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CHECK report for scAlign on tokay1

This page was generated on 2019-09-20 12:36:03 -0400 (Fri, 20 Sep 2019).

Package 1480/1770HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scAlign 1.1.2
Nelson Johansen
Snapshot Date: 2019-09-19 17:00:30 -0400 (Thu, 19 Sep 2019)
URL: https://git.bioconductor.org/packages/scAlign
Branch: master
Last Commit: ce3f0bb
Last Changed Date: 2019-09-18 14:02:37 -0400 (Wed, 18 Sep 2019)
malbec1 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
merida1 OS X 10.11.6 El Capitan / x86_64  ERROR  ERROR  skipped  skipped 

Summary

Package: scAlign
Version: 1.1.2
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scAlign.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings scAlign_1.1.2.tar.gz
StartedAt: 2019-09-20 06:06:11 -0400 (Fri, 20 Sep 2019)
EndedAt: 2019-09-20 06:14:37 -0400 (Fri, 20 Sep 2019)
EllapsedTime: 505.9 seconds
RetCode: 1
Status:  ERROR  
CheckDir: scAlign.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scAlign.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings scAlign_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/scAlign.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.1.2'
* 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', 'PMA'
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 ... OK
* 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
* 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 ... 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'
scAlignCreateObject : : 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<-
* 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' ... ERROR
Running examples in 'scAlign-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PlotTSNE
> ### Title: Creates tsne plot
> ### Aliases: PlotTSNE
> 
> ### ** Examples
> 
> 
>  library(SingleCellExperiment)
> 
>  ## Input data, 1000 genes x 100 cells
>  data = matrix( rnorm(1000*100,mean=0,sd=1), 1000, 100)
>  rownames(data) = paste0("gene", seq_len(1000))
>  colnames(data) = paste0("cell", seq_len(100))
> 
>  age    = c(rep("young",50), rep("old",50))
>  labels = c(c(rep("type1",25), rep("type2",25)), c(rep("type1",25), rep("type2",25)))
> 
>  ctrl.data = data[,which(age == "young")]
>  stim.data = data[,which(age == "old")]
> 
>  ## Build the SCE object for input to scAlign using Seurat preprocessing and variable gene selection
>  ctrlSCE <- SingleCellExperiment(
+                assays = list(scale.data = data[,which(age == "young")]))
> 
>  stimSCE <- SingleCellExperiment(
+                assays = list(scale.data = data[,which(age == "old")]))
> 
>  ## Build the scAlign class object and compute PCs
>  scAlignHSC = scAlignCreateObject(sce.objects = list("YOUNG"=ctrlSCE,
+                                                      "OLD"=stimSCE),
+                                   labels = list(labels[which(age == "young")],
+                                                 labels[which(age == "old")]),
+                                   pca.reduce = FALSE,
+                                   cca.reduce = FALSE,
+                                   project.name = "scAlign_Kowalcyzk_HSC")
> 
>  ## Run scAlign with high_var_genes
>  scAlignHSC = scAlign(scAlignHSC,
+                     options=scAlignOptions(steps=100,
+                                            log.every=100,
+                                            norm=TRUE,
+                                            early.stop=FALSE),
+                     encoder.data="scale.data",
+                     supervised='none',
+                     run.encoder=TRUE,
+                     run.decoder=FALSE,
+                     log.results=FALSE,
+                     log.dir=file.path('~/models','gene_input'),
+                     device="CPU")
Error in value[[3L]](cond) : 
  Error with system install of tensorflow, check R for Tensorflow docs.
Calls: scAlign ... tryCatch -> tryCatchList -> tryCatchOne -> 
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
PlotTSNE     50.36  13.67   27.16
scAlignMulti  9.17   0.35    9.27
scAlign       7.69   0.13    7.51
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         })
     }, error = function(e) {
         stop("Error with system install of tensorflow, check R for Tensorflow docs.")
     })
  4: tryCatchList(expr, classes, parentenv, handlers)
  5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  6: value[[3L]](cond)
  7: stop("Error with system install of tensorflow, check R for Tensorflow docs.")
  
  == testthat results  ===========================================================
  [ OK: 2 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: Alignment produces consistent results (@test-scalign.R#77) 
  
  Error: testthat unit tests failed
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  [1] "Step: 100    Loss: 41.542"
  [1] "Step: 200    Loss: 38.5748"
  [1] "Step: 300    Loss: 31.1811"
  [1] "Step: 400    Loss: 33.5432"
  [1] "Step: 500    Loss: 31.7264"
  [1] "============== Alignment Complete =============="
  -- 1. Failure: Alignment produces consistent results (@test-scalign.R#96)  -----
  `class_acc` is not more than 0.5. Difference: -0.0101
  
  == testthat results  ===========================================================
  [ OK: 2 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: Alignment produces consistent results (@test-scalign.R#96) 
  
  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: 3 ERRORs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/scAlign.Rcheck/00check.log'
for details.

Installation output

scAlign.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/scAlign_1.1.2.tar.gz && rm -rf scAlign.buildbin-libdir && mkdir scAlign.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scAlign.buildbin-libdir scAlign_1.1.2.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL scAlign_1.1.2.zip && rm scAlign_1.1.2.tar.gz scAlign_1.1.2.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  635k  100  635k    0     0  15.0M      0 --:--:-- --:--:-- --:--:-- 16.7M

install for i386

* 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
    PlotTSNE                                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  
    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

install for x64

* installing *source* package 'scAlign' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scAlign' as scAlign_1.1.2.zip
* DONE (scAlign)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'scAlign' successfully unpacked and MD5 sums checked

Tests output

scAlign.Rcheck/tests_i386/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: 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)
> 
> test_check("scAlign")
Loading required package: scAlign
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
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, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: Seurat

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:DelayedArray':

    simplify

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
Loading required package: PMA
[1] "Computing CCA using Seurat."

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-- 1. Error: Alignment produces consistent results (@test-scalign.R#77)  -------
Error with system install of tensorflow, check R for Tensorflow docs.
1: scAlign(scAlignCB, options = scAlignOptions(steps = 500, log.every = 500, norm = TRUE, 
       batch.norm.layer = TRUE, early.stop = FALSE), encoder.data = "scale.data", supervised = "none", 
       run.encoder = TRUE, run.decoder = FALSE, log.dir = file.path("~/models_temp", 
           "gene_input"), device = "CPU") at testthat/test-scalign.R:77
2: .check_tensorflow()
3: tryCatch({
       with(tf$Session() %as% sess, {
           sess$run(tf$Print("", list("Passed"), "TensorFlow check: "))
       })
   }, error = function(e) {
       stop("Error with system install of tensorflow, check R for Tensorflow docs.")
   })
4: tryCatchList(expr, classes, parentenv, handlers)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: value[[3L]](cond)
7: stop("Error with system install of tensorflow, check R for Tensorflow docs.")

== testthat results  ===========================================================
[ OK: 2 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
1. Error: Alignment produces consistent results (@test-scalign.R#77) 

Error: testthat unit tests failed
Execution halted

scAlign.Rcheck/tests_x64/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-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: 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, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: Seurat

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:DelayedArray':

    simplify

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
Loading required package: PMA
C:\Python37\lib\site-packages\tensorflow\python\framework\dtypes.py:516: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint8 = np.dtype([("qint8", np.int8, 1)])
C:\Python37\lib\site-packages\tensorflow\python\framework\dtypes.py:517: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint8 = np.dtype([("quint8", np.uint8, 1)])
C:\Python37\lib\site-packages\tensorflow\python\framework\dtypes.py:518: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint16 = np.dtype([("qint16", np.int16, 1)])
C:\Python37\lib\site-packages\tensorflow\python\framework\dtypes.py:519: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint16 = np.dtype([("quint16", np.uint16, 1)])
C:\Python37\lib\site-packages\tensorflow\python\framework\dtypes.py:520: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint32 = np.dtype([("qint32", np.int32, 1)])
C:\Python37\lib\site-packages\tensorflow\python\framework\dtypes.py:525: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  np_resource = np.dtype([("resource", np.ubyte, 1)])
C:\Python37\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:541: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint8 = np.dtype([("qint8", np.int8, 1)])
C:\Python37\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:542: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint8 = np.dtype([("quint8", np.uint8, 1)])
C:\Python37\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:543: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint16 = np.dtype([("qint16", np.int16, 1)])
C:\Python37\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:544: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint16 = np.dtype([("quint16", np.uint16, 1)])
C:\Python37\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:545: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint32 = np.dtype([("qint32", np.int32, 1)])
C:\Python37\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:550: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  np_resource = np.dtype([("resource", np.ubyte, 1)])
WARNING:tensorflow:From C:\Python37\lib\site-packages\tensorflow\python\util\deprecation_wrapper.py:119: The name tf.Session is deprecated. Please use tf.compat.v1.Session instead.

2019-09-20 06:13:39.637421: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2
WARNING:tensorflow:From C:\Python37\lib\site-packages\tensorflow\python\util\deprecation.py:320: Print (from tensorflow.python.ops.logging_ops) is deprecated and will be removed after 2018-08-20.
Instructions for updating:
Use tf.print instead of tf.Print. Note that tf.print returns a no-output operator that directly prints the output. Outside of defuns or eager mode, this operator will not be executed unless it is directly specified in session.run or used as a control dependency for other operators. This is only a concern in graph mode. Below is an example of how to ensure tf.print executes in graph mode:
```python
    sess = tf.compat.v1.Session()
    with sess.as_default():
        tensor = tf.range(10)
        print_op = tf.print(tensor)
        with tf.control_dependencies([print_op]):
          out = tf.add(tensor, tensor)
        sess.run(out)
    ```
Additionally, to use tf.print in python 2.7, users must make sure to import
the following:

  `from __future__ import print_function`

TensorFlow check: [Passed]
[1] "Computing CCA using Seurat."

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TensorFlow check: [Passed]
WARNING:tensorflow:From C:\Python37\lib\site-packages\tensorflow\python\util\deprecation_wrapper.py:119: The name tf.ConfigProto is deprecated. Please use tf.compat.v1.ConfigProto instead.

WARNING:tensorflow:From C:\Python37\lib\site-packages\tensorflow\python\util\deprecation_wrapper.py:119: The name tf.GPUOptions is deprecated. Please use tf.compat.v1.GPUOptions instead.

[1] "============== Step 1/3: Encoder training ==============="
[1] "Graph construction"
WARNING:tensorflow:From C:\Python37\lib\site-packages\tensorflow\python\util\deprecation_wrapper.py:119: The name tf.placeholder is deprecated. Please use tf.compat.v1.placeholder instead.

WARNING:tensorflow:From C:\Python37\lib\site-packages\tensorflow\python\util\deprecation.py:320: DatasetV1.make_initializable_iterator (from tensorflow.python.data.ops.dataset_ops) is deprecated and will be removed in a future version.
Instructions for updating:
Use `for ... in dataset:` to iterate over a dataset. If using `tf.estimator`, return the `Dataset` object directly from your input function. As a last resort, you can use `tf.compat.v1.data.make_initializable_iterator(dataset)`.
WARNING:tensorflow:From C:\Python37\lib\site-packages\tensorflow\python\util\deprecation_wrapper.py:119: The name tf.variable_scope is deprecated. Please use tf.compat.v1.variable_scope instead.

WARNING:tensorflow:
The TensorFlow contrib module will not be included in TensorFlow 2.0.
For more information, please see:
  * https://github.com/tensorflow/community/blob/master/rfcs/20180907-contrib-sunset.md
  * https://github.com/tensorflow/addons
  * https://github.com/tensorflow/io (for I/O related ops)
If you depend on functionality not listed there, please file an issue.

WARNING:tensorflow:From C:\Python37\lib\site-packages\tensorflow\python\util\deprecation.py:320: dense (from tensorflow.python.layers.core) is deprecated and will be removed in a future version.
Instructions for updating:
Use keras.layers.dense instead.
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:From C:\Python37\lib\site-packages\tensorflow\python\util\deprecation.py:320: batch_normalization (from tensorflow.python.layers.normalization) is deprecated and will be removed in a future version.
Instructions for updating:
Use keras.layers.BatchNormalization instead.  In particular, `tf.control_dependencies(tf.GraphKeys.UPDATE_OPS)` should not be used (consult the `tf.keras.layers.batch_normalization` documentation).
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:From C:\Python37\lib\site-packages\tensorflow\python\util\deprecation.py:320: dropout (from tensorflow.python.layers.core) is deprecated and will be removed in a future version.
Instructions for updating:
Use keras.layers.dropout instead.
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:From C:\Python37\lib\site-packages\tensorflow\python\ops\init_ops.py:1251: calling VarianceScaling.__init__ (from tensorflow.python.ops.init_ops) with dtype is deprecated and will be removed in a future version.
Instructions for updating:
Call initializer instance with the dtype argument instead of passing it to the constructor
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
WARNING:tensorflow:Entity > could not be transformed and will be executed as-is. Please report this to the AutgoGraph team. When filing the bug, set the verbosity to 10 (on Linux, `export AUTOGRAPH_VERBOSITY=10`) and attach the full output. Cause: converting >: AssertionError: Bad argument number for Name: 3, expecting 4
[1] "Adding source walker loss"
WARNING:tensorflow:From C:/Users/biocbuild/bbs-3.10-bioc/R/library/reticulate/python\rpytools\call.py:13: add_dispatch_support..wrapper (from tensorflow.python.ops.array_ops) is deprecated and will be removed in a future version.
Instructions for updating:
Use tf.where in 2.0, which has the same broadcast rule as np.where
WARNING:tensorflow:From C:\Python37\lib\site-packages\tensorflow\python\util\deprecation_wrapper.py:119: The name tf.losses.softmax_cross_entropy is deprecated. Please use tf.compat.v1.losses.softmax_cross_entropy instead.

WARNING:tensorflow:From C:\Python37\lib\site-packages\tensorflow\python\util\deprecation_wrapper.py:119: The name tf.summary.histogram is deprecated. Please use tf.compat.v1.summary.histogram instead.

WARNING:tensorflow:From C:\Python37\lib\site-packages\tensorflow\python\util\deprecation_wrapper.py:119: The name tf.summary.scalar is deprecated. Please use tf.compat.v1.summary.scalar instead.

[1] "Adding target walker loss"
WARNING:tensorflow:From C:\Python37\lib\site-packages\tensorflow\python\util\deprecation_wrapper.py:119: The name tf.train.get_or_create_global_step is deprecated. Please use tf.compat.v1.train.get_or_create_global_step instead.

WARNING:tensorflow:From C:\Python37\lib\site-packages\tensorflow\python\util\deprecation_wrapper.py:119: The name tf.train.exponential_decay is deprecated. Please use tf.compat.v1.train.exponential_decay instead.

WARNING:tensorflow:From C:\Python37\lib\site-packages\tensorflow\python\util\deprecation_wrapper.py:119: The name tf.losses.get_total_loss is deprecated. Please use tf.compat.v1.losses.get_total_loss instead.

WARNING:tensorflow:From C:\Python37\lib\site-packages\tensorflow\python\util\deprecation_wrapper.py:119: The name tf.train.AdamOptimizer is deprecated. Please use tf.compat.v1.train.AdamOptimizer instead.

WARNING:tensorflow:From C:\Python37\lib\site-packages\tensorflow\python\util\deprecation_wrapper.py:119: The name tf.summary.merge_all is deprecated. Please use tf.compat.v1.summary.merge_all instead.

WARNING:tensorflow:From C:\Python37\lib\site-packages\tensorflow\python\util\deprecation_wrapper.py:119: The name tf.logging.set_verbosity is deprecated. Please use tf.compat.v1.logging.set_verbosity instead.

WARNING:tensorflow:From C:\Python37\lib\site-packages\tensorflow\python\util\deprecation_wrapper.py:119: The name tf.logging.FATAL is deprecated. Please use tf.compat.v1.logging.FATAL instead.

[1] "Done random initialization"
[1] "Step: 1    Loss: 61.1994"
[1] "Step: 100    Loss: 41.542"
[1] "Step: 200    Loss: 38.5748"
[1] "Step: 300    Loss: 31.1811"
[1] "Step: 400    Loss: 33.5432"
[1] "Step: 500    Loss: 31.7264"
[1] "============== Alignment Complete =============="
-- 1. Failure: Alignment produces consistent results (@test-scalign.R#96)  -----
`class_acc` is not more than 0.5. Difference: -0.0101

== testthat results  ===========================================================
[ OK: 2 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
1. Failure: Alignment produces consistent results (@test-scalign.R#96) 

Error: testthat unit tests failed
Execution halted

Example timings

scAlign.Rcheck/examples_i386/scAlign-Ex.timings

nameusersystemelapsed

scAlign.Rcheck/examples_x64/scAlign-Ex.timings

nameusersystemelapsed
PlotTSNE50.3613.6727.16
gaussianKernel0.650.020.56
scAlign7.690.137.51
scAlignCreateObject0.450.040.50
scAlignMulti9.170.359.27
scAlignOptions000