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BioC 3.4: CHECK report for MSnID on zin1

This page was generated on 2016-09-21 03:39:17 -0700 (Wed, 21 Sep 2016).

Package 787/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnID 1.7.3
Vlad Petyuk
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnID
Last Changed Rev: 118642 / Revision: 121152
Last Changed Date: 2016-06-15 23:19:01 -0700 (Wed, 15 Jun 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MSnID
Version: 1.7.3
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MSnID_1.7.3.tar.gz
StartedAt: 2016-09-20 09:39:57 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 09:42:39 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 162.3 seconds
RetCode: 0
Status:  OK 
CheckDir: MSnID.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MSnID_1.7.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/MSnID.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.7.3’
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... 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’
.read_mzIDs.mzR: no visible binding for global variable ‘i’
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable ‘spectrumID’
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable ‘name’
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable ‘mass’
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable ‘location’
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable ‘modification’
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable ‘DatabaseAccess’
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable ‘DatabaseDescription’
.read_mzIDs.mzR.engine.single.file: no visible binding for global
  variable ‘DBseqLength’
infer_parsimonious_accessions,MSnID : infer_acc: no visible binding for
  global variable ‘accession’
infer_parsimonious_accessions,MSnID : infer_acc: no visible binding for
  global variable ‘pepSeq’
recalibrate,MSnID: no visible global function definition for ‘median’
recalibrate,MSnID: no visible global function definition for ‘density’
Undefined global functions or variables:
  DBseqLength DatabaseAccess DatabaseDescription accession density i
  location mass median modification name optim pepSeq quantile rnorm
  spectrumID
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/MSnID.Rcheck/00check.log’
for details.


MSnID.Rcheck/00install.out:

* 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
* DONE (MSnID)

MSnID.Rcheck/MSnID-Ex.timings:

nameusersystemelapsed
MSnID-class0.0000.0000.001
MSnIDFilter-class0.4440.0120.457
accessions0.2680.0000.266
apply_filter0.4040.0000.405
assess_missed_cleavages0.1600.0080.166
assess_termini0.1760.0040.181
correct_peak_selection0.2440.0000.245
data0.0960.0000.095
evaluate_filter0.3640.0040.368
id_quality0.0880.0000.088
infer_parsimonious_accessions0.6960.0040.702
mass_measurement_error0.2360.0040.243
optimize_filter1.2920.0561.343
peptides0.0760.0000.075
psms0.2440.0000.244
read_mzIDs0.0000.0000.001
recalibrate0.0920.0000.090