CHECK report for scAlign on malbec1
This page was generated on 2021-05-06 12:29:00 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the scAlign package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
|
| scAlign 1.4.0 (landing page) Nelson Johansen
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
URL: https://git.bioconductor.org/packages/scAlign |
Branch: RELEASE_3_12 |
Last Commit: 0309fa7 |
Last Changed Date: 2020-10-27 11:45:16 -0400 (Tue, 27 Oct 2020) |
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | | |
| merida1 | macOS 10.14.6 Mojave / x86_64 | ... NOT SUPPORTED ... | |
Summary
Command output
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### Running command:
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### /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.
Installation output
scAlign.Rcheck/00install.out
Tests output
scAlign.Rcheck/tests/testthat.Rout
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
Example timings
scAlign.Rcheck/scAlign-Ex.timings