BioC 3.1: CHECK report for MSnID on zin2

Package: MSnID

Version: 1.2.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings MSnID_1.2.0.tar.gz

StartedAt: 2015-10-09 03:49:27 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 03:52:16 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 168.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MSnID.Rcheck

Warnings: 3

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings MSnID_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/MSnID.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.2.0’
* 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 ... [11s/11s] WARNING
Found the following significant warnings:
  Warning: replacing previous import by ‘data.table::melt’ when loading ‘MSnID’
  Warning: replacing previous import by ‘data.table::dcast’ when loading ‘MSnID’
See ‘/home/biocbuild/bbs-3.1-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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'optimize_filter':
optimize_filter
  Code: function(filterObj, msnidObj, fdr.max, method, level, n.iter,
                 mc.cores = NULL)
  Docs: function(filterObj, msnidObj, fdr.max, method, level, n.iter)
  Argument names in code not in docs:
    mc.cores

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'optimize_filter':
  ‘mc.cores’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [9s/9s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [57s/57s]
 [57s/58s] 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: 3 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.1-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 by ‘data.table::melt’ when loading ‘MSnID’
Warning: replacing previous import by ‘data.table::dcast’ when loading ‘MSnID’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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 by ‘data.table::melt’ when loading ‘MSnID’
Warning: replacing previous import by ‘data.table::dcast’ when loading ‘MSnID’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (MSnID)

name	user	system	elapsed
MSnID-class	0.001	0.000	0.001
MSnIDFilter-class	0.461	0.004	0.468
accessions	0.260	0.000	0.261
apply_filter	0.362	0.016	0.378
assess_missed_cleavages	0.184	0.000	0.184
assess_termini	0.196	0.000	0.200
correct_peak_selection	0.280	0.000	0.283
data	0.095	0.008	0.103
evaluate_filter	0.400	0.000	0.399
id_quality	0.098	0.000	0.098
mass_measurement_error	0.09	0.00	0.09
optimize_filter	1.630	0.028	1.785
peptides	0.08	0.00	0.08
psms	0.089	0.000	0.088
read_mzIDs	0.000	0.000	0.001
recalibrate	0.098	0.000	0.098