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BioC 3.6: CHECK report for BLMA on tokay1

This page was generated on 2017-08-16 13:37:54 -0400 (Wed, 16 Aug 2017).

Package 146/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BLMA 1.1.0
Tin Nguyen
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BLMA
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BLMA
Version: 1.1.0
Command: rm -rf BLMA.buildbin-libdir BLMA.Rcheck && mkdir BLMA.buildbin-libdir BLMA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BLMA.buildbin-libdir BLMA_1.1.0.tar.gz >BLMA.Rcheck\00install.out 2>&1 && cp BLMA.Rcheck\00install.out BLMA-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BLMA.buildbin-libdir --install="check:BLMA-install.out" --force-multiarch --no-vignettes --timings BLMA_1.1.0.tar.gz
StartedAt: 2017-08-15 22:05:06 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:18:34 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 807.9 seconds
RetCode: 0
Status:  OK  
CheckDir: BLMA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BLMA.buildbin-libdir BLMA.Rcheck && mkdir BLMA.buildbin-libdir BLMA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BLMA.buildbin-libdir BLMA_1.1.0.tar.gz >BLMA.Rcheck\00install.out 2>&1 && cp BLMA.Rcheck\00install.out BLMA-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BLMA.buildbin-libdir --install="check:BLMA-install.out" --force-multiarch --no-vignettes --timings BLMA_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BLMA.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BLMA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BLMA' version '1.1.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'ROntoTools' 'GSA' 'PADOG' 'limma' 'graph' 'parallel' 'Biobase'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'BLMA' 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
addCLT: warning in pnorm(mean(x), 1/2, sqrt(1/(12 * n)), lower = TRUE):
  partial argument match of 'lower' to 'lower.tail'
additiveMethod: warning in pnorm(sum(x), n/2, sqrt(n/12), lower =
  TRUE): partial argument match of 'lower' to 'lower.tail'
bilevelAnalysisGeneset : <anonymous>: warning in topTable(fit2, adjust
  = "none", sort.by = "logFC", number = nrow(d) * percent, p.value =
  pCutoff): partial argument match of 'adjust' to 'adjust.method'
bilevelAnalysisPathway : <anonymous>: warning in topTable(fit2, adjust
  = "none", sort.by = "logFC", number = nrow(d) * percent, p.value =
  pCutoff): partial argument match of 'adjust' to 'adjust.method'
fisherMethod: warning in pchisq(-2 * sum(log(x)), df = 2 * length(x),
  lower = FALSE): partial argument match of 'lower' to 'lower.tail'
intraAnalysisGene : <anonymous>: warning in topTable(fit2, adjust =
  "none", sort.by = "none", number = Inf): partial argument match of
  'adjust' to 'adjust.method'
intraAnalysisGene: warning in topTable(fit2, adjust = "none", sort.by =
  "none", number = Inf): partial argument match of 'adjust' to
  'adjust.method'
bilevelAnalysisPathway : <anonymous>: no visible global function
  definition for 'Summary'
intraAnalysisGene: no visible binding for global variable 'd'
Undefined global functions or variables:
  Summary d
Consider adding
  importFrom("methods", "Summary")
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
bilevelAnalysisGeneset 180.33   0.44  180.77
bilevelAnalysisPathway  85.20   0.39   85.60
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
bilevelAnalysisGeneset 172.98   2.73  175.73
bilevelAnalysisPathway  97.06   0.42   97.49
bilevelAnalysisGene      5.71   0.11    5.81
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/BLMA.Rcheck/00check.log'
for details.


BLMA.Rcheck/00install.out:


install for i386

* installing *source* package 'BLMA' ...
** 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 'BLMA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BLMA' as BLMA_1.1.0.zip
* DONE (BLMA)

BLMA.Rcheck/examples_i386/BLMA-Ex.timings:

nameusersystemelapsed
addCLT000
bilevelAnalysisClassic0.010.000.02
bilevelAnalysisGene3.580.033.61
bilevelAnalysisGeneset180.33 0.44180.77
bilevelAnalysisPathway85.20 0.3985.60
fisherMethod000
intraAnalysisClassic000
intraAnalysisGene0.610.000.61
loadKEGGPathways2.340.012.36
stoufferMethod000

BLMA.Rcheck/examples_x64/BLMA-Ex.timings:

nameusersystemelapsed
addCLT000
bilevelAnalysisClassic000
bilevelAnalysisGene5.710.115.81
bilevelAnalysisGeneset172.98 2.73175.73
bilevelAnalysisPathway97.06 0.4297.49
fisherMethod000
intraAnalysisClassic0.020.000.01
intraAnalysisGene0.700.000.71
loadKEGGPathways2.640.002.64
stoufferMethod000