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CHECK report for MSnID on malbec2

This page was generated on 2019-10-16 12:05:20 -0400 (Wed, 16 Oct 2019).

Package 1056/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnID 1.18.1
Vlad Petyuk
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/MSnID
Branch: RELEASE_3_9
Last Commit: d328143
Last Changed Date: 2019-07-03 03:08:09 -0400 (Wed, 03 Jul 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: MSnID
Version: 1.18.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MSnID.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MSnID_1.18.1.tar.gz
StartedAt: 2019-10-16 03:23:59 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:28:44 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 284.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: MSnID.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MSnID.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MSnID_1.18.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MSnID.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.18.1’
* 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 : : 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’
infer_parsimonious_accessions,MSnID: no visible binding for global
  variable ‘accession’
infer_parsimonious_accessions,MSnID: no visible binding for global
  variable ‘pepSeq’
infer_parsimonious_accessions,MSnID: no visible global function
  definition for ‘.’
infer_parsimonious_accessions,MSnID: no visible binding for global
  variable ‘num’
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 num 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
infer_parsimonious_accessions 151.381  0.739  27.507
optimize_filter                33.601  0.339  16.158
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/MSnID.Rcheck/00check.log’
for details.



Installation output

MSnID.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL MSnID
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)

Tests output

MSnID.Rcheck/tests/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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("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 Oct 16 03:28:40 2019 
*********************************************** 
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MSnID RUnit Tests - 19 test functions, 0 errors, 0 failures
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
378.088   1.938 118.762 

Example timings

MSnID.Rcheck/MSnID-Ex.timings

nameusersystemelapsed
MSnID-class0.0000.0000.001
MSnIDFilter-class1.9420.0130.386
accessions0.4970.0040.500
apply_filter3.6060.0120.757
assess_missed_cleavages0.2530.0000.235
assess_termini0.2610.0000.261
correct_peak_selection0.1350.0000.135
data0.7840.0040.226
evaluate_filter2.4760.0120.605
id_quality1.0470.0070.298
infer_parsimonious_accessions151.381 0.739 27.507
mass_measurement_error0.1400.0170.143
optimize_filter33.601 0.33916.158
peptides0.0700.0000.071
psms0.0810.0040.085
read_mzIDs0.0010.0000.000
recalibrate0.0940.0040.097