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CHECK report for uSORT on tokay2

This page was generated on 2019-04-09 12:27:18 -0400 (Tue, 09 Apr 2019).

Package 1666/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
uSORT 1.9.1
Hao Chen
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/uSORT
Branch: master
Last Commit: 2f70aeb
Last Changed Date: 2019-01-04 13:53:04 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: uSORT
Version: 1.9.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:uSORT.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings uSORT_1.9.1.tar.gz
StartedAt: 2019-04-09 06:33:29 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 06:38:18 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 289.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: uSORT.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:uSORT.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings uSORT_1.9.1.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/uSORT.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'uSORT/DESCRIPTION' ... OK
* this is package 'uSORT' version '1.9.1'
* package encoding: UTF-8
* 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 'uSORT' can be installed ... WARNING
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/uSORT.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
sWanderlust        21.79   0.13   21.93
autoSPIN           13.95   0.11   14.06
pca_gene_selection  3.14   0.00   13.09
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
sWanderlust 21.36   0.05   23.66
autoSPIN    14.76   0.04   15.66
* 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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/uSORT.Rcheck/00check.log'
for details.



Installation output

uSORT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/uSORT_1.9.1.tar.gz && rm -rf uSORT.buildbin-libdir && mkdir uSORT.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=uSORT.buildbin-libdir uSORT_1.9.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL uSORT_1.9.1.zip && rm uSORT_1.9.1.tar.gz uSORT_1.9.1.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
  0 1641k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1641k  100 1641k    0     0  1994k      0 --:--:-- --:--:-- --:--:-- 2011k

install for i386

* installing *source* package 'uSORT' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Note: break used in wrong context: no loop is visible 
** help
*** installing help indices
  converting help for package 'uSORT'
    finding HTML links ... done
    EXP_to_CellDataSet                      html  
    Rwanderlust                             html  
    SPIN                                    html  
    STS_sorting                             html  
    STS_sorting_wrapper                     html  
    STS_sortingcost                         html  
    autoSPIN                                html  
    clusterGenes1                           html  
    compareModels1                          html  
    diff_test_helper1                       html  
    differentialGeneTest1                   html  
    distance.function                       html  
    driving_force_gene_selection            html  
    elbow_detection                         html  
    fluidigmSC_analyzeGeneDetection         html  
    fluidigmSC_identifyExpOutliers          html  
    fluidigmSC_isElementIgnoreCase          html  
    fluidigmSC_readLinearExp                html  
    fluidigmSC_removeGenesByLinearExpForAllType
                                            html  
    fluidigmSC_removeGenesByLinearExpForAllType_log2
                                            html  
    monocle_wrapper                         html  
    neighborhood_sorting                    html  
    neighborhood_sorting_wrapper            html  
    neighborhood_sortingcost                html  
    pca_gene_selection                      html  
    sWanderlust                             html  
    scattering_quantification_per_gene      html  
    sorting_method_parameter_GUI            html  
    summed_local_variance                   html  
    summed_local_variance_cyclical          html  
    summed_local_variance_linear            html  
    trajectory_landmarks                    html  
    uSORT                                   html  
    uSORT_GUI                               html  
    uSORT_parameters_GUI                    html  
    uSORT_preProcess                        html  
    uSORT_sorting_wrapper                   html  
    uSORT_write_results                     html  
    variability_per_gene                    html  
    wanderlust_wrapper                      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 'uSORT' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'uSORT' as uSORT_1.9.1.zip
* DONE (uSORT)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'uSORT' successfully unpacked and MD5 sums checked

Tests output

uSORT.Rcheck/tests_i386/runTests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("uSORT")
No starting point specified, the first row will be used!
  Building lNN graph...
    lNN computed in: 0 seconds
    Randomly Select waypoints...
    Flock waypoints...
  Iteratively realign trajectory: 
    Running iterations... 1
      Correlation with previous iteration: 0.985578
    Running iterations... 2
      Correlation with previous iteration: 0.999728
    Running iterations... 3
      Correlation with previous iteration: 0.999974
  Wanderlust Sorting Done!


RUNIT TEST PROTOCOL -- Tue Apr 09 06:37:53 2019 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
uSORT RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   5.39    0.46    5.84 

uSORT.Rcheck/tests_x64/runTests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("uSORT")
No starting point specified, the first row will be used!
  Building lNN graph...
    lNN computed in: 0 seconds
    Randomly Select waypoints...
    Flock waypoints...
  Iteratively realign trajectory: 
    Running iterations... 1
      Correlation with previous iteration: 0.985372
    Running iterations... 2
      Correlation with previous iteration: 0.99972
    Running iterations... 3
      Correlation with previous iteration: 0.999971
  Wanderlust Sorting Done!


RUNIT TEST PROTOCOL -- Tue Apr 09 06:38:01 2019 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
uSORT RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   6.68    0.48    7.79 

Example timings

uSORT.Rcheck/examples_i386/uSORT-Ex.timings

nameusersystemelapsed
Rwanderlust0.620.060.69
SPIN0.080.000.08
STS_sortingcost0.010.000.02
autoSPIN13.95 0.1114.06
driving_force_gene_selection000
elbow_detection000
monocle_wrapper0.000.010.02
neighborhood_sortingcost0.070.000.06
pca_gene_selection 3.14 0.0013.09
sWanderlust21.79 0.1321.93
uSORT000
uSORT_GUI000
uSORT_preProcess1.30.01.3
uSORT_sorting_wrapper2.430.032.47
uSORT_write_results000

uSORT.Rcheck/examples_x64/uSORT-Ex.timings

nameusersystemelapsed
Rwanderlust0.770.020.78
SPIN0.060.000.06
STS_sortingcost0.020.000.01
autoSPIN14.76 0.0415.66
driving_force_gene_selection000
elbow_detection000
monocle_wrapper000
neighborhood_sortingcost0.050.000.05
pca_gene_selection3.340.143.50
sWanderlust21.36 0.0523.66
uSORT000
uSORT_GUI000
uSORT_preProcess1.720.001.72
uSORT_sorting_wrapper3.160.003.15
uSORT_write_results000