Package: scAlign

Version: 1.1.6

Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:scAlign.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings scAlign_1.1.6.tar.gz

StartedAt: 2019-12-17 07:03:10 -0500 (Tue, 17 Dec 2019)

EndedAt: 2019-12-17 07:09:55 -0500 (Tue, 17 Dec 2019)

EllapsedTime: 405.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: scAlign.Rcheck

Warnings: 4

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:scAlign.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings scAlign_1.1.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/scAlign.Rcheck’
* using R Under development (unstable) (2019-12-14 r77569)
* 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 ‘1.1.6’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scAlign’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... 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 ... NOTE
/usr/lib/python2.7/dist-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
* checking S3 generic/method consistency ... WARNING
/usr/lib/python2.7/dist-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
/usr/lib/python2.7/dist-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
/usr/lib/python2.7/dist-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
/usr/lib/python2.7/dist-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
.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 : <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<-
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
/usr/lib/python2.7/dist-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
/usr/lib/python2.7/dist-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
/usr/lib/python2.7/dist-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
/usr/lib/python2.7/dist-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
* checking Rd \usage sections ... NOTE
/usr/lib/python2.7/dist-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
PlotTSNE 35.982  5.963  19.888
* 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: 4 WARNINGs, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/scAlign.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL scAlign
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘scAlign’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
/usr/lib/python2.7/dist-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
/usr/lib/python2.7/dist-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
** testing if installed package can be loaded from final location
/usr/lib/python2.7/dist-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
** testing if installed package keeps a record of temporary installation path
* DONE (scAlign)

R Under development (unstable) (2019-12-14 r77569) -- "Unsuffered Consequences"
Copyright (C) 2019 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: 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
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
/usr/lib/python2.7/dist-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
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
WARNING: Logging before flag parsing goes to stderr.
W1217 07:08:59.862076 140689707673536 deprecation_wrapper.py:119] From /usr/local/lib/python2.7/dist-packages/tensorflow/python/util/deprecation_wrapper.py:119: The name tf.Session is deprecated. Please use tf.compat.v1.Session instead.

2019-12-17 07:08:59.887877: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-12-17 07:08:59.895911: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2397245000 Hz
2019-12-17 07:08:59.897035: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x55cc2e302140 executing computations on platform Host. Devices:
2019-12-17 07:08:59.897077: I tensorflow/compiler/xla/service/service.cc:175]   StreamExecutor device (0): <undefined>, <undefined>
W1217 07:08:59.902475 140689707673536 deprecation.py:323] From /usr/local/lib/python2.7/dist-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]
W1217 07:09:02.915209 140689707673536 deprecation_wrapper.py:119] From /usr/local/lib/python2.7/dist-packages/tensorflow/python/util/deprecation_wrapper.py:119: The name tf.ConfigProto is deprecated. Please use tf.compat.v1.ConfigProto instead.

W1217 07:09:02.916344 140689707673536 deprecation_wrapper.py:119] From /usr/local/lib/python2.7/dist-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"
W1217 07:09:02.932030 140689707673536 deprecation_wrapper.py:119] From /usr/local/lib/python2.7/dist-packages/tensorflow/python/util/deprecation_wrapper.py:119: The name tf.placeholder is deprecated. Please use tf.compat.v1.placeholder instead.

W1217 07:09:02.956711 140689707673536 deprecation.py:323] From /usr/local/lib/python2.7/dist-packages/tensorflow/python/util/deprecation.py:320: 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)`.
W1217 07:09:03.034645 140689707673536 deprecation_wrapper.py:119] From /usr/local/lib/python2.7/dist-packages/tensorflow/python/util/deprecation_wrapper.py:119: The name tf.variable_scope is deprecated. Please use tf.compat.v1.variable_scope instead.

W1217 07:09:03.865923 140689707673536 lazy_loader.py:50] 
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.

W1217 07:09:03.872339 140689707673536 deprecation.py:323] From /usr/local/lib/python2.7/dist-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.
W1217 07:09:04.502445 140689707673536 deprecation.py:323] From /usr/local/lib/python2.7/dist-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).
W1217 07:09:04.636362 140689707673536 deprecation.py:323] From /usr/local/lib/python2.7/dist-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.
W1217 07:09:04.952860 140689707673536 deprecation.py:506] From /usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/init_ops.py:1251: calling __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
[1] "Adding source walker loss"
W1217 07:09:05.787045 140689707673536 deprecation.py:323] From /home/biocbuild/bbs-3.11-bioc/R/library/reticulate/python/rpytools/call.py:13: where (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
W1217 07:09:05.930103 140689707673536 deprecation_wrapper.py:119] From /usr/local/lib/python2.7/dist-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.

W1217 07:09:06.001511 140689707673536 deprecation_wrapper.py:119] From /usr/local/lib/python2.7/dist-packages/tensorflow/python/util/deprecation_wrapper.py:119: The name tf.summary.histogram is deprecated. Please use tf.compat.v1.summary.histogram instead.

W1217 07:09:06.066340 140689707673536 deprecation_wrapper.py:119] From /usr/local/lib/python2.7/dist-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"
W1217 07:09:06.612191 140689707673536 deprecation_wrapper.py:119] From /usr/local/lib/python2.7/dist-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.

W1217 07:09:06.622867 140689707673536 deprecation_wrapper.py:119] From /usr/local/lib/python2.7/dist-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.

W1217 07:09:06.633604 140689707673536 deprecation_wrapper.py:119] From /usr/local/lib/python2.7/dist-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.

W1217 07:09:06.636976 140689707673536 deprecation_wrapper.py:119] From /usr/local/lib/python2.7/dist-packages/tensorflow/python/util/deprecation_wrapper.py:119: The name tf.train.AdamOptimizer is deprecated. Please use tf.compat.v1.train.AdamOptimizer instead.

W1217 07:09:08.294931 140689707673536 deprecation_wrapper.py:119] From /usr/local/lib/python2.7/dist-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.

W1217 07:09:08.305593 140689707673536 deprecation_wrapper.py:119] From /usr/local/lib/python2.7/dist-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.

W1217 07:09:08.307059 140689707673536 deprecation_wrapper.py:119] From /usr/local/lib/python2.7/dist-packages/tensorflow/python/util/deprecation_wrapper.py:119: The name tf.logging.FATAL is deprecated. Please use tf.compat.v1.logging.FATAL instead.

2019-12-17 07:09:08.550915: 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: 60.838"
[1] "Step: 100    Loss: 48.4254"
[1] "Step: 200    Loss: 40.8635"
[1] "Step: 300    Loss: 33.5267"
[1] "Step: 400    Loss: 33.9722"
[1] "Step: 500    Loss: 32.3504"
[1] "============== Alignment Complete =============="
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 3 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
181.788  29.462  71.265 

name	user	system	elapsed
PlotTSNE	35.982	5.963	19.888
gaussianKernel	0.528	0.004	0.495
scAlign	4.774	0.107	4.624
scAlignCreateObject	0.858	0.007	0.868
scAlignMulti	4.361	0.056	4.427
scAlignOptions	0.003	0.000	0.003