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CHECK report for specL on tokay1

This page was generated on 2019-04-13 11:24:38 -0400 (Sat, 13 Apr 2019).

Package 1484/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
specL 1.16.1
Christian Panse , Witold E. Wolski
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/specL
Branch: RELEASE_3_8
Last Commit: f49026a
Last Changed Date: 2019-01-04 13:51:19 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: specL
Version: 1.16.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:specL.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings specL_1.16.1.tar.gz
StartedAt: 2019-04-13 05:40:08 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:42:13 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 125.1 seconds
RetCode: 0
Status:  OK  
CheckDir: specL.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:specL.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings specL_1.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/specL.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.16.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... OK
* 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 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/specL.Rcheck/00check.log'
for details.



Installation output

specL.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/specL_1.16.1.tar.gz && rm -rf specL.buildbin-libdir && mkdir specL.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=specL.buildbin-libdir specL_1.16.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL specL_1.16.1.zip && rm specL_1.16.1.tar.gz specL_1.16.1.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  10.5M      0 --:--:-- --:--:-- --:--:-- 11.5M

install for i386

* installing *source* package 'specL' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'specL' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'specL' as specL_1.16.1.zip
* DONE (specL)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'specL' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

specL.Rcheck/tests_i386/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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:  0.000260416666666667 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:  0.375000953674316 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:  0.281252861022949 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:  0.343752145767212 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:  0.328127145767212 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 ...
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  137
length of genSwathIonLibSpecL   137
time taken:  0.203125953674316 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:  0.265625953674316 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:  0.125 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:  0.125003099441528 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:  0.250001907348633 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:  0.218751192092896 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:  0.265627861022949 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:  0.218750953674316 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:  0.203125953674316 secs
length of genSwathIonLibSpecL  after fragmentIonRange filtering 137


RUNIT TEST PROTOCOL -- Sat Apr 13 05:42:01 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 
   6.09    0.07    6.59 

specL.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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:  0.000260432561238607 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:  0.515625953674316 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:  0.406253099441528 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:  0.265627145767212 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:  0.359376907348633 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  137
length of genSwathIonLibSpecL   137
time taken:  0.281250953674316 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:  0.343748092651367 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:  0.171875953674316 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:  0.156250953674316 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:  0.390626907348633 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:  0.140626907348633 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:  0.156251192092896 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:  0.312499046325684 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:  0.296875 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:  0.421876192092896 secs
length of genSwathIonLibSpecL  after fragmentIonRange filtering 137


RUNIT TEST PROTOCOL -- Sat Apr 13 05:42:09 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 
   7.53    0.10    7.62 

Example timings

specL.Rcheck/examples_i386/specL-Ex.timings

nameusersystemelapsed
annotate.protein_id0.030.000.03
cdsw0.020.000.01
genSwathIonLib0.410.000.41
iRTpeptides000
peptideStd0.010.000.01
read.bibliospec000
specL-class000
specLSet-class000

specL.Rcheck/examples_x64/specL-Ex.timings

nameusersystemelapsed
annotate.protein_id0.030.000.04
cdsw0.010.000.01
genSwathIonLib0.70.00.7
iRTpeptides000
peptideStd0.020.000.02
read.bibliospec000
specL-class000
specLSet-class000