phemd 1.2.0
William S Chen
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/phemd |
| Branch: RELEASE_3_10 |
| Last Commit: 96eb7b2 |
| Last Changed Date: 2019-10-29 13:11:29 -0400 (Tue, 29 Oct 2019) |
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ ERROR ] | | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |  |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:phemd.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings phemd_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/phemd.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 ‘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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
groupSamples 12.988 0.020 13.072
compareSamples 12.780 0.036 13.032
generateGDM 12.752 0.016 12.925
Phemd-methods 12.444 0.108 12.693
getSampleHistsByCluster 12.520 0.020 12.569
plotCellYield 11.988 0.028 12.028
clusterIndividualSamples 11.932 0.052 12.280
plotGroupedSamplesDmap 11.892 0.024 11.924
getSampleCelltypeFreqs 11.432 0.004 11.453
plotEmbeddings 11.332 0.000 11.359
getCellYield 10.940 0.000 11.056
printClusterAssignments 10.484 0.016 10.528
plotHeatmaps 10.368 0.024 10.410
orderCellsMonocle 9.716 0.008 9.757
* 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, 3 WARNINGs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.10-bioc/meat/phemd.Rcheck/00check.log’
for details.