BioC 3.4: CHECK report for attract on moscato1

Package: attract

Version: 1.25.1

Command: rm -rf attract.buildbin-libdir attract.Rcheck && mkdir attract.buildbin-libdir attract.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=attract.buildbin-libdir attract_1.25.1.tar.gz >attract.Rcheck\00install.out 2>&1 && cp attract.Rcheck\00install.out attract-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=attract.buildbin-libdir --install="check:attract-install.out" --force-multiarch --no-vignettes --timings attract_1.25.1.tar.gz

StartedAt: 2016-09-20 04:09:29 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 04:19:12 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 583.5 seconds

RetCode: 0

Status:  OK

CheckDir: attract.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf attract.buildbin-libdir attract.Rcheck && mkdir attract.buildbin-libdir attract.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=attract.buildbin-libdir attract_1.25.1.tar.gz >attract.Rcheck\00install.out 2>&1 && cp attract.Rcheck\00install.out attract-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=attract.buildbin-libdir --install="check:attract-install.out" --force-multiarch --no-vignettes --timings attract_1.25.1.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/attract.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 'attract/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'attract' version '1.25.1'
* 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 'attract' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotsynexprs: warning in axis(1, at = tickMarks, lab = tickLabels):
  partial argument match of 'lab' to 'labels'
removeFlatGenes: warning in topTable(fit2, coef =
  (1:(length(my.contrasts))), adjust = "fdr", n = nrow(dat.fr)):
  partial argument match of 'n' to 'number'
removeFlatGenes: warning in topTable(fit2, coef =
  (1:(length(my.contrasts))), adjust = "fdr", n = nrow(dat.fr)):
  partial argument match of 'adjust' to 'adjust.method'
calcFuncSynexprs : calc.func.onesyngroup: no visible global function
  definition for 'new'
findAttractors: no visible global function definition for 'new'
findCorrPartners: no visible global function definition for 'new'
findOnepwaySynexprs: no visible global function definition for 'new'
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
calcFuncSynexprs 72.95   0.89   76.69
findAttractors   61.69   1.55   65.29
findCorrPartners  8.24   0.01    9.94
findSynexprs      7.00   0.00    8.49
plotsynexprs      6.87   0.02    8.59
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
calcFuncSynexprs 93.53   0.57   95.87
findAttractors   64.76   1.54   68.12
findCorrPartners  8.92   0.03   10.38
plotsynexprs      8.19   0.03    9.94
findSynexprs      8.08   0.00    9.53
* 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/attract.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'attract' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'attract' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'attract' as attract_1.25.1.zip
* DONE (attract)

name	user	system	elapsed
AttractorModuleSet-class	0	0	0
SynExpressionSet-class	0	0	0
attract-package	0	0	0
buildCorMatrix	0	0	0
buildKeggIncidenceMatrix	0	0	0
calcFuncSynexprs	72.95	0.89	76.69
calcInform	0	0	0
calcModfstat	0	0	0
calcRss	0	0	0
exprs.dat	0.21	0.00	0.20
filterDataSet	0.36	0.03	0.39
findAttractors	61.69	1.55	65.29
findCorrPartners	8.24	0.01	9.94
findOnepwaySynexprs	0	0	0
findSynexprs	7.00	0.00	8.49
flagPwayExists	0	0	0
getCustomGenes	0	0	0
getPwayGenes	0	0	0
loring.eset	0.18	0.00	0.19
plotsynexprs	6.87	0.02	8.59
removeFlatGenes	0.20	0.03	0.24
samp.info	0.02	0.00	0.01
subset.loring.eset	0.09	0.00	0.10

name	user	system	elapsed
AttractorModuleSet-class	0	0	0
SynExpressionSet-class	0	0	0
attract-package	0	0	0
buildCorMatrix	0	0	0
buildKeggIncidenceMatrix	0	0	0
calcFuncSynexprs	93.53	0.57	95.87
calcInform	0	0	0
calcModfstat	0	0	0
calcRss	0	0	0
exprs.dat	0.17	0.02	0.18
filterDataSet	0.32	0.02	0.33
findAttractors	64.76	1.54	68.12
findCorrPartners	8.92	0.03	10.38
findOnepwaySynexprs	0	0	0
findSynexprs	8.08	0.00	9.53
flagPwayExists	0	0	0
getCustomGenes	0	0	0
getPwayGenes	0.02	0.00	0.01
loring.eset	0.14	0.02	0.16
plotsynexprs	8.19	0.03	9.94
removeFlatGenes	0.17	0.00	0.17
samp.info	0	0	0
subset.loring.eset	0.11	0.00	0.11