William S Chen
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/phemd |
| Branch: RELEASE_3_9 |
| Last Commit: b0f5bb8 |
| Last Changed Date: 2019-05-07 19:16:20 -0400 (Tue, 07 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:43:25 -0400 (Wed, 16 Oct 2019).
| Package 1203/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| phemd 1.0.1 William S Chen
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: phemd |
| Version: 1.0.1 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:phemd.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings phemd_1.0.1.tar.gz |
| StartedAt: 2019-10-16 05:57:33 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:09:41 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 727.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: phemd.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:phemd.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings phemd_1.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/phemd.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.0.1'
* 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 ... OK
* loading checks for arch 'x64'
** 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 ... NOTE
createDataObj: no visible global function definition for
'packageVersion'
getSampleHistsByCluster: no visible global function definition for
'GetIdent'
Undefined global functions or variables:
GetIdent packageVersion
Consider adding
importFrom("utils", "packageVersion")
to your NAMESPACE file.
* 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
clusterIndividualSamples 11.72 0.31 12.09
plotEmbeddings 11.74 0.27 12.00
plotHeatmaps 11.55 0.19 11.73
plotCellYield 10.89 0.41 11.31
printClusterAssignments 11.13 0.14 11.27
plotGroupedSamplesDmap 10.82 0.17 11.00
getCellYield 10.06 0.22 10.28
getSampleCelltypeFreqs 9.77 0.29 10.06
groupSamples 9.35 0.31 9.66
Phemd-methods 8.99 0.55 9.53
compareSamples 9.13 0.38 9.52
getSampleHistsByCluster 9.16 0.29 9.44
generateGDM 9.15 0.23 9.39
orderCellsMonocle 8.28 0.29 8.60
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
clusterIndividualSamples 13.86 0.23 14.33
getSampleCelltypeFreqs 13.86 0.14 14.00
plotGroupedSamplesDmap 13.51 0.22 13.73
generateGDM 13.42 0.18 13.61
Phemd-methods 12.71 0.21 12.92
plotHeatmaps 12.61 0.22 12.83
getCellYield 12.50 0.15 12.65
plotEmbeddings 12.32 0.15 12.47
printClusterAssignments 12.12 0.14 12.28
getSampleHistsByCluster 11.74 0.18 11.93
compareSamples 11.58 0.16 11.75
plotCellYield 11.54 0.17 11.72
groupSamples 11.08 0.18 11.27
orderCellsMonocle 8.43 0.14 8.56
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/phemd.Rcheck/00check.log'
for details.
phemd.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/phemd_1.0.1.tar.gz && rm -rf phemd.buildbin-libdir && mkdir phemd.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=phemd.buildbin-libdir phemd_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL phemd_1.0.1.zip && rm phemd_1.0.1.tar.gz phemd_1.0.1.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 729k 100 729k 0 0 10.1M 0 --:--:-- --:--:-- --:--:-- 11.3M
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
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
* MD5 sums
packaged installation of 'phemd' as phemd_1.0.1.zip
* DONE (phemd)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'phemd' successfully unpacked and MD5 sums checked
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phemd.Rcheck/examples_i386/phemd-Ex.timings
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phemd.Rcheck/examples_x64/phemd-Ex.timings
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