Package: scAlign

Version: 1.0.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:scAlign.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings scAlign_1.0.0.tar.gz

StartedAt: 2019-10-16 04:48:14 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:55:01 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 407.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: scAlign.Rcheck

Warnings: 4

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:scAlign.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings scAlign_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/scAlign.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... OK
* 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’
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
PlotTSNE     18.482  1.651  17.562
scAlign       5.738  0.012   5.940
scAlignMulti  5.570  0.075   5.463
* 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, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/scAlign.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL scAlign
###
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* installing to library ‘/home/biocbuild/bbs-3.9-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 version 3.6.1 (2019-07-05) -- "Action of the Toes"
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
/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
WARNING: Logging before flag parsing goes to stderr.
W1016 04:53:22.243566 140145663666112 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.

2019-10-16 04:53:22.274543: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2019-10-16 04:53:22.285016: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2397050000 Hz
2019-10-16 04:53:22.285797: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x56514422d6d0 executing computations on platform Host. Devices:
2019-10-16 04:53:22.285839: I tensorflow/compiler/xla/service/service.cc:175]   StreamExecutor device (0): , 
W1016 04:53:22.300853 140145663666112 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]
W1016 04:53:26.546740 140145663666112 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.

W1016 04:53:26.547775 140145663666112 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"
W1016 04:53:26.562552 140145663666112 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.

W1016 04:53:26.587905 140145663666112 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)`.
W1016 04:53:26.664391 140145663666112 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.

W1016 04:53:27.374087 140145663666112 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.

W1016 04:53:27.377695 140145663666112 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.
W1016 04:53:27.839626 140145663666112 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).
W1016 04:53:27.918771 140145663666112 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.
W1016 04:53:28.195904 140145663666112 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"
W1016 04:53:28.987401 140145663666112 deprecation.py:323] From /home/biocbuild/bbs-3.9-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
W1016 04:53:29.176408 140145663666112 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.

W1016 04:53:29.244261 140145663666112 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.

W1016 04:53:29.284802 140145663666112 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"
W1016 04:53:29.880929 140145663666112 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.

W1016 04:53:29.892719 140145663666112 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.

W1016 04:53:29.904870 140145663666112 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.

W1016 04:53:29.908596 140145663666112 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.

W1016 04:53:31.644558 140145663666112 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.

W1016 04:53:31.654500 140145663666112 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.

W1016 04:53:31.655956 140145663666112 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.

2019-10-16 04:53:31.907149: 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: 68.8778    Alignment: 0.8316"
[1] "Step: 100    Loss: 45.6738    Alignment: 0.7731"
[1] "Step: 200    Loss: 33.7138    Alignment: 0.7646"
[1] "Step: 300    Loss: 27.1238    Alignment: 0.7385"
[1] "Step: 400    Loss: 25.5209    Alignment: 0.7201"
[1] "Step: 500    Loss: 23.8217    Alignment: 0.7155"
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 3 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
395.464  54.473 110.769 

name	user	system	elapsed
PlotTSNE	18.482	1.651	17.562
gaussianKernel	0.525	0.024	0.500
scAlign	5.738	0.012	5.940
scAlignCreateObject	0.838	0.004	0.952
scAlignMulti	5.570	0.075	5.463
scAlignOptions	0.002	0.000	0.002