Package: specL

Version: 1.12.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings specL_1.12.0.tar.gz

StartedAt: 2018-04-12 03:04:23 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:05:05 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 42.0 seconds

RetCode: 0

Status:  OK

CheckDir: specL.Rcheck

Warnings: 0

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings specL_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/specL.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 ‘1.12.0’
* 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 ‘specL’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
* 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
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/specL.Rcheck/00check.log’
for details.

* installing *source* package ‘specL’ ...
** libs
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -c lower_bound.cpp -o lower_bound.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o specL.so lower_bound.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/specL.Rcheck/specL/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (specL)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("specL")

Attaching package: 'specL'

The following objects are masked from 'package:protViz':

    plot.psm, plot.psmSet, summary.psmSet

start protein annotation ...
time taken:  0.000313822428385417 minutes
start protein annotation ...
time taken:  0.00030363400777181 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:  0.330523729324341 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:  0.253906965255737 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:  0.251364469528198 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:  0.25685977935791 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:  0.0109732151031494 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:  0.0118322372436523 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:  0.21054744720459 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:  0.262960433959961 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:  0.00963091850280762 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:  0.0114467144012451 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:  0.143426656723022 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:  0.133475780487061 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:  0.247844219207764 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:  0.133816003799438 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:  0.134555101394653 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:  0.251485586166382 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:  0.199050664901733 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:  0.204360008239746 secs
length of genSwathIonLibSpecL  after fragmentIonRange filtering 137


RUNIT TEST PROTOCOL -- Thu Apr 12 03:05:03 2018 
*********************************************** 
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 
  6.352   0.264   6.706 

name	user	system	elapsed
annotate.protein_id	0.024	0.004	0.032
cdsw	0.036	0.000	0.040
genSwathIonLib	0.440	0.008	0.449
iRTpeptides	0.004	0.000	0.004
peptideStd	0.008	0.000	0.007
read.bibliospec	0.000	0.000	0.001
specL-class	0.004	0.000	0.001
specLSet-class	0.000	0.000	0.001