Package: Sconify

Version: 1.3.1

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Sconify.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Sconify_1.3.1.tar.gz

StartedAt: 2019-04-09 05:48:04 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:50:56 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 171.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Sconify.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Sconify.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Sconify_1.3.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Sconify.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 'Sconify/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Sconify' version '1.3.1'
* 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 'Sconify' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'flowCore::view' by 'tibble::view' when loading 'Sconify'
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Sconify.Rcheck/00install.out' for details.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
SconeValues 18.44   0.02   18.46
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
SconeValues   15   0.01   15.02
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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/Sconify.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/Sconify_1.3.1.tar.gz && rm -rf Sconify.buildbin-libdir && mkdir Sconify.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Sconify.buildbin-libdir Sconify_1.3.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Sconify_1.3.1.zip && rm Sconify_1.3.1.tar.gz Sconify_1.3.1.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 3903k  100 3903k    0     0  6416k      0 --:--:-- --:--:-- --:--:-- 6494k

install for i386

* installing *source* package 'Sconify' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'flowCore::view' by 'tibble::view' when loading 'Sconify'
Note: wrong number of arguments to '/' 
Note: wrong number of arguments to 'asinh' 
** help
*** installing help indices
  converting help for package 'Sconify'
    finding HTML links ... done
    AddTsne                                 html  
    FcsToTibble                             html  
    Fnn                                     html  
    GetKnnDe                                html  
    GetMarkerNames                          html  
    Impute                                  html  
    ImputeTesting                           html  
    LogTransformQ                           html  
    MakeHist                                html  
    MakeKnnList                             html  
    MeaningOfLife                           html  
    MultipleDonorStatistics                 html  
    ParseMarkers                            html  
    PostProcessing                          html  
    ProcessMultipleFiles                    html  
    QCorrectionThresholding                 html  
    QuantNormalize                          html  
    QuantNormalizeElements                  html  
    RunStatistics                           html  
    SconeValues                             html  
    SplitFile                               html  
    StringToNumbers                         html  
    SubsampleAndTsne                        html  
    TsneVis                                 html  
    bz.gmcsf.final                          html  
    bz.gmcsf.final.norm.scale               html  
    exist                                   html  
    funct.markers                           html  
    input.markers                           html  
    markers                                 html  
    wand.combined                           html  
    wand.final                              html  
    wand.ideal.k                            html  
    wand.il7                                html  
    wand.scone                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'flowCore::view' by 'tibble::view' when loading 'Sconify'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'flowCore::view' by 'tibble::view' when loading 'Sconify'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'Sconify' ...
** testing if installed package can be loaded
Warning: replacing previous import 'flowCore::view' by 'tibble::view' when loading 'Sconify'
* MD5 sums
packaged installation of 'Sconify' as Sconify_1.3.1.zip
* DONE (Sconify)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'Sconify' successfully unpacked and MD5 sums checked

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.

> library(testthat)
> library(Sconify)
Warning message:
replacing previous import 'flowCore::view' by 'tibble::view' when loading 'Sconify' 
> 
> test_check("Sconify")
Read the 100 x 27 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000
Computing input similarities...
Building tree...
Done in 0.01 seconds (sparsity = 0.969400)!
Learning embedding...
Iteration 50: error is 51.307006 (50 iterations in 0.02 seconds)
Iteration 100: error is 51.304569 (50 iterations in 0.02 seconds)
Iteration 150: error is 51.185404 (50 iterations in 0.01 seconds)
Iteration 200: error is 53.929916 (50 iterations in 0.02 seconds)
Iteration 250: error is 50.648088 (50 iterations in 0.01 seconds)
Iteration 300: error is 1.647179 (50 iterations in 0.00 seconds)
Iteration 350: error is 1.236908 (50 iterations in 0.02 seconds)
Iteration 400: error is 0.559941 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.225498 (50 iterations in 0.02 seconds)
Iteration 500: error is 0.148656 (50 iterations in 0.02 seconds)
Iteration 550: error is 0.148795 (50 iterations in 0.00 seconds)
Iteration 600: error is 0.148284 (50 iterations in 0.00 seconds)
Iteration 650: error is 0.146528 (50 iterations in 0.02 seconds)
Iteration 700: error is 0.146981 (50 iterations in 0.02 seconds)
Iteration 750: error is 0.148942 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.148249 (50 iterations in 0.02 seconds)
Iteration 850: error is 0.149091 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.148009 (50 iterations in 0.00 seconds)
Iteration 950: error is 0.148015 (50 iterations in 0.02 seconds)
Iteration 1000: error is 0.148468 (50 iterations in 0.02 seconds)
Fitting performed in 0.25 seconds.
Read the 1000 x 27 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000
Computing input similarities...
Building tree...
Done in 0.22 seconds (sparsity = 0.129120)!
Learning embedding...
Iteration 50: error is 65.749256 (50 iterations in 0.31 seconds)
Iteration 100: error is 60.770488 (50 iterations in 0.23 seconds)
Iteration 150: error is 60.351428 (50 iterations in 0.22 seconds)
Iteration 200: error is 60.210398 (50 iterations in 0.23 seconds)
Iteration 250: error is 60.142781 (50 iterations in 0.25 seconds)
Iteration 300: error is 1.349444 (50 iterations in 0.19 seconds)
Iteration 350: error is 1.235469 (50 iterations in 0.17 seconds)
Iteration 400: error is 1.202541 (50 iterations in 0.17 seconds)
Iteration 450: error is 1.187985 (50 iterations in 0.17 seconds)
Iteration 500: error is 1.181907 (50 iterations in 0.17 seconds)
Iteration 550: error is 1.177415 (50 iterations in 0.17 seconds)
Iteration 600: error is 1.173799 (50 iterations in 0.17 seconds)
Iteration 650: error is 1.170708 (50 iterations in 0.16 seconds)
Iteration 700: error is 1.167752 (50 iterations in 0.16 seconds)
Iteration 750: error is 1.165944 (50 iterations in 0.16 seconds)
Iteration 800: error is 1.163787 (50 iterations in 0.16 seconds)
Iteration 850: error is 1.162121 (50 iterations in 0.16 seconds)
Iteration 900: error is 1.160670 (50 iterations in 0.16 seconds)
Iteration 950: error is 1.158592 (50 iterations in 0.16 seconds)
Iteration 1000: error is 1.156991 (50 iterations in 0.16 seconds)
Fitting performed in 3.72 seconds.
== testthat results  ===========================================================
OK: 72 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  17.57    0.40   18.00 

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.

> library(testthat)
> library(Sconify)
Warning message:
replacing previous import 'flowCore::view' by 'tibble::view' when loading 'Sconify' 
> 
> test_check("Sconify")
Read the 100 x 27 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000
Computing input similarities...
Building tree...
Done in 0.01 seconds (sparsity = 0.967400)!
Learning embedding...
Iteration 50: error is 50.236316 (50 iterations in 0.02 seconds)
Iteration 100: error is 52.577886 (50 iterations in 0.00 seconds)
Iteration 150: error is 54.527303 (50 iterations in 0.00 seconds)
Iteration 200: error is 50.328422 (50 iterations in 0.02 seconds)
Iteration 250: error is 52.718126 (50 iterations in 0.02 seconds)
Iteration 300: error is 1.505131 (50 iterations in 0.01 seconds)
Iteration 350: error is 1.099232 (50 iterations in 0.02 seconds)
Iteration 400: error is 0.848987 (50 iterations in 0.00 seconds)
Iteration 450: error is 0.513371 (50 iterations in 0.02 seconds)
Iteration 500: error is 0.332426 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.246356 (50 iterations in 0.00 seconds)
Iteration 600: error is 0.212012 (50 iterations in 0.00 seconds)
Iteration 650: error is 0.201043 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.197410 (50 iterations in 0.02 seconds)
Iteration 750: error is 0.178025 (50 iterations in 0.00 seconds)
Iteration 800: error is 0.179253 (50 iterations in 0.02 seconds)
Iteration 850: error is 0.181227 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.181054 (50 iterations in 0.00 seconds)
Iteration 950: error is 0.180072 (50 iterations in 0.00 seconds)
Iteration 1000: error is 0.179836 (50 iterations in 0.02 seconds)
Fitting performed in 0.19 seconds.
Read the 1000 x 27 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000
Computing input similarities...
Building tree...
Done in 0.22 seconds (sparsity = 0.129120)!
Learning embedding...
Iteration 50: error is 65.084180 (50 iterations in 0.22 seconds)
Iteration 100: error is 60.919360 (50 iterations in 0.20 seconds)
Iteration 150: error is 60.404073 (50 iterations in 0.20 seconds)
Iteration 200: error is 60.212449 (50 iterations in 0.20 seconds)
Iteration 250: error is 60.127174 (50 iterations in 0.20 seconds)
Iteration 300: error is 1.342582 (50 iterations in 0.14 seconds)
Iteration 350: error is 1.231863 (50 iterations in 0.12 seconds)
Iteration 400: error is 1.200928 (50 iterations in 0.12 seconds)
Iteration 450: error is 1.186617 (50 iterations in 0.12 seconds)
Iteration 500: error is 1.178861 (50 iterations in 0.12 seconds)
Iteration 550: error is 1.172108 (50 iterations in 0.11 seconds)
Iteration 600: error is 1.167107 (50 iterations in 0.12 seconds)
Iteration 650: error is 1.163700 (50 iterations in 0.12 seconds)
Iteration 700: error is 1.160374 (50 iterations in 0.14 seconds)
Iteration 750: error is 1.158673 (50 iterations in 0.13 seconds)
Iteration 800: error is 1.156364 (50 iterations in 0.12 seconds)
Iteration 850: error is 1.155679 (50 iterations in 0.12 seconds)
Iteration 900: error is 1.154518 (50 iterations in 0.12 seconds)
Iteration 950: error is 1.152617 (50 iterations in 0.12 seconds)
Iteration 1000: error is 1.151602 (50 iterations in 0.12 seconds)
Fitting performed in 2.92 seconds.
== testthat results  ===========================================================
OK: 72 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  17.84    0.32   18.15