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 ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
##############################################################################
##############################################################################
###
### 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.
* 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)