Multiple platform build/check report for BioC 3.11 - CHECK report for uSORT on tokay2

Package: uSORT

Version: 1.14.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:uSORT.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings uSORT_1.14.0.tar.gz

StartedAt: 2020-10-17 09:08:42 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 09:13:19 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 276.7 seconds

RetCode: 0

Status: WARNINGS

CheckDir: uSORT.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:uSORT.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings uSORT_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/uSORT.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.14.0'
* 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-3.11-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 (user + system) or elapsed time > 5s
             user system elapsed
sWanderlust 19.72   0.23   19.96
autoSPIN    11.67   0.01   11.69
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
sWanderlust 26.02   0.08   26.11
autoSPIN    18.48   0.00   18.48
* 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-3.11-bioc/meat/uSORT.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/uSORT_1.14.0.tar.gz && rm -rf uSORT.buildbin-libdir && mkdir uSORT.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=uSORT.buildbin-libdir uSORT_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL uSORT_1.14.0.zip && rm uSORT_1.14.0.tar.gz uSORT_1.14.0.zip
###
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  % 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 1641k  100 1641k    0     0  17.7M      0 --:--:-- --:--:-- --:--:-- 19.3M

install for i386

* installing *source* package 'uSORT' ...
** using staged installation
** 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_1.14.0.zip
* DONE (uSORT)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'uSORT' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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: 0.985372
    Running iterations... 2
      Correlation with previous iteration: 0.99972
    Running iterations... 3
      Correlation with previous iteration: 0.999971
  Wanderlust Sorting Done!


RUNIT TEST PROTOCOL -- Sat Oct 17 09:12:57 2020 
*********************************************** 
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 
   5.32    0.46    5.79


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 -- Sat Oct 17 09:13:03 2020 
*********************************************** 
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 
   5.75    0.39    6.14

name	user	system	elapsed
Rwanderlust	0.62	0.02	0.64
SPIN	0.04	0.00	0.05
STS_sortingcost	0.00	0.02	0.02
autoSPIN	11.67	0.01	11.69
driving_force_gene_selection	0	0	0
elbow_detection	0	0	0
monocle_wrapper	0	0	0
neighborhood_sortingcost	0.05	0.00	0.04
pca_gene_selection	3.17	0.08	3.89
sWanderlust	19.72	0.23	19.96
uSORT	0	0	0
uSORT_GUI	0	0	0
uSORT_preProcess	1.98	0.08	2.06
uSORT_sorting_wrapper	2.27	0.13	2.39
uSORT_write_results	0	0	0

name	user	system	elapsed
Rwanderlust	0.81	0.00	0.81
SPIN	0.05	0.02	0.07
STS_sortingcost	0.00	0.01	0.02
autoSPIN	18.48	0.00	18.48
driving_force_gene_selection	0	0	0
elbow_detection	0	0	0
monocle_wrapper	0	0	0
neighborhood_sortingcost	0.08	0.00	0.08
pca_gene_selection	4.10	0.03	4.14
sWanderlust	26.02	0.08	26.11
uSORT	0	0	0
uSORT_GUI	0	0	0
uSORT_preProcess	2.06	0.00	2.06
uSORT_sorting_wrapper	2.24	0.00	2.23
uSORT_write_results	0.01	0.00	0.02

CHECK report for uSORT on tokay2

Summary

Command output

Installation output

Tests output

Example timings