BioC 3.4: CHECK report for IPO on moscato1

Package: IPO

Version: 0.99.5

Command: rm -rf IPO.buildbin-libdir IPO.Rcheck && mkdir IPO.buildbin-libdir IPO.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IPO.buildbin-libdir IPO_0.99.5.tar.gz >IPO.Rcheck\00install.out 2>&1 && cp IPO.Rcheck\00install.out IPO-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=IPO.buildbin-libdir --install="check:IPO-install.out" --force-multiarch --no-vignettes --timings IPO_0.99.5.tar.gz

StartedAt: 2016-09-20 10:48:35 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 11:00:25 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 709.3 seconds

RetCode: 0

Status:  OK

CheckDir: IPO.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf IPO.buildbin-libdir IPO.Rcheck && mkdir IPO.buildbin-libdir IPO.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IPO.buildbin-libdir IPO_0.99.5.tar.gz >IPO.Rcheck\00install.out 2>&1 && cp IPO.Rcheck\00install.out IPO-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=IPO.buildbin-libdir --install="check:IPO-install.out" --force-multiarch --no-vignettes --timings IPO_0.99.5.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/IPO.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IPO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IPO' version '0.99.5'
* 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 'IPO' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL (>= 2) + file LICENSE
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'D:/biocbld/bbs-3.4-bioc/meat/IPO.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'IPO' ...
** R
** inst
** preparing package for lazy loading
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.12.6)
than is installed on your system (0.12.7). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.12.6)
than is installed on your system (0.12.7). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.

install for x64

* installing *source* package 'IPO' ...
** testing if installed package can be loaded
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.12.6)
than is installed on your system (0.12.7). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
* MD5 sums
packaged installation of 'IPO' as IPO_0.99.5.zip
* DONE (IPO)

name	user	system	elapsed
IPO-package	0	0	0
attachList	0	0	0
calcPPS	0.78	0.03	2.73
calculateXcmsSet	0.98	0.03	1.01
combineParams	0.00	0.02	0.02
createModel	0.14	0.00	0.16
decode	0	0	0
findIsotopes.CAMERA	0.70	0.03	0.73
findIsotopes.IPO	0.96	0.03	0.99
getBbdParameter	0.01	0.00	0.01
getCcdParameter	0	0	0
getDefaultRetCorCenterSample	0	0	0
getDefaultRetGroupStartingParams	0	0	0
getDefaultXcmsSetStartingParams	0	0	0
getNormalizedResponse	0	0	0
getRGTVValues	0	0	0
optimizeRetGroup	0	0	0
optimizeXcmsSet	0	0	0
toMatrix	0	0	0
typeCastParams	0	0	0
writeParamsTable	0.01	0.00	0.01
writeRScript	0	0	0

name	user	system	elapsed
IPO-package	0	0	0
attachList	0.02	0.00	0.02
calcPPS	0.74	0.02	1.71
calculateXcmsSet	1.33	0.00	1.33
combineParams	0.01	0.00	0.02
createModel	0.19	0.00	0.19
decode	0	0	0
findIsotopes.CAMERA	0.84	0.01	0.85
findIsotopes.IPO	0.84	0.03	0.88
getBbdParameter	0.02	0.00	0.01
getCcdParameter	0	0	0
getDefaultRetCorCenterSample	0	0	0
getDefaultRetGroupStartingParams	0	0	0
getDefaultXcmsSetStartingParams	0	0	0
getNormalizedResponse	0	0	0
getRGTVValues	0	0	0
optimizeRetGroup	0	0	0
optimizeXcmsSet	0	0	0
toMatrix	0	0	0
typeCastParams	0	0	0
writeParamsTable	0	0	0
writeRScript	0.02	0.00	0.01