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CHECK report for scAlign on malbec1

This page was generated on 2020-04-15 12:15:36 -0400 (Wed, 15 Apr 2020).

Package 1521/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scAlign 1.2.0
Nelson Johansen
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/scAlign
Branch: RELEASE_3_10
Last Commit: 0254014
Last Changed Date: 2019-10-29 13:11:38 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  ERROR  ERROR  skipped  skipped 
merida1 OS X 10.11.6 El Capitan / x86_64  ERROR  ERROR  skipped  skipped 

Summary

Package: scAlign
Version: 1.2.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:scAlign.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings scAlign_1.2.0.tar.gz
StartedAt: 2020-04-15 06:29:12 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:35:44 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 392.1 seconds
RetCode: 0
Status:  OK 
CheckDir: scAlign.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:scAlign.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings scAlign_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/scAlign.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.2.0’
* 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', '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 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’
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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
PlotTSNE     36.732  5.624  20.724
scAlignMulti  5.424  0.072   5.400
scAlign       5.032  0.084   4.869
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/scAlign.Rcheck/00check.log’
for details.

Installation output

scAlign.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL scAlign
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-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)

Tests output

scAlign.Rcheck/tests/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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
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:tensorflow:From /home/biocbuild/.virtualenvs/r-reticulate/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.

2020-04-15 06:34:39.890526: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2020-04-15 06:34:39.899267: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2397160000 Hz
2020-04-15 06:34:39.900222: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x55d357427d90 executing computations on platform Host. Devices:
2020-04-15 06:34:39.900263: I tensorflow/compiler/xla/service/service.cc:175]   StreamExecutor device (0): <undefined>, <undefined>
WARNING:tensorflow:From /home/biocbuild/.virtualenvs/r-reticulate/lib/python2.7/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 /home/biocbuild/.virtualenvs/r-reticulate/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/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/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/lib/python2.7/site-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)`.
WARNING:tensorflow:From /home/biocbuild/.virtualenvs/r-reticulate/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.

WARNING:tensorflow:From /home/biocbuild/.virtualenvs/r-reticulate/lib/python2.7/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:From /home/biocbuild/.virtualenvs/r-reticulate/lib/python2.7/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:From /home/biocbuild/.virtualenvs/r-reticulate/lib/python2.7/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:From /home/biocbuild/.virtualenvs/r-reticulate/lib/python2.7/site-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"
WARNING:tensorflow:From /home/biocbuild/bbs-3.10-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
WARNING:tensorflow:From /home/biocbuild/.virtualenvs/r-reticulate/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/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/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/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/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/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/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/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/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/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.

2020-04-15 06:34:49.239489: 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: 59.9368"
[1] "Step: 100    Loss: 44.4347"
[1] "Step: 200    Loss: 39.912"
[1] "Step: 300    Loss: 32.9516"
[1] "Step: 400    Loss: 32.1901"
[1] "Step: 500    Loss: 30.4001"
[1] "============== Alignment Complete =============="
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 3 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
189.656  30.500  75.632

Example timings

scAlign.Rcheck/scAlign-Ex.timings

nameusersystemelapsed
PlotTSNE36.732 5.62420.724
gaussianKernel0.5080.0080.485
scAlign5.0320.0844.869
scAlignCreateObject1.0240.0081.033
scAlignMulti5.4240.0725.400
scAlignOptions0.0080.0000.008