BioC 3.6: CHECK report for MSnID on malbec1

Package: MSnID

Version: 1.11.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MSnID_1.11.0.tar.gz

StartedAt: 2017-08-16 00:56:56 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:59:48 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 172.2 seconds

RetCode: 0

Status:  OK

CheckDir: MSnID.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MSnID_1.11.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/MSnID.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.11.0’
* 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 ‘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 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 ... 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 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/MSnID.Rcheck/00check.log’
for details.

* installing *source* package ‘MSnID’ ...
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MSnID)

name	user	system	elapsed
MSnID-class	0.000	0.000	0.001
MSnIDFilter-class	0.392	0.008	0.377
accessions	0.308	0.000	0.308
apply_filter	0.460	0.000	0.429
assess_missed_cleavages	0.396	0.000	0.398
assess_termini	0.180	0.000	0.181
correct_peak_selection	0.080	0.000	0.082
data	0.088	0.000	0.077
evaluate_filter	0.200	0.004	0.190
id_quality	0.292	0.000	0.290
infer_parsimonious_accessions	0.756	0.020	0.756
mass_measurement_error	0.076	0.000	0.075
optimize_filter	1.516	0.060	1.472
peptides	0.068	0.000	0.068
psms	0.080	0.000	0.081
read_mzIDs	0	0	0
recalibrate	0.300	0.000	0.298