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This page was generated on 2023-10-27 11:34:20 -0400 (Fri, 27 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_64R Under development (unstable) (2023-10-22 r85388) -- "Unsuffered Consequences" 4594
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-10-23 r85389 ucrt) -- "Unsuffered Consequences" 4308
merida1macOS 12.6.4 Montereyx86_64R Under development (unstable) (2023-10-23 r85395) -- "Unsuffered Consequences" 3776
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1500/2217HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phemd 1.19.0  (landing page)
William S Chen
Snapshot Date: 2023-10-26 14:00:13 -0400 (Thu, 26 Oct 2023)
git_url: https://git.bioconductor.org/packages/phemd
git_branch: devel
git_last_commit: 0982798
git_last_commit_date: 2023-10-24 11:44:02 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    ERROR  skippedskipped

CHECK results for phemd on nebbiolo1


To the developers/maintainers of the phemd package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/phemd.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: phemd
Version: 1.19.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:phemd.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings phemd_1.19.0.tar.gz
StartedAt: 2023-10-26 23:59:08 -0400 (Thu, 26 Oct 2023)
EndedAt: 2023-10-27 00:07:26 -0400 (Fri, 27 Oct 2023)
EllapsedTime: 498.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: phemd.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:phemd.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings phemd_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/phemd.Rcheck’
* using R Under development (unstable) (2023-10-22 r85388)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘phemd/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘phemd’ version ‘1.19.0’
* 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 ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
':::' call which should be '::': ‘monocle:::reducedDimA<-’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘VGAM:::VGAM.weights.function’ ‘monocle:::extract_ddrtree_ordering’
  ‘monocle:::extract_good_branched_ordering’
  ‘monocle:::findNearestPointOnMST’ ‘monocle:::projPointOnLine’
  ‘monocle:::project_point_to_line_segment’ ‘monocle:::reducedDimK<-’
  ‘monocle:::reducedDimW<-’ ‘monocle:::select_root_cell’
  ‘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
newCellDataSetUpdated: no visible global function definition for
  ‘isSparseMatrix’
orderCellsUpdated: no visible binding for '<<-' assignment to
  ‘next_node’
orderCellsUpdated: no visible global function definition for
  ‘pq_helper’
orderCellsUpdated: no visible global function definition for
  ‘select_root_cell’
project2MSTUpdated: no visible global function definition for ‘nei’
Undefined global functions or variables:
  isSparseMatrix nei pq_helper select_root_cell
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'as(<dsCMatrix>, "dsTMatrix")' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
Phemd-methods            8.504  0.232   8.737
compareSamples           8.352  0.164   8.516
getCellYield             8.025  0.224   8.249
printClusterAssignments  8.070  0.112   8.183
plotCellYield            7.794  0.024   7.819
clusterIndividualSamples 7.521  0.223   7.744
plotGroupedSamplesDmap   7.122  0.044   7.167
getSampleHistsByCluster  7.059  0.027   7.088
groupSamples             7.017  0.068   7.086
getSampleCelltypeFreqs   6.943  0.059   7.003
generateGDM              6.903  0.060   6.964
orderCellsMonocle        6.706  0.148   6.855
plotHeatmaps             6.518  0.056   6.576
plotEmbeddings           6.200  0.052   6.252
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘phemd.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/phemd.Rcheck/00check.log’
for details.



Installation output

phemd.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL phemd
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* 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
** 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 (phemd)

Tests output


Example timings

phemd.Rcheck/phemd-Ex.timings

nameusersystemelapsed
GDM0.4400.0080.448
Phemd-methods8.5040.2328.737
aggregateSamples1.5150.0401.555
assignCellClusterNearestNode000
batchIDs0.2910.0160.307
bindSeuratObj1.1760.0321.209
celltypeFreqs0.3030.0040.308
clusterIndividualSamples7.5210.2237.744
compareSamples8.3520.1648.516
createDataObj0.3280.0040.331
drawColnames45000
embedCells2.5540.0042.558
generateGDM6.9030.0606.964
getArithmeticCentroids0.0010.0000.000
getCellYield8.0250.2248.249
getSampleCelltypeFreqs6.9430.0597.003
getSampleHistsByCluster7.0590.0277.088
getSampleSizes0.0010.0000.000
groupSamples7.0170.0687.086
identifyCentroids0.0000.0000.001
monocleInfo0.3220.0400.362
orderCellsMonocle6.7060.1486.855
phateInfo0.3020.0000.302
plotCellYield7.7940.0247.819
plotEmbeddings6.2000.0526.252
plotGroupedSamplesDmap7.1220.0447.167
plotHeatmaps6.5180.0566.576
pooledCells0.3750.0160.390
printClusterAssignments8.0700.1128.183
rawExpn0.3130.0000.313
removeTinySamples0.6480.0000.648
retrieveRefClusters000
sNames0.3020.0000.302
selectFeatures1.8570.0031.861
selectMarkers0.3090.0000.310
seuratInfo0.3090.0000.309
subsampledBool0.3530.0000.352
subsampledIdx0.3200.0000.319