BioC 2.14: CHECK report for isobar on petty

Package: isobar

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch isobar_1.10.0.tar.gz

StartedAt: 2014-10-07 22:38:22 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:43:03 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 280.9 seconds

RetCode: 0

Status:  OK

CheckDir: isobar.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch isobar_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/isobar.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘isobar/DESCRIPTION’ ... OK
* this is package ‘isobar’ version ‘1.10.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘isobar’ can be installed ... [15s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘distr’
A package should be listed in only one of these fields.
* 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.as.matrix’ ‘.as.vect’ ‘.convertPeptideModif’
  ‘.proteinGroupAsConciseDataFrame’ ‘.read.idfile’ ‘.sum.bool’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
shared.ratios.sign: no visible binding for global variable ‘ratio’
shared.ratios.sign: no visible binding for global variable ‘g’
spectra.count2: no visible binding for global variable ‘peptide’
coerce,IBSpectra-MSnSet: no visible binding for global variable ‘o’
* 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 ... [75s/76s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
NoiseModel-class 22.436  0.169  22.848
peptide.count     9.592  0.052   9.700
calculate.dNSAF   9.408  0.036   9.553
subsetIBSpectra   5.116  0.038   5.174
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/isobar.Rcheck/00check.log’
for details.

* installing *source* package ‘isobar’ ...
** R
** data
** inst
** preparing package for lazy loading
in method for ‘coerce’ with signature ‘"MSnSet","IBSpectra"’: no definition for class “MSnSet”
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “MSnSet”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (isobar)

name	user	system	elapsed
IBSpectra-class	1.094	0.048	1.143
NoiseModel-class	22.436	0.169	22.848
ProteinGroup-class	0.508	0.023	0.538
TlsParameter-class	0.002	0.000	0.003
Tlsd-class	0.003	0.001	0.004
calculate-pvalues	0.029	0.001	0.033
calculate.dNSAF	9.408	0.036	9.553
calculate.emPAI	0.719	0.019	0.791
distr-methods	0.556	0.014	0.598
fit-distr	1.827	0.046	1.979
getPtmInfo	0.001	0.000	0.001
groupMemberPeptides	0.701	0.028	0.730
isobar-analysis	0.770	0.021	0.797
isobar-data	0.413	0.018	0.431
isobar-import	2.202	0.044	2.287
isobar-log	3.555	0.043	3.616
isobar-plots	3.066	0.091	3.193
isobar-preprocessing	3.226	0.090	3.368
number.ranges	0.002	0.000	0.002
observedKnownSites	0.829	0.012	0.861
peptide.count	9.592	0.052	9.700
proteinInfo-methods	0.412	0.014	0.428
proteinNameAndDescription	0.436	0.015	0.451
ratio-summ	0.790	0.018	0.810
sanitize	0.001	0.000	0.002
spectra.count2	0.711	0.018	0.731
subsetIBSpectra	5.116	0.038	5.174
utils	0.001	0.000	0.001