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CHECK report for scAlign on merida1

This page was generated on 2019-08-31 12:22:57 -0400 (Sat, 31 Aug 2019).

Package 1477/1766HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scAlign 1.1.1
Nelson Johansen
Snapshot Date: 2019-08-30 17:00:18 -0400 (Fri, 30 Aug 2019)
URL: https://git.bioconductor.org/packages/scAlign
Branch: master
Last Commit: ebd63db
Last Changed Date: 2019-08-09 15:04:31 -0400 (Fri, 09 Aug 2019)
malbec1 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
tokay1 Windows Server 2012 R2 Standard / x64  ERROR  ERROR  skipped  skipped 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: scAlign
Version: 1.1.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scAlign.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scAlign_1.1.1.tar.gz
StartedAt: 2019-08-31 04:58:20 -0400 (Sat, 31 Aug 2019)
EndedAt: 2019-08-31 05:04:54 -0400 (Sat, 31 Aug 2019)
EllapsedTime: 394.6 seconds
RetCode: 1
Status:  ERROR 
CheckDir: scAlign.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scAlign.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scAlign_1.1.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/scAlign.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scAlign/DESCRIPTION’ ... OK
* this is package ‘scAlign’ version ‘1.1.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘scAlign’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
* 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 ... NOTE
.check_all_args: no visible global function definition for ‘metadata’
.check_all_args: no visible global function definition for ‘assays’
.data_setup: no visible global function definition for ‘assays’
.data_setup: no visible global function definition for ‘assay’
scAlign: no visible global function definition for ‘metadata’
scAlign: no visible global function definition for ‘metadata<-’
scAlignCreateObject: no visible global function definition for
  ‘colData<-’
scAlignCreateObject: no visible global function definition for
  ‘metadata’
scAlignCreateObject: no visible global function definition for
  ‘metadata<-’
scAlignCreateObject: no visible global function definition for ‘assays’
scAlignCreateObject: no visible global function definition for ‘assay’
scAlignCreateObject: no visible global function definition for
  ‘GetCellEmbeddings’
scAlignCreateObject: no visible global function definition for
  ‘GetGeneLoadings’
scAlignMulti: no visible global function definition for ‘metadata’
scAlignMulti: no visible global function definition for ‘metadata<-’
scAlignMulti: no visible global function definition for ‘assays’
scAlignMulti: no visible global function definition for ‘assay’
Undefined global functions or variables:
  GetCellEmbeddings GetGeneLoadings assay assays colData<- metadata
  metadata<-
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'scAlignOptions':
scAlignOptions
  Code: function(steps = 15000, batch.size = 150, learning.rate =
                 1e-04, log.every = 5000, architecture = "large",
                 batch.norm.layer = FALSE, dropout.layer = TRUE,
                 num.dim = 32, perplexity = 30, betas = 0, norm = TRUE,
                 full.norm = FALSE, early.stop = FALSE, walker.loss =
                 TRUE, reconc.loss = FALSE, walker.weight = 1,
                 classifier.weight = 1, classifier.delay = NA,
                 gpu.device = "0", seed = 1234)
  Docs: function(steps = 15000, batch.size = 150, learning.rate =
                 1e-04, log.every = 5000, architecture = "large",
                 batch.norm.layer = TRUE, dropout.layer = TRUE, num.dim
                 = 32, perplexity = 30, betas = 0, norm = TRUE,
                 full.norm = FALSE, early.stop = FALSE, walker.loss =
                 TRUE, reconc.loss = FALSE, walker.weight = 1,
                 classifier.weight = 1, classifier.delay = NA,
                 gpu.device = "0", seed = 1234)
  Mismatches in argument default values:
    Name: 'batch.norm.layer' Code: FALSE Docs: TRUE

* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
PlotTSNE     55.322 31.865  17.860
scAlignMulti  7.023  0.343   6.931
scAlign       5.970  0.527   5.681
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [1] "Step: 100    Loss: 9.0929"
  [1] "Step: 200    Loss: 9.267"
  [1] "Step: 300    Loss: 8.8361"
  [1] "Step: 400    Loss: 8.8351"
  [1] "Step: 500    Loss: 8.8307"
  [1] "============== Alignment Complete =============="
  ── 1. Failure: Alignment produces consistent results (@test-scalign.R#95)  ─────
  `class_acc` is not more than 0.5. Difference: -0.307
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 2 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: Alignment produces consistent results (@test-scalign.R#95) 
  
  Error: testthat unit tests failed
  Execution halted
* 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 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/scAlign.Rcheck/00check.log’
for details.

Installation output

scAlign.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL scAlign
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘scAlign’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (scAlign)

Tests output

scAlign.Rcheck/tests/testthat.Rout.fail


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)
> 
> test_check("scAlign")
Loading required package: scAlign
TensorFlow check: [Passed]
[1] "Computing CCA using Seurat."

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TensorFlow check: [Passed]
[1] "============== Step 1/3: Encoder training ==============="
[1] "Graph construction"
[1] "Adding source walker loss"
[1] "Adding target walker loss"
[1] "Done random initialization"
[1] "Step: 1    Loss: 10.0713"
[1] "Step: 100    Loss: 9.0929"
[1] "Step: 200    Loss: 9.267"
[1] "Step: 300    Loss: 8.8361"
[1] "Step: 400    Loss: 8.8351"
[1] "Step: 500    Loss: 8.8307"
[1] "============== Alignment Complete =============="
── 1. Failure: Alignment produces consistent results (@test-scalign.R#95)  ─────
`class_acc` is not more than 0.5. Difference: -0.307

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 2 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
1. Failure: Alignment produces consistent results (@test-scalign.R#95) 

Error: testthat unit tests failed
Execution halted

Example timings

scAlign.Rcheck/scAlign-Ex.timings

nameusersystemelapsed
PlotTSNE55.32231.86517.860
gaussianKernel0.4630.0440.407
scAlign5.9700.5275.681
scAlignCreateObject0.8090.0260.836
scAlignMulti7.0230.3436.931
scAlignOptions0.0040.0010.005