Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:33:44 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the specL package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1762/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
specL 1.24.0 (landing page) Christian Panse
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: specL |
Version: 1.24.0 |
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:specL.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings specL_1.24.0.tar.gz |
StartedAt: 2021-05-06 07:11:35 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 07:12:54 -0400 (Thu, 06 May 2021) |
EllapsedTime: 79.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: specL.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:specL.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings specL_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/specL.Rcheck' * using R version 4.0.5 (2021-03-31) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'specL/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'specL' version '1.24.0' * 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 '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 * 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 ... 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 .retentiontimePlotFile : <anonymous>: no visible global function definition for 'head' summary,specLSet : <anonymous>: no visible binding for global variable 'iRTpeptides' Undefined global functions or variables: head iRTpeptides Consider adding importFrom("utils", "head") 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 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 ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.12-bioc/meat/specL.Rcheck/00check.log' for details.
specL.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/specL_1.24.0.tar.gz && rm -rf specL.buildbin-libdir && mkdir specL.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=specL.buildbin-libdir specL_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL specL_1.24.0.zip && rm specL_1.24.0.tar.gz specL_1.24.0.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 486k 100 486k 0 0 10.3M 0 --:--:-- --:--:-- --:--:-- 10.5M install for i386 * installing *source* package 'specL' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'specL' finding HTML links ... done annotate.protein_id html cdsw html genSwathIonLib html iRTpeptides html ms1.p2069 html peptideStd html plot-methods html read.bibliospec html show-methods html specL-class html specLSet-class html write.spectronaut-methods html ** 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 install for x64 * installing *source* package 'specL' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'specL' as specL_1.24.0.zip * DONE (specL) * installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library' package 'specL' successfully unpacked and MD5 sums checked
specL.Rcheck/tests_i386/runTests.Rout R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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: 0.000260432561238607 minutes start protein annotation ... time taken: 0.000260432561238607 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: 0.484376907348633 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: 0.500001907348633 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: 0.421875953674316 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: 0.296875953674316 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: 0.015625 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: 0.0156259536743164 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: 0.234375 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: 0.343752145767212 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: 0.015625 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 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: 0.171877861022949 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: 0.203123807907104 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: 0.265628099441528 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: 0.15625 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: 0.171874046325684 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: 0.390627145767212 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: 0.359375953674316 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: 0.281249046325684 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 RUNIT TEST PROTOCOL -- Thu May 06 07:12:39 2021 *********************************************** 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 8.01 0.18 8.29 |
specL.Rcheck/tests_x64/runTests.Rout R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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 minutes start protein annotation ... time taken: 0.000260416666666667 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: 0.343750953674316 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: 0.328127145767212 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: 0.296875953674316 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: 0.328126907348633 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: 0.015625 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: 0.0156240463256836 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: 0.250002145767212 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: 0.328126907348633 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 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 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: 0.15625 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: 0.140628099441528 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: 0.296876907348633 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: 0.171875 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: 0.15625 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: 0.296877861022949 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: 0.296877861022949 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: 0.25 secs length of genSwathIonLibSpecL after fragmentIonRange filtering 137 RUNIT TEST PROTOCOL -- Thu May 06 07:12:47 2021 *********************************************** 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 6.87 0.06 6.96 |
specL.Rcheck/examples_i386/specL-Ex.timings
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specL.Rcheck/examples_x64/specL-Ex.timings
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