Tyler J Burns
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/Sconify |
| Branch: RELEASE_3_8 |
| Last Commit: 940b0c7 |
| Last Changed Date: 2019-01-04 13:49:48 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:29:04 -0400 (Sat, 13 Apr 2019).
| Package 1402/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Sconify 1.2.1 Tyler J Burns
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: Sconify |
| Version: 1.2.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Sconify.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Sconify_1.2.1.tar.gz |
| StartedAt: 2019-04-13 05:21:04 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 05:24:41 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 217.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Sconify.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Sconify.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Sconify_1.2.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/Sconify.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.2.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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-3.8-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 16.38 0.05 16.43
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
SconeValues 15.36 0 15.36
* 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-3.8-bioc/meat/Sconify.Rcheck/00check.log'
for details.
Sconify.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/Sconify_1.2.1.tar.gz && rm -rf Sconify.buildbin-libdir && mkdir Sconify.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Sconify.buildbin-libdir Sconify_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL Sconify_1.2.1.zip && rm Sconify_1.2.1.tar.gz Sconify_1.2.1.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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 3907k 100 3907k 0 0 49.5M 0 --:--:-- --:--:-- --:--:-- 51.5M
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
Warning: replacing previous import 'flowCore::view' by 'tibble::view' when loading 'Sconify'
In R CMD INSTALL
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_1.2.1.zip
* DONE (Sconify)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'Sconify' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
Sconify.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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 0.02 seconds (sparsity = 0.966800)!
Learning embedding...
Iteration 50: error is 53.372795 (50 iterations in 0.03 seconds)
Iteration 100: error is 49.428287 (50 iterations in 0.02 seconds)
Iteration 150: error is 53.596468 (50 iterations in 0.01 seconds)
Iteration 200: error is 51.375760 (50 iterations in 0.02 seconds)
Iteration 250: error is 54.796896 (50 iterations in 0.03 seconds)
Iteration 300: error is 1.207049 (50 iterations in 0.02 seconds)
Iteration 350: error is 0.338639 (50 iterations in 0.02 seconds)
Iteration 400: error is 0.209484 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.202799 (50 iterations in 0.02 seconds)
Iteration 500: error is 0.180327 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.177162 (50 iterations in 0.02 seconds)
Iteration 600: error is 0.170801 (50 iterations in 0.00 seconds)
Iteration 650: error is 0.171840 (50 iterations in 0.00 seconds)
Iteration 700: error is 0.171266 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.171872 (50 iterations in 0.02 seconds)
Iteration 800: error is 0.170119 (50 iterations in 0.02 seconds)
Iteration 850: error is 0.169780 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.171110 (50 iterations in 0.02 seconds)
Iteration 950: error is 0.172480 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.172774 (50 iterations in 0.02 seconds)
Fitting performed in 0.31 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 0.23 seconds (sparsity = 0.129120)!
Learning embedding...
Iteration 50: error is 64.513064 (50 iterations in 0.33 seconds)
Iteration 100: error is 60.646861 (50 iterations in 0.23 seconds)
Iteration 150: error is 60.287010 (50 iterations in 0.23 seconds)
Iteration 200: error is 60.165518 (50 iterations in 0.25 seconds)
Iteration 250: error is 60.107585 (50 iterations in 0.25 seconds)
Iteration 300: error is 1.345357 (50 iterations in 0.19 seconds)
Iteration 350: error is 1.238910 (50 iterations in 0.19 seconds)
Iteration 400: error is 1.205141 (50 iterations in 0.17 seconds)
Iteration 450: error is 1.193526 (50 iterations in 0.17 seconds)
Iteration 500: error is 1.186653 (50 iterations in 0.17 seconds)
Iteration 550: error is 1.181970 (50 iterations in 0.17 seconds)
Iteration 600: error is 1.176705 (50 iterations in 0.17 seconds)
Iteration 650: error is 1.172287 (50 iterations in 0.17 seconds)
Iteration 700: error is 1.169272 (50 iterations in 0.17 seconds)
Iteration 750: error is 1.166801 (50 iterations in 0.17 seconds)
Iteration 800: error is 1.164774 (50 iterations in 0.17 seconds)
Iteration 850: error is 1.163117 (50 iterations in 0.17 seconds)
Iteration 900: error is 1.162166 (50 iterations in 0.17 seconds)
Iteration 950: error is 1.160573 (50 iterations in 0.17 seconds)
Iteration 1000: error is 1.159279 (50 iterations in 0.17 seconds)
Fitting performed in 3.91 seconds.
== testthat results ===========================================================
OK: 72 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
20.70 0.46 21.14
|
Sconify.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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 0.02 seconds (sparsity = 0.964800)!
Learning embedding...
Iteration 50: error is 53.372867 (50 iterations in 0.02 seconds)
Iteration 100: error is 50.647447 (50 iterations in 0.01 seconds)
Iteration 150: error is 53.577251 (50 iterations in 0.02 seconds)
Iteration 200: error is 53.744513 (50 iterations in 0.01 seconds)
Iteration 250: error is 53.239776 (50 iterations in 0.02 seconds)
Iteration 300: error is 1.584865 (50 iterations in 0.02 seconds)
Iteration 350: error is 1.215493 (50 iterations in 0.01 seconds)
Iteration 400: error is 0.922714 (50 iterations in 0.00 seconds)
Iteration 450: error is 0.614236 (50 iterations in 0.02 seconds)
Iteration 500: error is 0.246677 (50 iterations in 0.02 seconds)
Iteration 550: error is 0.187553 (50 iterations in 0.00 seconds)
Iteration 600: error is 0.185667 (50 iterations in 0.01 seconds)
Iteration 650: error is 0.168665 (50 iterations in 0.02 seconds)
Iteration 700: error is 0.166504 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.165694 (50 iterations in 0.00 seconds)
Iteration 800: error is 0.165511 (50 iterations in 0.02 seconds)
Iteration 850: error is 0.164504 (50 iterations in 0.02 seconds)
Iteration 900: error is 0.166452 (50 iterations in 0.00 seconds)
Iteration 950: error is 0.165577 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.165580 (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 64.868386 (50 iterations in 0.25 seconds)
Iteration 100: error is 60.643398 (50 iterations in 0.17 seconds)
Iteration 150: error is 60.280059 (50 iterations in 0.19 seconds)
Iteration 200: error is 60.161243 (50 iterations in 0.19 seconds)
Iteration 250: error is 60.103916 (50 iterations in 0.20 seconds)
Iteration 300: error is 1.332839 (50 iterations in 0.14 seconds)
Iteration 350: error is 1.231967 (50 iterations in 0.14 seconds)
Iteration 400: error is 1.201398 (50 iterations in 0.16 seconds)
Iteration 450: error is 1.188392 (50 iterations in 0.16 seconds)
Iteration 500: error is 1.179567 (50 iterations in 0.16 seconds)
Iteration 550: error is 1.173760 (50 iterations in 0.16 seconds)
Iteration 600: error is 1.170859 (50 iterations in 0.16 seconds)
Iteration 650: error is 1.168283 (50 iterations in 0.16 seconds)
Iteration 700: error is 1.166202 (50 iterations in 0.16 seconds)
Iteration 750: error is 1.164666 (50 iterations in 0.16 seconds)
Iteration 800: error is 1.161817 (50 iterations in 0.16 seconds)
Iteration 850: error is 1.158717 (50 iterations in 0.16 seconds)
Iteration 900: error is 1.156903 (50 iterations in 0.14 seconds)
Iteration 950: error is 1.155697 (50 iterations in 0.14 seconds)
Iteration 1000: error is 1.154032 (50 iterations in 0.16 seconds)
Fitting performed in 3.28 seconds.
== testthat results ===========================================================
OK: 72 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
19.60 0.29 19.89
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Sconify.Rcheck/examples_i386/Sconify-Ex.timings
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Sconify.Rcheck/examples_x64/Sconify-Ex.timings
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