BioC 3.2: CHECK report for MSnID on moscato1

Package: MSnID

Version: 1.3.1

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_1.3.1.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_1.3.1.tar.gz

StartedAt: 2015-08-20 07:43:06 -0700 (Thu, 20 Aug 2015)

EndedAt: 2015-08-20 07:49:25 -0700 (Thu, 20 Aug 2015)

EllapsedTime: 379.4 seconds

RetCode: 0

Status:  OK

CheckDir: MSnID.Rcheck

Warnings: 0

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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_1.3.1.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_1.3.1.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-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 '1.3.1'
* 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 ... OK
* 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' ... [15s] OK
** running examples for arch 'x64' ... [15s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [59s]
 [60s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [72s]
 [72s] 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
  '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
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

install for x64

* installing *source* package 'MSnID' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSnID' as MSnID_1.3.1.zip
* DONE (MSnID)

name	user	system	elapsed
MSnID-class	0	0	0
MSnIDFilter-class	0.54	0.02	0.58
accessions	0.35	0.00	0.34
apply_filter	0.31	0.01	0.33
assess_missed_cleavages	0.56	0.00	0.56
assess_termini	0.61	0.00	0.61
correct_peak_selection	0.37	0.00	0.37
data	0.35	0.00	0.36
evaluate_filter	0.66	0.02	0.67
id_quality	0.23	0.00	0.24
mass_measurement_error	0.22	0.02	0.23
optimize_filter	2.76	0.11	2.89
peptides	0.16	0.01	0.17
psms	0.19	0.00	0.19
read_mzIDs	0	0	0
recalibrate	0.12	0.00	0.12

name	user	system	elapsed
MSnID-class	0	0	0
MSnIDFilter-class	0.69	0.01	0.70
accessions	0.30	0.00	0.29
apply_filter	0.53	0.03	0.58
assess_missed_cleavages	0.45	0.00	0.45
assess_termini	0.38	0.00	0.38
correct_peak_selection	0.4	0.0	0.4
data	0.16	0.02	0.17
evaluate_filter	0.58	0.01	0.60
id_quality	0.14	0.02	0.15
mass_measurement_error	0.11	0.03	0.14
optimize_filter	2.98	0.10	3.33
peptides	0.13	0.01	0.14
psms	0.12	0.00	0.13
read_mzIDs	0	0	0
recalibrate	0.13	0.00	0.12