BioC 3.1: CHECK report for MSnID on moscato2

Package: MSnID

Version: 1.2.0

Command: rm -rf MSnID.buildbin-libdir MSnID.Rcheck && mkdir MSnID.buildbin-libdir MSnID.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSnID.buildbin-libdir MSnID_1.2.0.tar.gz >MSnID.Rcheck\00install.out 2>&1 && cp MSnID.Rcheck\00install.out MSnID-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=MSnID.buildbin-libdir --install="check:MSnID-install.out" --force-multiarch --no-vignettes --timings MSnID_1.2.0.tar.gz

StartedAt: 2015-10-09 04:11:41 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 04:16:54 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 313.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MSnID.Rcheck

Warnings: 3

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### Running command:
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###   rm -rf MSnID.buildbin-libdir MSnID.Rcheck && mkdir MSnID.buildbin-libdir MSnID.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSnID.buildbin-libdir MSnID_1.2.0.tar.gz >MSnID.Rcheck\00install.out 2>&1 && cp MSnID.Rcheck\00install.out MSnID-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=MSnID.buildbin-libdir --install="check:MSnID-install.out" --force-multiarch --no-vignettes --timings MSnID_1.2.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/MSnID.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'MSnID' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import by 'data.table::dcast' when loading 'MSnID'
  Warning: replacing previous import by 'data.table::melt' when loading 'MSnID'
See 'E:/biocbld/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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [11s] OK
** running examples for arch 'x64' ... [12s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [47s]
 [47s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [66s]
 [66s] 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
  'E:/biocbld/bbs-3.1-bioc/meat/MSnID.Rcheck/00check.log'
for details.

install for i386

* 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::dcast' when loading 'MSnID'
Warning: replacing previous import by 'data.table::melt' 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::dcast' when loading 'MSnID'
Warning: replacing previous import by 'data.table::melt' when loading 'MSnID'
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'MSnID' ...
** 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'
* MD5 sums
packaged installation of 'MSnID' as MSnID_1.2.0.zip
* DONE (MSnID)

name	user	system	elapsed
MSnID-class	0	0	0
MSnIDFilter-class	0.42	0.01	0.44
accessions	0.24	0.00	0.24
apply_filter	0.32	0.02	0.35
assess_missed_cleavages	0.36	0.00	0.36
assess_termini	0.39	0.00	0.39
correct_peak_selection	0.25	0.00	0.25
data	0.25	0.00	0.25
evaluate_filter	0.42	0.00	0.42
id_quality	0.24	0.02	0.25
mass_measurement_error	0.25	0.00	0.25
optimize_filter	1.99	0.06	2.37
peptides	0.10	0.02	0.11
psms	0.09	0.01	0.11
read_mzIDs	0	0	0
recalibrate	0.12	0.00	0.13

name	user	system	elapsed
MSnID-class	0	0	0
MSnIDFilter-class	0.53	0.01	0.56
accessions	0.3	0.0	0.3
apply_filter	0.31	0.02	0.49
assess_missed_cleavages	0.53	0.00	0.53
assess_termini	0.27	0.00	0.27
correct_peak_selection	0.28	0.01	0.29
data	0.11	0.00	0.11
evaluate_filter	0.42	0.02	0.44
id_quality	0.11	0.00	0.11
mass_measurement_error	0.26	0.01	0.28
optimize_filter	1.97	0.11	2.10
peptides	0.11	0.00	0.10
psms	0.26	0.02	0.29
read_mzIDs	0	0	0
recalibrate	0.13	0.00	0.12