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BioC 3.6: CHECK report for M3Drop on tokay1

This page was generated on 2017-08-16 13:37:07 -0400 (Wed, 16 Aug 2017).

Package 746/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3Drop 1.3.0
Tallulah Andrews
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/M3Drop
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: M3Drop
Version: 1.3.0
Command: rm -rf M3Drop.buildbin-libdir M3Drop.Rcheck && mkdir M3Drop.buildbin-libdir M3Drop.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=M3Drop.buildbin-libdir M3Drop_1.3.0.tar.gz >M3Drop.Rcheck\00install.out 2>&1 && cp M3Drop.Rcheck\00install.out M3Drop-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=M3Drop.buildbin-libdir --install="check:M3Drop-install.out" --force-multiarch --no-vignettes --timings M3Drop_1.3.0.tar.gz
StartedAt: 2017-08-16 00:33:00 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:37:03 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 243.1 seconds
RetCode: 0
Status:  OK  
CheckDir: M3Drop.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf M3Drop.buildbin-libdir M3Drop.Rcheck && mkdir M3Drop.buildbin-libdir M3Drop.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=M3Drop.buildbin-libdir M3Drop_1.3.0.tar.gz >M3Drop.Rcheck\00install.out 2>&1 && cp M3Drop.Rcheck\00install.out M3Drop-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=M3Drop.buildbin-libdir --install="check:M3Drop-install.out" --force-multiarch --no-vignettes --timings M3Drop_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/M3Drop.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 'M3Drop/DESCRIPTION' ... OK
* this is package 'M3Drop' version '1.3.0'
* 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 'M3Drop' 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 ... NOTE
Package in Depends field not imported from: 'numDeriv'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bg__filter_cells: no visible binding for global variable 'x'
bg__get_extreme_residuals: no visible binding for global variable 'x'
Undefined global functions or variables:
  x
* 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 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
M3D_getmarkers   67.76   0.00   67.77
M3D_Get_Extremes 11.44   0.11   11.54
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
M3D_getmarkers   79.94   0.00   79.95
M3D_Get_Extremes 12.62   0.33   12.95
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/M3Drop.Rcheck/00check.log'
for details.


M3Drop.Rcheck/00install.out:


install for i386

* installing *source* package 'M3Drop' ...
** R
** 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 'M3Drop' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'M3Drop' as M3Drop_1.3.0.zip
* DONE (M3Drop)

M3Drop.Rcheck/examples_i386/M3Drop-Ex.timings:

nameusersystemelapsed
Brennecke_getVariableGenes2.910.053.12
Fitting_Dropout_Models000
M3D_Clean_Data0.600.050.64
M3D_Differential_Expression3.730.083.82
M3D_Dropout_Models2.720.042.76
M3D_Expression_Heatmap0.760.000.77
M3D_Get_Extremes11.44 0.1111.54
M3D_Get_Heatmap_Cell_Clusters0.760.020.78
M3D_Test_Shift2.280.012.30
M3D_ThreeSet_Venn0.180.000.17
M3D_getmarkers67.76 0.0067.77

M3Drop.Rcheck/examples_x64/M3Drop-Ex.timings:

nameusersystemelapsed
Brennecke_getVariableGenes3.020.033.05
Fitting_Dropout_Models000
M3D_Clean_Data0.790.040.81
M3D_Differential_Expression4.140.124.27
M3D_Dropout_Models2.790.062.86
M3D_Expression_Heatmap0.850.020.89
M3D_Get_Extremes12.62 0.3312.95
M3D_Get_Heatmap_Cell_Clusters1.030.001.03
M3D_Test_Shift3.300.043.35
M3D_ThreeSet_Venn0.230.000.23
M3D_getmarkers79.94 0.0079.95