BioC 3.5: CHECK report for isobar on tokay2

Package: isobar

Version: 1.22.0

Command: rm -rf isobar.buildbin-libdir isobar.Rcheck && mkdir isobar.buildbin-libdir isobar.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=isobar.buildbin-libdir isobar_1.22.0.tar.gz >isobar.Rcheck\00install.out 2>&1 && cp isobar.Rcheck\00install.out isobar-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=isobar.buildbin-libdir --install="check:isobar-install.out" --force-multiarch --no-vignettes --timings isobar_1.22.0.tar.gz

StartedAt: 2017-10-18 00:47:39 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:52:13 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 274.7 seconds

RetCode: 0

Status:  OK

CheckDir: isobar.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf isobar.buildbin-libdir isobar.Rcheck && mkdir isobar.buildbin-libdir isobar.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=isobar.buildbin-libdir isobar_1.22.0.tar.gz >isobar.Rcheck\00install.out 2>&1 && cp isobar.Rcheck\00install.out isobar-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=isobar.buildbin-libdir --install="check:isobar-install.out" --force-multiarch --no-vignettes --timings isobar_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/isobar.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'isobar/DESCRIPTION' ... OK
* this is package 'isobar' version '1.22.0'
* 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 'isobar' 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
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.calcProbXGreaterThanY.orig: no visible global function definition for
  'd'
.plot.pairs: possible error in
  png(sprintf("pairwise_correlation_%s.png", name), title = "Pairwise
  Correlation plot", width = 1000, height = 1000, pointsize = 14):
  unused argument (title = "Pairwise Correlation plot")
.read.peaklist: no visible binding for global variable 'type'
.round.distr: no visible global function definition for 'param'
.write.summarized.table: no visible binding for global variable 'name'
distrprint: no visible global function definition for 'param'
distrprint : <anonymous>: no visible global function definition for
  'param'
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'
twodistr.plot: no visible global function definition for 'd'
ProteinGroup,data.frame-missing: no visible binding for global variable
  'peptide'
coerce,IBSpectra-MSnSet: no visible global function definition for 'mz'
coerce,IBSpectra-MSnSet: no visible binding for global variable 'o'
coerce,MSnSet-IBSpectra: no visible global function definition for
  'qual'
df,Tlsd: no visible global function definition for 'param'
estimateRatio,IBSpectra-ANY-missing-missing-character-missing: no
  visible binding for global variable 'i'
estimateRatio,IBSpectra-ANY-missing-missing-missing-character: no
  visible binding for global variable 'i'
estimateRatioNumeric,numeric-numeric-NoiseModel: no visible binding for
  global variable 'center.var'
location,Tlsd: no visible global function definition for 'param'
plotRatio,IBSpectra-character-character-character: no visible binding
  for global variable 'pch'
plotRatio,IBSpectra-character-character-character: no visible binding
  for global variable 'noise.model.col'
plotRatio,IBSpectra-character-character-character: no visible binding
  for global variable 'pch.p'
scale,Tlsd: no visible global function definition for 'param'
Undefined global functions or variables:
  center.var d g i mz name noise.model.col o param pch pch.p peptide
  qual ratio type
* 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
Examples with CPU or elapsed time > 5s
                 user system elapsed
NoiseModel-class   14   0.12   14.14
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
NoiseModel-class 13.99   0.03   14.03
fit-distr         4.97   0.07    5.05
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/isobar.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'isobar' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'isobar' as isobar_1.22.0.zip
* DONE (isobar)

name	user	system	elapsed
IBSpectra-class	0.69	0.05	0.74
NoiseModel-class	14.00	0.12	14.14
ProteinGroup-class	0.28	0.00	0.28
TlsParameter-class	0	0	0
Tlsd-class	0	0	0
calculate-pvalues	0.03	0.00	0.03
calculate.dNSAF	2.61	0.00	2.61
calculate.emPAI	0.69	0.01	0.80
distr-methods	0.07	0.00	0.32
fit-distr	3.60	0.25	3.85
getPtmInfo	0	0	0
groupMemberPeptides	0.42	0.03	0.45
isobar-analysis	0.33	0.05	0.38
isobar-data	0.28	0.00	0.28
isobar-import	1.81	0.03	1.84
isobar-log	1.63	0.00	1.63
isobar-plots	1.61	0.03	1.64
isobar-preprocessing	2.39	0.03	2.42
number.ranges	0	0	0
observedKnownSites	0.36	0.00	0.36
peptide.count	3.39	0.00	3.39
proteinInfo-methods	0.23	0.00	0.23
proteinNameAndDescription	0.36	0.02	0.38
ratio-summ	0.70	0.01	0.72
sanitize	0	0	0
spectra.count2	0.49	0.00	0.48
subsetIBSpectra	2.14	0.02	2.16
utils	0	0	0

name	user	system	elapsed
IBSpectra-class	0.94	0.04	0.98
NoiseModel-class	13.99	0.03	14.03
ProteinGroup-class	0.42	0.00	0.42
TlsParameter-class	0	0	0
Tlsd-class	0	0	0
calculate-pvalues	0.06	0.00	0.06
calculate.dNSAF	3.52	0.00	3.52
calculate.emPAI	0.84	0.04	0.87
distr-methods	0.06	0.03	0.09
fit-distr	4.97	0.07	5.05
getPtmInfo	0	0	0
groupMemberPeptides	0.58	0.00	0.57
isobar-analysis	0.40	0.02	0.43
isobar-data	0.33	0.02	0.34
isobar-import	1.86	0.00	1.86
isobar-log	2.56	0.00	2.56
isobar-plots	1.92	0.11	2.03
isobar-preprocessing	2.18	0.03	2.21
number.ranges	0	0	0
observedKnownSites	0.53	0.00	0.53
peptide.count	3.22	0.00	3.22
proteinInfo-methods	0.21	0.00	0.22
proteinNameAndDescription	0.27	0.00	0.26
ratio-summ	0.58	0.00	0.58
sanitize	0	0	0
spectra.count2	0.31	0.00	0.31
subsetIBSpectra	1.78	0.00	1.78
utils	0	0	0