Package: MSnID

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSnID.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSnID_1.20.0.tar.gz

StartedAt: 2020-04-15 04:05:46 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:09:42 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 236.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MSnID.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSnID.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSnID_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/MSnID.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSnID/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSnID’ version ‘1.20.0’
* 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 ‘MSnID’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.construct_optimization_grid : <anonymous>: no visible global function
  definition for ‘quantile’
.get_num_pep_for_fdr: no visible global function definition for ‘rnorm’
.optimize_filter: no visible global function definition for ‘optim’
.read_mzIDs.mzR: no visible binding for global variable ‘i’
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable ‘spectrumID’
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable ‘name’
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable ‘mass’
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable ‘location’
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable ‘modification’
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable ‘DatabaseAccess’
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable ‘DatabaseDescription’
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable ‘DBseqLength’
infer_parsimonious_accessions,MSnID : infer_acc: no visible binding for
  global variable ‘accession’
infer_parsimonious_accessions,MSnID : infer_acc: no visible binding for
  global variable ‘N’
infer_parsimonious_accessions,MSnID : infer_acc: no visible binding for
  global variable ‘pepSeq’
recalibrate,MSnID: no visible global function definition for ‘median’
recalibrate,MSnID: no visible global function definition for ‘density’
Undefined global functions or variables:
  DBseqLength DatabaseAccess DatabaseDescription N accession density i
  location mass median modification name optim pepSeq quantile rnorm
  spectrumID
Consider adding
  importFrom("stats", "density", "median", "optim", "quantile", "rnorm")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'read_mzIDs.Rd':
  ‘[mzR]{mzR-package}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
infer_parsimonious_accessions 9.802   4.84   2.477
optimize_filter               3.972   1.65  10.749
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/MSnID.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MSnID
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘MSnID’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MSnID)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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("MSnID")
Note, the anticipated/suggested columns in the
peptide-to-spectrum matching results are:
-----------------------------------------------
accession
calculatedMassToCharge
chargeState
experimentalMassToCharge
isDecoy
peptide
spectrumFile
spectrumID
Reading from mzIdentMLs ...

reading c_elegans.mzid.gz... DONE!
Reading from mzIdentMLs ...



RUNIT TEST PROTOCOL -- Wed Apr 15 04:09:36 2020 
*********************************************** 
Number of test functions: 17 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MSnID RUnit Tests - 17 test functions, 0 errors, 0 failures
Number of test functions: 17 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 75.148  20.178  64.653 

name	user	system	elapsed
MSnID-class	0	0	0
MSnIDFilter-class	0.501	0.179	0.362
accessions	0.736	0.390	0.419
apply_filter	1.426	0.846	0.683
assess_missed_cleavages	2.283	0.201	0.467
assess_termini	0.255	0.018	0.275
correct_peak_selection	0.112	0.019	0.132
data	0.613	1.239	0.314
evaluate_filter	1.009	1.367	0.381
id_quality	0.819	0.931	0.301
infer_parsimonious_accessions	9.802	4.840	2.477
mass_measurement_error	1.739	0.029	0.162
optimize_filter	3.972	1.650	10.749
peptides	0.587	0.220	0.141
psms	0.786	0.021	0.147
read_mzIDs	0.000	0.000	0.001
recalibrate	0.128	0.025	0.155