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BioC 3.4: CHECK report for DEGreport on tokay1

This page was generated on 2017-04-15 16:18:50 -0400 (Sat, 15 Apr 2017).

Package 311/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEGreport 1.10.1
Lorena Pantano
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/DEGreport
Last Changed Rev: 126447 / Revision: 128728
Last Changed Date: 2017-02-03 19:03:51 -0500 (Fri, 03 Feb 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
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DEGreport
Version: 1.10.1
Command: rm -rf DEGreport.buildbin-libdir DEGreport.Rcheck && mkdir DEGreport.buildbin-libdir DEGreport.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DEGreport.buildbin-libdir DEGreport_1.10.1.tar.gz >DEGreport.Rcheck\00install.out 2>&1 && cp DEGreport.Rcheck\00install.out DEGreport-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=DEGreport.buildbin-libdir --install="check:DEGreport-install.out" --force-multiarch --no-vignettes --timings DEGreport_1.10.1.tar.gz
StartedAt: 2017-04-14 21:53:19 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:55:46 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 147.3 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-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DEGreport.buildbin-libdir DEGreport_1.10.1.tar.gz >DEGreport.Rcheck\00install.out 2>&1 && cp DEGreport.Rcheck\00install.out DEGreport-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=DEGreport.buildbin-libdir --install="check:DEGreport-install.out" --force-multiarch --no-vignettes --timings DEGreport_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/DEGreport.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.10.1'
* 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 ... 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'
.mds: no visible binding for global variable 'one'
.mds: no visible binding for global variable 'two'
.mds: no visible binding for global variable 'label'
.plot_base: no visible binding for global variable 'value'
.plot_base: no visible binding for global variable 'variable'
.plot_cluster: no visible binding for global variable 'x'
.plot_cluster: no visible binding for global variable 'value'
.plot_cluster: no visible binding for global variable 'group'
.run_cluster_profiler: no visible global function definition for
  'enrichGO'
.run_cluster_profiler: no visible global function definition for
  'simplify'
.table_w_fc: no visible global function definition for 'colData'
.table_w_fc : <anonymous>: no visible global function definition for
  'results'
.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'
degPlot: no visible global function definition for 'colData'
degPlot : <anonymous>: no visible global function definition for
  'plotCounts'
degPlot : <anonymous>: no visible binding for global variable 'count'
degPlot : <anonymous>: no visible binding for global variable
  'treatment'
degResults: no visible global function definition for 'assay'
degResults: no visible global function definition for 'rlog'
degResults: no visible global function definition for 'results'
degResults: no visible global function definition for 'colData'
degResults: no visible global function definition for 'rowMax'
degVolcano: no visible binding for global variable 'logFC'
degVolcano: no visible binding for global variable 'V1'
degVolcano: no visible binding for global variable 'V2'
degVolcano: no visible binding for global variable 'adj.P.Val'
degVolcano: no visible binding for global variable 'x'
degVolcano: no visible binding for global variable 'y'
Undefined global functions or variables:
  MulticoreParam V1 V2 adj.P.Val assay bplapply coda.samples colData
  comp count enrichGO group jags.model keys label log2FoldChange logFC
  one plotCounts results rlog rowMax simplify treatment two value
  variable x y
* 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 12.86   0.23   13.09
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
degResults 13.73   0.18    13.9
* 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-3.4-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_1.10.1.zip
* DONE (DEGreport)

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

nameusersystemelapsed
degMB0.350.000.35
degMV0.330.000.32
degMean0.250.010.27
degObj000
degPR0.190.000.19
degPatterns0.800.070.86
degRank0.010.000.02
degResults12.86 0.2313.09
degVB0.450.020.47
degVar0.300.000.29
degVolcano0.650.000.66

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

nameusersystemelapsed
degMB0.390.020.40
degMV0.370.000.38
degMean0.350.010.36
degObj000
degPR0.220.000.22
degPatterns0.980.000.98
degRank0.020.000.02
degResults13.73 0.1813.90
degVB0.380.010.39
degVar0.360.000.36
degVolcano0.790.000.80