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BioC 3.6: CHECK report for DEGreport on tokay1

This page was generated on 2017-08-16 13:32:55 -0400 (Wed, 16 Aug 2017).

Package 334/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEGreport 1.13.8
Lorena Pantano
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DEGreport
Last Changed Rev: 131015 / Revision: 131943
Last Changed Date: 2017-07-06 13:48:39 -0400 (Thu, 06 Jul 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: DEGreport
Version: 1.13.8
Command: rm -rf DEGreport.buildbin-libdir DEGreport.Rcheck && mkdir DEGreport.buildbin-libdir DEGreport.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DEGreport.buildbin-libdir DEGreport_1.13.8.tar.gz >DEGreport.Rcheck\00install.out 2>&1 && cp DEGreport.Rcheck\00install.out DEGreport-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DEGreport.buildbin-libdir --install="check:DEGreport-install.out" --force-multiarch --no-vignettes --timings DEGreport_1.13.8.tar.gz
StartedAt: 2017-08-15 22:54:11 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:59:56 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 344.4 seconds
RetCode: 0
Status:  OK  
CheckDir: DEGreport.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DEGreport.buildbin-libdir DEGreport.Rcheck && mkdir DEGreport.buildbin-libdir DEGreport.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DEGreport.buildbin-libdir DEGreport_1.13.8.tar.gz >DEGreport.Rcheck\00install.out 2>&1 && cp DEGreport.Rcheck\00install.out DEGreport-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DEGreport.buildbin-libdir --install="check:DEGreport-install.out" --force-multiarch --no-vignettes --timings DEGreport_1.13.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/DEGreport.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 'DEGreport/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DEGreport' version '1.13.8'
* checking package namespace information ... NOTE
  Namespace with empty importFrom: 'S4Vectors'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'DEGreport' 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
.convertIDs: no visible global function definition for 'keys'
.run_cluster_profiler: no visible global function definition for
  'enrichGO'
.run_cluster_profiler: no visible global function definition for
  'simplify'
.table_w_fc : <anonymous>: no visible binding for global variable
  'log2FoldChange'
.table_w_fc: no visible binding for global variable 'comp'
.table_w_fc: no visible binding for global variable 'log2FoldChange'
degBI: no visible global function definition for 'bplapply'
degBI: no visible global function definition for 'MulticoreParam'
degBIcmd: no visible global function definition for 'jags.model'
degBIcmd: no visible global function definition for 'coda.samples'
degCheckFactors: no visible binding for global variable 'value'
degMDS: no visible binding for global variable 'one'
degMDS: no visible binding for global variable 'two'
degMDS: no visible binding for global variable 'label'
degPlot: no visible global function definition for
  'SummarizedExperiment'
degPlot: no visible global function definition for 'SimpleList'
degPlot: no visible binding for global variable '.'
degPlotWide : <anonymous>: no visible binding for global variable
  'count'
Undefined global functions or variables:
  . MulticoreParam SimpleList SummarizedExperiment bplapply
  coda.samples comp count enrichGO jags.model keys label log2FoldChange
  one simplify two value
* 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
degResults 7.28   0.04    7.31
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
degResults 7.39   0.04    7.44
degQC      5.86   0.02    5.87
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/DEGreport.Rcheck/00check.log'
for details.


DEGreport.Rcheck/00install.out:


install for i386

* installing *source* package 'DEGreport' ...
** 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 'DEGreport' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEGreport' as DEGreport_1.13.8.zip
* DONE (DEGreport)

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

nameusersystemelapsed
degCheckFactors2.110.042.16
degCovariates2.190.082.26
degFilter0.240.000.23
degMB0.450.030.49
degMDS1.350.051.39
degMV0.510.000.51
degMean0.230.000.23
degObj000
degPCA2.020.052.07
degPR0.190.000.19
degPatterns1.140.001.14
degPlotWide3.470.063.53
degQC3.500.033.53
degRank000
degResults7.280.047.31
degVB0.340.000.34
degVar0.270.000.27
degVolcano0.460.000.47

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

nameusersystemelapsed
degCheckFactors2.670.042.71
degCovariates2.750.072.82
degFilter0.180.010.21
degMB0.490.020.50
degMDS1.340.031.37
degMV0.640.000.64
degMean0.280.000.28
degObj0.020.000.02
degPCA1.270.091.36
degPR0.210.000.22
degPatterns1.270.021.28
degPlotWide4.370.064.44
degQC5.860.025.87
degRank000
degResults7.390.047.44
degVB0.400.000.41
degVar0.300.000.29
degVolcano0.580.020.59