Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2022-04-13 12:07:17 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for scAlign on tokay2


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? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1702/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scAlign 1.8.0  (landing page)
Nelson Johansen
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/scAlign
git_branch: RELEASE_3_14
git_last_commit: 9693380
git_last_commit_date: 2021-10-26 12:51:07 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: scAlign
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:scAlign.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings scAlign_1.8.0.tar.gz
StartedAt: 2022-04-13 02:16:50 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 02:20:34 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 224.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: scAlign.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:scAlign.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings scAlign_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/scAlign.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.8.0'
* 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 ... ERROR
Running examples in 'scAlign-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gaussianKernel
> ### Title: Computes gaussian kernel matrix
> ### Aliases: gaussianKernel
> 
> ### ** Examples
> 
> 
> ## Input data, 100 cells x 10 features
> data = matrix(sample.int(1000, 100*10, TRUE), 100, 10)
> rownames(data) = paste0("cell", seq_len(100))
> colnames(data) = paste0("gene", seq_len(10))
> 
> result = gaussianKernel(data, nrow(data))
Error in py_call_impl(callable, dots$args, dots$keywords) : 
  ValueError: Tried to convert 'shape' to a tensor and failed. Error: Cannot convert a partially known TensorShape to a Tensor: (None, 1)

Detailed traceback:
  File "C:\Python37\lib\site-packages\tensorflow_core\python\ops\array_ops.py", line 131, in reshape
    result = gen_array_ops.reshape(tensor, shape, name)
  File "C:\Python37\lib\site-packages\tensorflow_core\python\ops\gen_array_ops.py", line 8116, in reshape
    "Reshape", tensor=tensor, shape=shape, name=name)
  File "C:\Python37\lib\site-packages\tensorflow_core\python\framework\op_def_library.py", line 545, in _apply_op_helper
    (input_name, err))
Calls: gaussianKernel ... tryCatchList -> force -> <Anonymous> -> py_call_impl
Execution halted
* 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 ERROR, 1 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/scAlign.Rcheck/00check.log'
for details.


Installation output

scAlign.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch scAlign
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.14-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

Tests output

scAlign.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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

Attaching package: 'BiocGenerics'

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
2022-04-13 02:20:26.789519: 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 
  11.78    1.17   13.48 

Example timings

scAlign.Rcheck/scAlign-Ex.timings

nameusersystemelapsed
PlotTSNE5.290.957.04