Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-09-29 11:35:50 -0400 (Fri, 29 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 1505/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phemd 1.16.0  (landing page)
William S Chen
Snapshot Date: 2023-09-28 14:00:15 -0400 (Thu, 28 Sep 2023)
git_url: https://git.bioconductor.org/packages/phemd
git_branch: RELEASE_3_17
git_last_commit: fb3f157
git_last_commit_date: 2023-08-22 18:03:33 -0400 (Tue, 22 Aug 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    OK    WARNINGS    OK  UNNEEDED, same version is already published

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: 1.16.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:phemd.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings phemd_1.16.0.tar.gz
StartedAt: 2023-09-28 23:54:22 -0400 (Thu, 28 Sep 2023)
EndedAt: 2023-09-29 00:02:27 -0400 (Fri, 29 Sep 2023)
EllapsedTime: 484.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: phemd.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:phemd.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings phemd_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/phemd.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* 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 ‘1.16.0’
* 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
plotGroupedSamplesDmap   8.174  0.176   8.351
clusterIndividualSamples 8.062  0.216   8.278
compareSamples           8.047  0.164   8.211
getSampleHistsByCluster  7.910  0.128   8.038
groupSamples             7.665  0.120   7.785
Phemd-methods            7.448  0.096   7.543
plotHeatmaps             7.394  0.108   7.502
printClusterAssignments  7.162  0.036   7.197
getCellYield             7.059  0.096   7.156
getSampleCelltypeFreqs   7.041  0.024   7.065
plotCellYield            6.870  0.040   6.910
generateGDM              6.637  0.076   6.713
plotEmbeddings           6.345  0.028   6.373
orderCellsMonocle        5.666  0.044   5.710
* 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-3.17-bioc/meat/phemd.Rcheck/00check.log’
for details.



Installation output

phemd.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL phemd
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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
GDM0.420.060.48
Phemd-methods7.4480.0967.543
aggregateSamples1.4800.0161.496
assignCellClusterNearestNode000
batchIDs0.3160.0000.316
bindSeuratObj1.2200.0681.289
celltypeFreqs0.3470.0040.351
clusterIndividualSamples8.0620.2168.278
compareSamples8.0470.1648.211
createDataObj0.3240.0000.324
drawColnames45000
embedCells2.4320.0042.437
generateGDM6.6370.0766.713
getArithmeticCentroids000
getCellYield7.0590.0967.156
getSampleCelltypeFreqs7.0410.0247.065
getSampleHistsByCluster7.9100.1288.038
getSampleSizes000
groupSamples7.6650.1207.785
identifyCentroids000
monocleInfo0.2980.0000.298
orderCellsMonocle5.6660.0445.710
phateInfo0.3420.0000.342
plotCellYield6.870.046.91
plotEmbeddings6.3450.0286.373
plotGroupedSamplesDmap8.1740.1768.351
plotHeatmaps7.3940.1087.502
pooledCells0.3390.0000.339
printClusterAssignments7.1620.0367.197
rawExpn0.3230.0000.323
removeTinySamples0.6620.0000.662
retrieveRefClusters000
sNames0.3180.0000.318
selectFeatures1.9350.0001.935
selectMarkers0.3230.0000.322
seuratInfo0.3350.0000.335
subsampledBool0.340.000.34
subsampledIdx0.3790.0000.379