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) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:48:44 -0400 (Wed, 15 Apr 2020).
| Package 1255/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| phemd 1.2.0 William S Chen
| 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 | |
| Package: phemd |
| Version: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:phemd.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings phemd_1.2.0.tar.gz |
| StartedAt: 2020-04-15 04:34:36 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:44:09 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 572.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: phemd.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:phemd.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings phemd_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/phemd.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (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 ... 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 ... 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 ... OK
* 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
Phemd-methods 12.918 0.145 13.088
compareSamples 12.390 0.211 12.612
groupSamples 12.287 0.218 12.515
generateGDM 12.194 0.250 12.469
clusterIndividualSamples 11.949 0.217 12.184
plotGroupedSamplesDmap 11.940 0.188 12.144
getSampleCelltypeFreqs 11.862 0.192 12.064
getCellYield 11.659 0.187 11.907
printClusterAssignments 11.510 0.262 11.786
plotCellYield 11.375 0.205 11.625
getSampleHistsByCluster 11.358 0.210 11.582
plotHeatmaps 10.686 0.189 10.889
plotEmbeddings 10.685 0.166 10.877
orderCellsMonocle 10.188 0.182 10.384
* 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 NOTE
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/phemd.Rcheck/00check.log’
for details.
phemd.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL phemd ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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)
phemd.Rcheck/phemd-Ex.timings
| name | user | system | elapsed | |
| GDM | 0.744 | 0.008 | 0.753 | |
| Phemd-methods | 12.918 | 0.145 | 13.088 | |
| aggregateSamples | 2.612 | 0.009 | 2.625 | |
| assignCellClusterNearestNode | 0.005 | 0.000 | 0.006 | |
| batchIDs | 0.533 | 0.001 | 0.534 | |
| bindSeuratObj | 1.563 | 0.021 | 1.589 | |
| celltypeFreqs | 0.464 | 0.001 | 0.465 | |
| clusterIndividualSamples | 11.949 | 0.217 | 12.184 | |
| compareSamples | 12.390 | 0.211 | 12.612 | |
| createDataObj | 0.504 | 0.001 | 0.505 | |
| drawColnames45 | 0.007 | 0.000 | 0.006 | |
| embedCells | 4.344 | 0.027 | 4.380 | |
| generateGDM | 12.194 | 0.250 | 12.469 | |
| getArithmeticCentroids | 0.006 | 0.000 | 0.006 | |
| getCellYield | 11.659 | 0.187 | 11.907 | |
| getSampleCelltypeFreqs | 11.862 | 0.192 | 12.064 | |
| getSampleHistsByCluster | 11.358 | 0.210 | 11.582 | |
| getSampleSizes | 0.006 | 0.000 | 0.007 | |
| groupSamples | 12.287 | 0.218 | 12.515 | |
| identifyCentroids | 0.004 | 0.000 | 0.004 | |
| monocleInfo | 0.549 | 0.001 | 0.551 | |
| orderCellsMonocle | 10.188 | 0.182 | 10.384 | |
| phateInfo | 0.514 | 0.001 | 0.515 | |
| plotCellYield | 11.375 | 0.205 | 11.625 | |
| plotEmbeddings | 10.685 | 0.166 | 10.877 | |
| plotGroupedSamplesDmap | 11.940 | 0.188 | 12.144 | |
| plotHeatmaps | 10.686 | 0.189 | 10.889 | |
| pooledCells | 0.518 | 0.001 | 0.520 | |
| printClusterAssignments | 11.510 | 0.262 | 11.786 | |
| rawExpn | 0.519 | 0.002 | 0.521 | |
| removeTinySamples | 0.990 | 0.002 | 0.993 | |
| retrieveRefClusters | 0.006 | 0.000 | 0.006 | |
| sNames | 0.508 | 0.001 | 0.509 | |
| selectFeatures | 3.032 | 0.005 | 3.038 | |
| selectMarkers | 0.548 | 0.001 | 0.550 | |
| seuratInfo | 0.551 | 0.001 | 0.552 | |
| subsampledBool | 0.563 | 0.000 | 0.564 | |
| subsampledIdx | 0.561 | 0.001 | 0.563 | |