Back to Multiple platform build/check report for BioC 3.10
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

CHECK report for M3Drop on tokay1

This page was generated on 2020-04-15 12:27:30 -0400 (Wed, 15 Apr 2020).

Package 933/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3Drop 1.12.0
Tallulah Andrews
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/M3Drop
Branch: RELEASE_3_10
Last Commit: 5552690
Last Changed Date: 2019-10-29 13:10:13 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: M3Drop
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:M3Drop.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings M3Drop_1.12.0.tar.gz
StartedAt: 2020-04-15 04:23:39 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:37:15 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 815.9 seconds
RetCode: 0
Status:  OK  
CheckDir: M3Drop.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:M3Drop.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings M3Drop_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/M3Drop.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.12.0'
* 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
* 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 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.
Missing or unexported object: 'scater::exprs'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
M3DropConvertData: no visible global function definition for 'assays'
NBumiConvertData: no visible global function definition for 'assays'
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:
  assays x
* checking Rd files ... NOTE
prepare_Rd: NBumi_FSOther.Rd:8-10: Dropping empty section \usage
prepare_Rd: NBumi_TradDE.Rd:7-8: Dropping empty section \usage
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
NewSimulations 149.66   2.34  152.00
Imputation     118.76   0.25  119.05
M3D_getmarkers  35.88   0.17   36.05
M3D_ConverData   5.56   0.20    7.02
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
NewSimulations 171.53   1.08  173.05
Imputation     118.63   0.11  118.78
M3D_getmarkers  45.73   0.02   45.79
M3D_ConverData   8.32   0.26    9.65
* 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-3.10-bioc/meat/M3Drop.Rcheck/00check.log'
for details.



Installation output

M3Drop.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/M3Drop_1.12.0.tar.gz && rm -rf M3Drop.buildbin-libdir && mkdir M3Drop.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=M3Drop.buildbin-libdir M3Drop_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL M3Drop_1.12.0.zip && rm M3Drop_1.12.0.tar.gz M3Drop_1.12.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 56165  100 56165    0     0  1528k      0 --:--:-- --:--:-- --:--:-- 1714k

install for i386

* installing *source* package 'M3Drop' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'M3Drop'
    finding HTML links ... done
    Brennecke_getVariableGenes              html  
    Consensus_FS                            html  
    Fitting_Dropout_Models                  html  
    Imputation                              html  
    M3D_Clean_Data                          html  
    M3D_ConverData                          html  
    M3D_Differential_Expression             html  
    M3D_Dropout_Models                      html  
    M3D_Expression_Heatmap                  html  
    M3D_Get_Extremes                        html  
    M3D_Get_Heatmap_Cell_Clusters           html  
    M3D_Plotting                            html  
    M3D_Simulations                         html  
    M3D_Test_Shift                          html  
    M3D_ThreeSet_Venn                       html  
    M3D_TraditionalDE                       html  
    M3D_calc_var                            html  
    M3D_getmarkers                          html  
    M3D_horz_res                            html  
    NBumi_CheckFit                          html  
    NBumi_CoExpression                      html  
    NBumi_CompareModels                     html  
    NBumi_ConvertToInteger                  html  
    NBumi_ConvrtData                        html  
    NBumi_FSDrop                            html  
    NBumi_FSHighVar                         html  
    NBumi_FSOther                           html  
    NBumi_FitDisp                           html  
    NBumi_FitDispVsMean                     html  
    NBumi_FitModel                          html  
    NBumi_HVG                               html  
    NBumi_TradDE                            html  
    NewSimulations                          html  
    Other_FS                                html  
    PoissonUMIFeatureSelectionDropouts      html  
    bg__fit_gamma                           html  
    bg__get_stats                           html  
    bg__mean2disp                           html  
    bg__shift_size                          html  
    bg__var_vs_drop                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'M3Drop' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'M3Drop' as M3Drop_1.12.0.zip
* DONE (M3Drop)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'M3Drop' successfully unpacked and MD5 sums checked

Tests output


Example timings

M3Drop.Rcheck/examples_i386/M3Drop-Ex.timings

nameusersystemelapsed
Brennecke_getVariableGenes2.240.212.54
Consensus_FS0.310.000.31
Fitting_Dropout_Models000
Imputation118.76 0.25119.05
M3D_Clean_Data0.940.091.03
M3D_ConverData5.560.207.02
M3D_Differential_Expression1.220.061.29
M3D_Dropout_Models1.890.132.01
M3D_Expression_Heatmap0.250.000.25
M3D_Get_Extremes1.660.061.72
M3D_Get_Heatmap_Cell_Clusters0.20.00.2
M3D_Simulations000
M3D_Test_Shift0.680.000.67
M3D_ThreeSet_Venn0.060.000.07
M3D_TraditionalDE0.010.000.01
M3D_getmarkers35.88 0.1736.05
M3D_horz_res000
NBumi_CheckFit1.680.141.81
NBumi_CoExpression1.150.191.34
NBumi_CompareModels2.550.092.64
NBumi_ConvertToInteger000
NBumi_ConvrtData0.400.030.42
NBumi_FSDrop1.590.001.59
NBumi_FSHighVar1.310.041.35
NBumi_FSOther0.020.000.01
NBumi_FitDisp000
NBumi_FitDispVsMean0.510.000.52
NBumi_FitModel1.350.011.36
NBumi_HVG0.90.00.9
NBumi_TradDE000
NewSimulations149.66 2.34152.00
Other_FS0.200.000.21
PoissonUMIFeatureSelectionDropouts0.800.000.79
bg__fit_gamma000
bg__get_stats000
bg__mean2disp000
bg__shift_size000
bg__var_vs_drop000

M3Drop.Rcheck/examples_x64/M3Drop-Ex.timings

nameusersystemelapsed
Brennecke_getVariableGenes3.330.063.39
Consensus_FS0.750.000.75
Fitting_Dropout_Models000
Imputation118.63 0.11118.78
M3D_Clean_Data1.030.131.15
M3D_ConverData8.320.269.65
M3D_Differential_Expression2.470.102.56
M3D_Dropout_Models1.110.001.11
M3D_Expression_Heatmap0.280.010.30
M3D_Get_Extremes1.840.061.91
M3D_Get_Heatmap_Cell_Clusters0.20.00.2
M3D_Simulations000
M3D_Test_Shift1.410.071.47
M3D_ThreeSet_Venn0.060.000.06
M3D_TraditionalDE0.020.000.02
M3D_getmarkers45.73 0.0245.79
M3D_horz_res000
NBumi_CheckFit2.030.062.11
NBumi_CoExpression0.860.020.88
NBumi_CompareModels2.890.062.96
NBumi_ConvertToInteger000
NBumi_ConvrtData0.550.010.57
NBumi_FSDrop1.940.072.00
NBumi_FSHighVar0.830.110.93
NBumi_FSOther0.010.000.02
NBumi_FitDisp000
NBumi_FitDispVsMean0.580.030.61
NBumi_FitModel0.830.030.86
NBumi_HVG0.860.060.92
NBumi_TradDE000
NewSimulations171.53 1.08173.05
Other_FS0.830.171.00
PoissonUMIFeatureSelectionDropouts0.790.000.79
bg__fit_gamma000
bg__get_stats000
bg__mean2disp000
bg__shift_size000
bg__var_vs_drop000