Nelson Johansen
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/scAlign |
| Branch: RELEASE_3_9 |
| Last Commit: ef247aa |
| Last Changed Date: 2019-05-02 11:54:15 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:04:51 -0400 (Wed, 16 Oct 2019).
| Package 1459/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scAlign 1.0.0 Nelson Johansen
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | ERROR | ERROR | skipped | skipped | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: scAlign |
| Version: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2019-10-16 06:34:13 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:44:48 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 635.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scAlign.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-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 ‘1.0.0’
* 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 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 ... 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
* 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 ... 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 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 40.086 12.581 26.190
scAlignMulti 10.611 0.712 10.543
scAlign 9.431 0.201 9.851
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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 NOTE
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/scAlign.Rcheck/00check.log’
for details.
scAlign.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL scAlign ### ############################################################################## ############################################################################## * 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)
scAlign.Rcheck/tests/testthat.Rout
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: 71.5262 Alignment: 0.887"
[1] "Step: 100 Loss: 47.4968 Alignment: 0.7896"
[1] "Step: 200 Loss: 34.4268 Alignment: 0.7719"
[1] "Step: 300 Loss: 28.8995 Alignment: 0.7811"
[1] "Step: 400 Loss: 25.903 Alignment: 0.7808"
[1] "Step: 500 Loss: 25.0049 Alignment: 0.7755"
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 3 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
>
> proc.time()
user system elapsed
829.588 464.764 191.971
scAlign.Rcheck/scAlign-Ex.timings
| name | user | system | elapsed | |
| PlotTSNE | 40.086 | 12.581 | 26.190 | |
| gaussianKernel | 0.907 | 0.098 | 0.887 | |
| scAlign | 9.431 | 0.201 | 9.851 | |
| scAlignCreateObject | 1.298 | 0.064 | 1.378 | |
| scAlignMulti | 10.611 | 0.712 | 10.543 | |
| scAlignOptions | 0.004 | 0.001 | 0.005 | |