Nelson Johansen
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/scAlign |
| git_branch: RELEASE_3_13 |
| git_last_commit: 8ef122b |
| git_last_commit_date: 2021-05-19 12:43:01 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:21 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the scAlign package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scAlign.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1679/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scAlign 1.6.0 (landing page) Nelson Johansen
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: scAlign |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:scAlign.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings scAlign_1.6.0.tar.gz |
| StartedAt: 2021-10-15 05:05:48 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 05:09:48 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 240.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scAlign.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:scAlign.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings scAlign_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/scAlign.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'scAlign/DESCRIPTION' ... OK
* this is package 'scAlign' version '1.6.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'SingleCellExperiment', 'Seurat', 'tensorflow', 'purrr', 'irlba',
'Rtsne', 'ggplot2', 'FNN'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... 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'
PlotTSNE: no visible global function definition for 'assays'
PlotTSNE: no visible binding for global variable 'scAlignHSC'
PlotTSNE: 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'
scAlignCreateObject : <anonymous>: no visible global function
definition for 'assay'
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<- scAlignHSC
* 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 ... WARNING
Files not of a type allowed in a 'data' directory:
'DESCRIPTION' 'LICENSE' 'NAMESPACE' 'NEWS' 'README.md'
Please use e.g. 'inst/extdata' for non-R data files
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PlotTSNE 68.82 19.55 19.44
scAlignMulti 6.16 0.61 5.95
scAlign 5.41 0.43 5.06
* 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 WARNING, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/scAlign.Rcheck/00check.log'
for details.
scAlign.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch scAlign
###
##############################################################################
##############################################################################
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
* installing *source* package 'scAlign' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'scAlign'
finding HTML links ... done
GetCrit html
PlotTSNE html
RunMultiCCA html
UpdateW html
alignment_score html
cellbench html
compute_kernel_matrix html
decoderModel_add_mse_loss html
decoderModel_calc_projection html
decoderModel_create_train_op html
decoderModel_emb_to_proj html
decoderModel_train_decoder html
decoder_large html
decoder_medium html
decoder_small html
define_kernel_matrix html
dot-check_all_args html
dot-check_tensorflow html
dot-data_setup html
dot-early_stop html
dot-is.wholenumber html
dot-learning_rate html
dot-plotTSNE html
encoderModel_add_logit_loss html
encoderModel_add_semisup_loss_data_driven
html
encoderModel_calc_embedding html
encoderModel_calc_logit html
encoderModel_create_train_op html
encoderModel_data_to_embedding html
encoderModel_embedding_to_logit html
encoderModel_gaussian_kernel html
encoderModel_train_encoder html
encoderModel_train_encoder_multi html
encoder_large html
encoder_medium html
encoder_small html
gaussianKernel html
l2n html
scAlign html
scAlignArguments html
scAlignCreateObject html
scAlignMulti html
scAlignOptions 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
* DONE (scAlign)
Making 'packages.html' ... done
scAlign.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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)
>
> test_check("scAlign")
Loading required package: scAlign
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: Seurat
Attaching SeuratObject
Attaching package: 'Seurat'
The following object is masked from 'package:SummarizedExperiment':
Assays
Loading required package: tensorflow
Loading required package: purrr
Attaching package: 'purrr'
The following object is masked from 'package:GenomicRanges':
reduce
The following object is masked from 'package:IRanges':
reduce
The following object is masked from 'package:testthat':
is_null
Loading required package: irlba
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Loading required package: Rtsne
Loading required package: ggplot2
Loading required package: FNN
2021-10-15 05:09:41.197805: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2
TensorFlow check: [Passed]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
>
> proc.time()
user system elapsed
11.51 1.25 13.32
scAlign.Rcheck/scAlign-Ex.timings
| name | user | system | elapsed | |
| PlotTSNE | 68.82 | 19.55 | 19.44 | |
| gaussianKernel | 0.50 | 0.00 | 0.47 | |
| scAlign | 5.41 | 0.43 | 5.06 | |
| scAlignCreateObject | 2.54 | 0.02 | 2.56 | |
| scAlignMulti | 6.16 | 0.61 | 5.95 | |
| scAlignOptions | 0.01 | 0.00 | 0.02 | |