BioC 3.3: CHECK report for attract on moscato2

Package: attract

Version: 1.24.0

Command: rm -rf attract.buildbin-libdir attract.Rcheck && mkdir attract.buildbin-libdir attract.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=attract.buildbin-libdir attract_1.24.0.tar.gz >attract.Rcheck\00install.out 2>&1 && cp attract.Rcheck\00install.out attract-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=attract.buildbin-libdir --install="check:attract-install.out" --force-multiarch --no-vignettes --timings attract_1.24.0.tar.gz

StartedAt: 2016-10-13 01:07:30 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 01:17:13 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 582.9 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 && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=attract.buildbin-libdir attract_1.24.0.tar.gz >attract.Rcheck\00install.out 2>&1 && cp attract.Rcheck\00install.out attract-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=attract.buildbin-libdir --install="check:attract-install.out" --force-multiarch --no-vignettes --timings attract_1.24.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-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 '1.24.0'
* 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 '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'
findAttractors: no visible global function definition for
  'count.fields'
findAttractors: no visible global function definition for 'read.table'
findAttractors : evalPway: no visible global function definition for
  't.test'
Undefined global functions or variables:
  count.fields read.table t.test
Consider adding
  importFrom("stats", "t.test")
  importFrom("utils", "count.fields", "read.table")
to your NAMESPACE file.
* 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 77.98   0.97  103.64
findCorrPartners  9.24   0.09   10.37
plotsynexprs      7.69   0.03    8.87
findSynexprs      7.58   0.02    9.08
findAttractors    6.97   0.02    8.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
calcFuncSynexprs 105.05   1.00  108.94
findCorrPartners  10.95   0.00   12.04
findAttractors    10.52   0.03   12.14
plotsynexprs      10.00   0.03   11.05
findSynexprs       9.28   0.00   10.95
* 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
  'E:/biocbld/bbs-3.3-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_1.24.0.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	77.98	0.97	103.64
calcInform	0	0	0
calcModfstat	0	0	0
calcRss	0	0	0
exprs.dat	0.19	0.00	0.19
filterDataSet	0.34	0.00	0.34
findAttractors	6.97	0.02	8.47
findCorrPartners	9.24	0.09	10.37
findOnepwaySynexprs	0	0	0
findSynexprs	7.58	0.02	9.08
flagPwayExists	0	0	0
getCustomGenes	0	0	0
getPwayGenes	0	0	0
loring.eset	0.28	0.01	0.30
plotsynexprs	7.69	0.03	8.87
removeFlatGenes	0.18	0.00	0.19
samp.info	0	0	0
subset.loring.eset	0.10	0.00	0.09

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	105.05	1.00	108.94
calcInform	0	0	0
calcModfstat	0	0	0
calcRss	0	0	0
exprs.dat	0.27	0.00	0.27
filterDataSet	0.44	0.00	0.44
findAttractors	10.52	0.03	12.14
findCorrPartners	10.95	0.00	12.04
findOnepwaySynexprs	0	0	0
findSynexprs	9.28	0.00	10.95
flagPwayExists	0	0	0
getCustomGenes	0	0	0
getPwayGenes	0	0	0
loring.eset	0.24	0.00	0.23
plotsynexprs	10.00	0.03	11.05
removeFlatGenes	0.19	0.00	0.18
samp.info	0.01	0.00	0.02
subset.loring.eset	0.13	0.00	0.13