 137 length of genSwathIonLibSpecL 137 time taken: 0.363688945770264 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 RUNIT TEST PROTOCOL -- Tue Apr 9 03:54:54 2019 *********************************************** Number of test functions: 9 Number of errors: 0 Number of failures: 0 1 Test Suite : specL RUnit Tests - 9 test functions, 0 errors, 0 failures Number of test functions: 9 Number of errors: 0 Number of failures: 0 There were 13 warnings (use warnings() to see them) > > > proc.time() user system elapsed 7.812 0.299 8.166
specL.Rcheck/specL-Ex.timings
name | user | system | elapsed | |
annotate.protein_id | 0.039 | 0.011 | 0.055 | |
cdsw | 0.028 | 0.002 | 0.030 | |
genSwathIonLib | 0.500 | 0.015 | 0.517 | |
iRTpeptides | 0.005 | 0.001 | 0.006 | |
peptideStd | 0.009 | 0.001 | 0.010 | |
read.bibliospec | 0.001 | 0.000 | 0.001 | |
specL-class | 0.003 | 0.001 | 0.004 | |
specLSet-class | 0.003 | 0.001 | 0.004 | |