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BioC 3.5: CHECK report for M3Drop on tokay2

This page was generated on 2017-10-18 14:26:37 -0400 (Wed, 18 Oct 2017).

Package 736/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3Drop 1.2.0
Tallulah Andrews
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/M3Drop
Branch: RELEASE_3_5
Last Commit: d007dcf
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: M3Drop
Version: 1.2.0
Command: rm -rf M3Drop.buildbin-libdir M3Drop.Rcheck && mkdir M3Drop.buildbin-libdir M3Drop.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=M3Drop.buildbin-libdir M3Drop_1.2.0.tar.gz >M3Drop.Rcheck\00install.out 2>&1 && cp M3Drop.Rcheck\00install.out M3Drop-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=M3Drop.buildbin-libdir --install="check:M3Drop-install.out" --force-multiarch --no-vignettes --timings M3Drop_1.2.0.tar.gz
StartedAt: 2017-10-18 01:00:07 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 01:04:38 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 271.1 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-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=M3Drop.buildbin-libdir M3Drop_1.2.0.tar.gz >M3Drop.Rcheck\00install.out 2>&1 && cp M3Drop.Rcheck\00install.out M3Drop-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=M3Drop.buildbin-libdir --install="check:M3Drop-install.out" --force-multiarch --no-vignettes --timings M3Drop_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/M3Drop.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.2.0'
* 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   61.51   0.02   61.53
M3D_Get_Extremes 11.77   0.35   12.11
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
M3D_getmarkers   82.56   0.00   82.56
M3D_Get_Extremes 12.87   0.19   13.06
* 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-3.5-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_1.2.0.zip
* DONE (M3Drop)

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

nameusersystemelapsed
Brennecke_getVariableGenes2.970.043.03
Fitting_Dropout_Models000
M3D_Clean_Data0.580.040.61
M3D_Differential_Expression3.810.153.97
M3D_Dropout_Models2.550.062.61
M3D_Expression_Heatmap0.750.000.75
M3D_Get_Extremes11.77 0.3512.11
M3D_Get_Heatmap_Cell_Clusters0.790.010.81
M3D_Test_Shift2.350.022.36
M3D_ThreeSet_Venn0.160.000.15
M3D_getmarkers61.51 0.0261.53

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

nameusersystemelapsed
Brennecke_getVariableGenes3.420.063.48
Fitting_Dropout_Models000
M3D_Clean_Data0.850.151.02
M3D_Differential_Expression4.320.184.48
M3D_Dropout_Models3.300.123.42
M3D_Expression_Heatmap0.910.000.91
M3D_Get_Extremes12.87 0.1913.06
M3D_Get_Heatmap_Cell_Clusters0.920.010.94
M3D_Test_Shift2.500.072.56
M3D_ThreeSet_Venn0.190.000.19
M3D_getmarkers82.56 0.0082.56