Package: isobar

Version: 1.0.0

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch isobar_1.0.0.tar.gz

StartedAt: 2012-01-09 03:51:55 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 03:54:28 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 152.8 seconds

RetCode: 0

Status:  OK

CheckDir: isobar.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/isobar.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'isobar/DESCRIPTION' ... OK
* this is package 'isobar' version '1.0.0'
* 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 whether package 'isobar' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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
.create.or.load.xls.protein.tbl : <anonymous>: no visible binding for
  global variable 'ibspectra'
.create.or.load.xls.protein.tbl : <anonymous>: no visible binding for
  global variable 'protein.tbl'
.parse.spectrum : <anonymous>: no visible binding for '<<-' assignment
  to 'observedMasses'
.parse.spectrum : <anonymous>: no visible binding for global variable
  'observedMasses'
.parse.spectrum : <anonymous>: no visible binding for '<<-' assignment
  to 'observedIntensities'
.parse.spectrum : <anonymous>: no visible binding for global variable
  'observedIntensities'
shared.ratios.sign: no visible binding for global variable 'ratio'
shared.ratios.sign: no visible binding for global variable 'proteins'
shared.ratios.sign: no visible binding for global variable 'g'
* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                    old_size new_size compress
  ibspiked_set1.rda    1.4Mb    606Kb       xz
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'isobar' ...
** R
** data
** inst
** preparing package for lazy loading
in method for 'coerce' with signature '"ProteinGroup","data.frame.concise"': no definition for class "data.frame.concise"
in method for 'coerce' with signature '"IBSpectra","data.frame.concise"': no definition for class "data.frame.concise"
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 ...
*** tangling vignette sources ...
   'isobar-devel.Rnw' 
   'isobar.Rnw' using 'UTF-8' 
** testing if installed package can be loaded

* DONE (isobar)

name	user	system	elapsed
IBSpectra-class	0.62	0.00	0.62
NoiseModel-class	21.72	0.03	21.80
ProteinGroup-class	0.23	0.00	0.23
fit-distr	1.08	0.02	1.19
groupMemberPeptides	0.38	0.00	0.38
isobar-analysis	0.22	0.00	0.22
isobar-data	0.2	0.0	0.2
isobar-import	18.59	0.11	18.76
isobar-log	2.53	0.01	2.57
isobar-plots	2.34	0.00	2.35
isobar-preprocessing	2.48	0.02	2.50
number.ranges	0	0	0
proteinInfo-methods	0.19	0.02	0.20
ratio-summ	0.24	0.00	0.24
sanitize	0	0	0
subsetIBSpectra	3.06	0.00	3.06