BioC 3.2: CHECK report for MSnID on moscato1

Package: MSnID

Version: 1.4.0

Command: rm -rf MSnID.buildbin-libdir MSnID.Rcheck && mkdir MSnID.buildbin-libdir MSnID.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSnID.buildbin-libdir MSnID_1.4.0.tar.gz >MSnID.Rcheck\00install.out 2>&1 && cp MSnID.Rcheck\00install.out MSnID-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MSnID.buildbin-libdir --install="check:MSnID-install.out" --force-multiarch --no-vignettes --timings MSnID_1.4.0.tar.gz

StartedAt: 2016-04-23 05:08:20 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 05:16:06 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 466.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MSnID.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf MSnID.buildbin-libdir MSnID.Rcheck && mkdir MSnID.buildbin-libdir MSnID.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSnID.buildbin-libdir MSnID_1.4.0.tar.gz >MSnID.Rcheck\00install.out 2>&1 && cp MSnID.Rcheck\00install.out MSnID-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MSnID.buildbin-libdir --install="check:MSnID-install.out" --force-multiarch --no-vignettes --timings MSnID_1.4.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/MSnID.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.4.0'
* 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 'reshape2::dcast' by 'data.table::dcast' when loading 'MSnID'
  Warning: replacing previous import 'reshape2::melt' by 'data.table::melt' when loading 'MSnID'
See 'D:/biocbld/bbs-3.2-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 ... 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 ...
** running examples for arch 'i386' ... [16s] OK
** running examples for arch 'x64' ... [19s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [74s]
 [76s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [80s]
 [80s] 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
  'D:/biocbld/bbs-3.2-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 'reshape2::dcast' by 'data.table::dcast' when loading 'MSnID'
Warning: replacing previous import 'reshape2::melt' by 'data.table::melt' 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::dcast' by 'data.table::dcast' when loading 'MSnID'
Warning: replacing previous import 'reshape2::melt' by 'data.table::melt' when loading 'MSnID'

install for x64

* installing *source* package 'MSnID' ...
** 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'
* MD5 sums
packaged installation of 'MSnID' as MSnID_1.4.0.zip
* DONE (MSnID)

name	user	system	elapsed
MSnID-class	0	0	0
MSnIDFilter-class	0.50	0.02	0.57
accessions	0.34	0.02	0.36
apply_filter	0.39	0.01	0.41
assess_missed_cleavages	0.48	0.02	0.50
assess_termini	0.44	0.01	0.46
correct_peak_selection	0.31	0.02	0.32
data	0.33	0.00	0.33
evaluate_filter	0.75	0.00	0.75
id_quality	0.42	0.00	0.42
mass_measurement_error	0.32	0.00	0.34
optimize_filter	2.25	0.01	2.31
peptides	0.16	0.02	0.17
psms	0.46	0.01	0.49
read_mzIDs	0	0	0
recalibrate	0.30	0.00	0.29

name	user	system	elapsed
MSnID-class	0	0	0
MSnIDFilter-class	0.87	0.00	1.84
accessions	0.41	0.00	0.41
apply_filter	0.58	0.01	0.69
assess_missed_cleavages	0.42	0.02	0.43
assess_termini	0.43	0.01	0.46
correct_peak_selection	0.47	0.00	0.46
data	0.13	0.02	0.14
evaluate_filter	0.42	0.01	0.44
id_quality	0.2	0.0	0.2
mass_measurement_error	0.48	0.00	0.49
optimize_filter	2.29	0.02	2.45
peptides	0.13	0.01	0.14
psms	0.43	0.00	0.44
read_mzIDs	0	0	0
recalibrate	0.17	0.02	0.18