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BioC 3.3: CHECK report for MSnID on moscato2

This page was generated on 2016-10-13 12:53:06 -0700 (Thu, 13 Oct 2016).

Package 753/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnID 1.6.0
Vlad Petyuk
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/MSnID
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: MSnID
Version: 1.6.0
Command: rm -rf MSnID.buildbin-libdir MSnID.Rcheck && mkdir MSnID.buildbin-libdir MSnID.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSnID.buildbin-libdir MSnID_1.6.0.tar.gz >MSnID.Rcheck\00install.out 2>&1 && cp MSnID.Rcheck\00install.out MSnID-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=MSnID.buildbin-libdir --install="check:MSnID-install.out" --force-multiarch --no-vignettes --timings MSnID_1.6.0.tar.gz
StartedAt: 2016-10-13 06:37:25 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 06:43:49 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 383.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: MSnID.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MSnID.buildbin-libdir MSnID.Rcheck && mkdir MSnID.buildbin-libdir MSnID.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSnID.buildbin-libdir MSnID_1.6.0.tar.gz >MSnID.Rcheck\00install.out 2>&1 && cp MSnID.Rcheck\00install.out MSnID-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=MSnID.buildbin-libdir --install="check:MSnID-install.out" --force-multiarch --no-vignettes --timings MSnID_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/MSnID.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.6.0'
* 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 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 'E:/biocbld/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
* 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'E:/biocbld/bbs-3.3-bioc/meat/MSnID.Rcheck/00check.log'
for details.


MSnID.Rcheck/00install.out:


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_1.6.0.zip
* DONE (MSnID)

MSnID.Rcheck/examples_i386/MSnID-Ex.timings:

nameusersystemelapsed
MSnID-class000
MSnIDFilter-class0.690.000.90
accessions0.370.000.38
apply_filter0.440.031.11
assess_missed_cleavages0.580.000.57
assess_termini0.610.000.61
correct_peak_selection0.390.000.39
data0.390.020.41
evaluate_filter0.620.000.62
id_quality0.360.000.36
mass_measurement_error0.410.001.65
optimize_filter2.490.033.02
peptides0.160.000.15
psms0.170.000.17
read_mzIDs000
recalibrate0.390.020.41

MSnID.Rcheck/examples_x64/MSnID-Ex.timings:

nameusersystemelapsed
MSnID-class000
MSnIDFilter-class0.670.000.96
accessions0.290.000.30
apply_filter0.410.000.42
assess_missed_cleavages0.310.010.33
assess_termini0.480.020.50
correct_peak_selection0.130.000.12
data0.090.020.11
evaluate_filter0.510.030.55
id_quality0.110.000.11
mass_measurement_error0.080.030.11
optimize_filter2.010.052.19
peptides0.160.000.16
psms0.390.000.39
read_mzIDs000
recalibrate0.170.000.17