Package: phemd

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:phemd.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings phemd_1.2.0.tar.gz

StartedAt: 2020-04-15 05:28:53 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:40:23 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 690.3 seconds

RetCode: 1

Status:  ERROR

CheckDir: phemd.Rcheck

Warnings: NA

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:phemd.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings phemd_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/phemd.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'phemd/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'phemd' version '1.2.0'
* 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 whether package 'phemd' 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
* loading checks for arch 'i386'
** 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 ... WARNING
---- unloading
* loading checks for arch 'x64'
** checking whether the package can be loaded ... ERROR
Loading required package: monocle
Loading required package: Matrix
Loading required package: Biobase
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 object is masked from 'package:Matrix':

    which

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: VGAM
Loading required package: stats4
Loading required package: splines
Loading required package: DDRTree
Loading required package: irlba
Error in py_module_import(module, convert = convert) : 
  ImportError: No module named phate

It looks like this package has a loading problem: see the messages for
details.
** checking whether the package can be loaded with stated dependencies ...Loading required package: monocle
Loading required package: methods
Loading required package: Matrix
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: utils

Attaching package: 'utils'

The following objects are masked from 'package:Matrix':

    head, tail

Loading required package: graphics

Attaching package: 'graphics'

The following object is masked from 'package:Matrix':

    image

Loading required package: stats

Attaching package: 'stats'

The following objects are masked from 'package:Matrix':

    cov2cor, toeplitz, update

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 object is masked from 'package:Matrix':

    which

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: VGAM
Loading required package: stats4
Loading required package: splines
Loading required package: DDRTree
Loading required package: irlba
Error in py_module_import(module, convert = convert) : 
  ImportError: No module named phate

It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package.  All dependencies must be
declared in DESCRIPTION.
See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
** checking whether the package can be unloaded cleanly ... WARNING
---- unloading
** checking whether the namespace can be loaded with stated dependencies ... WARNING
Error in py_module_import(module, convert = convert) : 
  ImportError: No module named phate

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
** checking whether the namespace can be unloaded cleanly ... WARNING
---- unloading
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'VGAM:::VGAM.weights.function' 'pheatmap:::find_coordinates'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Error in py_module_import(module, convert = convert) : 
  ImportError: No module named phate
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
compareSamples           11.72   0.50   12.34
generateGDM              11.42   0.53   12.00
clusterIndividualSamples  9.36   0.33    9.75
getCellYield              9.27   0.39    9.65
Phemd-methods             8.89   0.54    9.44
plotGroupedSamplesDmap    9.10   0.19    9.28
getSampleHistsByCluster   8.82   0.20    9.03
orderCellsMonocle         8.41   0.43    8.83
groupSamples              8.47   0.25    8.72
printClusterAssignments   8.44   0.11    8.55
plotCellYield             7.95   0.15    8.11
getSampleCelltypeFreqs    7.80   0.17    7.97
plotEmbeddings            6.81   0.14    6.95
plotHeatmaps              6.65   0.20    6.86
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
plotGroupedSamplesDmap   10.78   0.09   11.11
clusterIndividualSamples  9.72   0.16    9.93
plotEmbeddings            9.33   0.09    9.43
groupSamples              9.14   0.12    9.26
getSampleHistsByCluster   9.11   0.09    9.20
Phemd-methods             9.13   0.06    9.18
getSampleCelltypeFreqs    8.93   0.08    9.02
printClusterAssignments   8.60   0.23    8.83
getCellYield              8.53   0.17    8.70
plotHeatmaps              8.41   0.13    8.53
plotCellYield             8.01   0.07    8.08
generateGDM               7.90   0.13    8.03
compareSamples            7.86   0.14    8.06
orderCellsMonocle         6.66   0.11    6.77
* 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 ERROR, 4 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/phemd.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/phemd_1.2.0.tar.gz && rm -rf phemd.buildbin-libdir && mkdir phemd.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=phemd.buildbin-libdir phemd_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL phemd_1.2.0.zip && rm phemd_1.2.0.tar.gz phemd_1.2.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

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100  479k  100  479k    0     0  3250k      0 --:--:-- --:--:-- --:--:-- 3331k

install for i386

* installing *source* package 'phemd' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'phemd'
    finding HTML links ... done
    GDM                                     html  
    Phemd-methods                           html  
    Phemd                                   html  
    aggregateSamples                        html  
    all_expn_data                           html  
    all_genes                               html  
    assignCellClusterNearestNode            html  
    batchIDs                                html  
    bindSeuratObj                           html  
    celltypeFreqs                           html  
    clusterIndividualSamples                html  
    compareSamples                          html  
    createDataObj                           html  
    drawColnames45                          html  
    embedCells                              html  
    gaussianffLocal                         html  
    generateGDM                             html  
    getArithmeticCentroids                  html  
    getCellYield                            html  
    getSampleCelltypeFreqs                  html  
    getSampleHistsByCluster                 html  
    getSampleSizes                          html  
    groupSamples                            html  
    heatmap_genes                           html  
    identifyCentroids                       html  
    monocleInfo                             html  
    orderCellsMonocle                       html  
    phateInfo                               html  
    plotCellYield                           html  
    plotEmbeddings                          html  
    plotGroupedSamplesDmap                  html  
    plotHeatmaps                            html  
    plotSummaryHistograms                   html  
    pooledCells                             html  
    printClusterAssignments                 html  
    rawExpn                                 html  
    removeTinySamples                       html  
    retrieveRefClusters                     html  
    sNames                                  html  
    selectFeatures                          html  
    selectMarkers                           html  
    selected_genes                          html  
    seuratInfo                              html  
    snames_data                             html  
    subsampledBool                          html  
    subsampledIdx                           html  
** 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

install for x64

* installing *source* package 'phemd' ...
** testing if installed package can be loaded
Error in py_module_import(module, convert = convert) : 
  ImportError: No module named phate
* MD5 sums
packaged installation of 'phemd' as phemd_1.2.0.zip
* DONE (phemd)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'phemd' successfully unpacked and MD5 sums checked