BioC 3.3: CHECK report for MSnID on oaxaca

Package: MSnID

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSnID_1.6.0.tar.gz

StartedAt: 2016-10-13 03:58:21 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 04:02:09 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 227.2 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 --no-vignettes --timings MSnID_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/MSnID.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.6.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘reshape2::melt’ by ‘data.table::melt’ when loading ‘MSnID’
  Warning: replacing previous import ‘reshape2::dcast’ by ‘data.table::dcast’ when loading ‘MSnID’
See ‘/Users/biocbuild/bbs-3.3-bioc/meat/MSnID.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 loading without being on the library search path ... 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’
recalibrate,MSnID: no visible global function definition for ‘median’
recalibrate,MSnID: no visible global function definition for ‘density’
Undefined global functions or variables:
  density median optim quantile rnorm
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 sizes of PDF files under ‘inst/doc’ ... 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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-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
Warning: replacing previous import ‘reshape2::melt’ by ‘data.table::melt’ when loading ‘MSnID’
Warning: replacing previous import ‘reshape2::dcast’ by ‘data.table::dcast’ when loading ‘MSnID’
Creating a generic function for ‘update’ from package ‘stats’ in package ‘MSnID’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘reshape2::melt’ by ‘data.table::melt’ when loading ‘MSnID’
Warning: replacing previous import ‘reshape2::dcast’ by ‘data.table::dcast’ when loading ‘MSnID’
* DONE (MSnID)

name	user	system	elapsed
MSnID-class	0.000	0.000	0.001
MSnIDFilter-class	0.369	0.011	0.403
accessions	0.192	0.006	0.198
apply_filter	0.211	0.017	0.228
assess_missed_cleavages	0.161	0.013	0.185
assess_termini	0.379	0.018	0.398
correct_peak_selection	0.105	0.010	0.116
data	0.086	0.010	0.096
evaluate_filter	0.436	0.014	0.449
id_quality	0.085	0.009	0.094
mass_measurement_error	0.090	0.005	0.095
optimize_filter	1.381	0.143	1.721
peptides	0.085	0.009	0.094
psms	0.282	0.007	0.288
read_mzIDs	0.001	0.001	0.001
recalibrate	0.108	0.013	0.120