##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:scAlign.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings scAlign_1.4.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/scAlign.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scAlign/DESCRIPTION’ ... OK
* this is package ‘scAlign’ version ‘1.4.0’
* 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 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’
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 ... WARNING
Codoc mismatches from documentation object 'PlotTSNE':
PlotTSNE
  Code: function(object, data.use, labels.use = "scAlign.labels", cols
                 = NULL, title = "", legend = "none", point.size = 3,
                 seed = 1234, ...)
  Docs: function(object, data.use, labels.use = "scAlign.labels", cols
                 = NULL, title = "", legend = "none", seed = 1234, ...)
  Argument names in code not in docs:
    point.size
  Mismatches in argument names:
    Position: 7 Code: point.size Docs: seed
    Position: 8 Code: seed Docs: ...

Codoc mismatches from documentation object 'scAlignCreateObject':
scAlignCreateObject
  Code: function(sce.objects, genes.use = NULL, labels = list(),
                 pca.reduce = FALSE, pcs.compute = 20, cca.reduce =
                 FALSE, ccs.compute = 15, cca.standardize = TRUE,
                 data.use = "scale.data", project.name =
                 "scAlignProject")
  Docs: function(sce.objects, genes.use = NULL, labels = list(),
                 pca.reduce = FALSE, pcs.compute = 20, cca.reduce =
                 FALSE, ccs.compute = 15, data.use = "scale.data",
                 project.name = "scAlignProject")
  Argument names in code not in docs:
    cca.standardize
  Mismatches in argument names:
    Position: 8 Code: cca.standardize Docs: data.use
    Position: 9 Code: data.use Docs: project.name

Codoc mismatches from documentation object 'scAlignOptions':
scAlignOptions
  Code: function(steps = 15000, steps.decoder = 10000, 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 = 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)
  Argument names in code not in docs:
    steps.decoder
  Mismatches in argument names (first 3):
    Position: 2 Code: steps.decoder Docs: batch.size
    Position: 3 Code: batch.size Docs: learning.rate
    Position: 4 Code: learning.rate Docs: log.every

* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
PlotTSNE 40.228  6.276  31.378
scAlign   5.512  0.056   5.308
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/scAlign.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL scAlign
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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)

R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
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
WARNING:tensorflow:From /home/biocbuild/.virtualenvs/r-reticulate/local/lib/python2.7/site-packages/tensorflow/python/util/deprecation_wrapper.py:119: The name tf.Session is deprecated. Please use tf.compat.v1.Session instead.

2021-05-06 05:44:36.090334: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2021-05-06 05:44:36.118213: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2397315000 Hz
2021-05-06 05:44:36.119228: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x55ab6031fc70 executing computations on platform Host. Devices:
2021-05-06 05:44:36.119268: I tensorflow/compiler/xla/service/service.cc:175]   StreamExecutor device (0): <undefined>, <undefined>
TensorFlow check: [Passed]
[1] "Computing CCA using Seurat."

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TensorFlow check: [Passed]
WARNING:tensorflow:From /home/biocbuild/.virtualenvs/r-reticulate/local/lib/python2.7/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 /home/biocbuild/.virtualenvs/r-reticulate/local/lib/python2.7/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 /home/biocbuild/.virtualenvs/r-reticulate/local/lib/python2.7/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 /home/biocbuild/.virtualenvs/r-reticulate/local/lib/python2.7/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.

[1] "Adding source walker loss"
WARNING:tensorflow:From /home/biocbuild/.virtualenvs/r-reticulate/local/lib/python2.7/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 /home/biocbuild/.virtualenvs/r-reticulate/local/lib/python2.7/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 /home/biocbuild/.virtualenvs/r-reticulate/local/lib/python2.7/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 /home/biocbuild/.virtualenvs/r-reticulate/local/lib/python2.7/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 /home/biocbuild/.virtualenvs/r-reticulate/local/lib/python2.7/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 /home/biocbuild/.virtualenvs/r-reticulate/local/lib/python2.7/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 /home/biocbuild/.virtualenvs/r-reticulate/local/lib/python2.7/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 /home/biocbuild/.virtualenvs/r-reticulate/local/lib/python2.7/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 /home/biocbuild/.virtualenvs/r-reticulate/local/lib/python2.7/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 /home/biocbuild/.virtualenvs/r-reticulate/local/lib/python2.7/site-packages/tensorflow/python/util/deprecation_wrapper.py:119: The name tf.logging.FATAL is deprecated. Please use tf.compat.v1.logging.FATAL instead.

2021-05-06 05:44:45.426440: W tensorflow/compiler/jit/mark_for_compilation_pass.cc:1412] (One-time warning): Not using XLA:CPU for cluster because envvar TF_XLA_FLAGS=--tf_xla_cpu_global_jit was not set.  If you want XLA:CPU, either set that envvar, or use experimental_jit_scope to enable XLA:CPU.  To confirm that XLA is active, pass --vmodule=xla_compilation_cache=1 (as a proper command-line flag, not via TF_XLA_FLAGS) or set the envvar XLA_FLAGS=--xla_hlo_profile.
[1] "Done random initialization"
[1] "Step: 1    Loss: 60.7268"
[1] "Step: 100    Loss: 47.1493"
[1] "Step: 200    Loss: 39.1225"
[1] "Step: 300    Loss: 35.231"
[1] "Step: 400    Loss: 33.5344"
[1] "Step: 500    Loss: 31.63"
[1] "============== Alignment Complete =============="
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
191.596  27.336  78.344