| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:06:52 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 | ||||
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To the developers/maintainers of the MetaNeighbor package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MetaNeighbor.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1102/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MetaNeighbor 1.14.0 (landing page) Stephan Fischer
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: MetaNeighbor |
| Version: 1.14.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetaNeighbor.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MetaNeighbor_1.14.0.tar.gz |
| StartedAt: 2022-04-12 22:32:57 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 22:36:31 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 214.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MetaNeighbor.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetaNeighbor.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MetaNeighbor_1.14.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MetaNeighbor.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MetaNeighbor/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MetaNeighbor' version '1.14.0'
* 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 'MetaNeighbor' can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.5Mb
sub-directories of 1Mb or more:
data 7.1Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
MetaNeighbor : <anonymous>: no visible binding for global variable
'cell_type'
ggPlotHeatmap: no visible binding for global variable 'target_ct'
ggPlotHeatmap: no visible binding for global variable 'ref_ct'
ggPlotHeatmap: no visible binding for global variable 'auroc'
is_reciprocal_top_hit: no visible binding for global variable 'auroc'
is_reciprocal_top_hit: no visible binding for global variable
'ref_cell_type'
is_reciprocal_top_hit: no visible binding for global variable
'target_cell_type'
is_reciprocal_top_hit: no visible binding for global variable
'reciprocal_cell_type'
is_reciprocal_top_hit: no visible binding for global variable
'is_reciprocal'
plotDotPlot: no visible binding for global variable 'cluster'
plotDotPlot: no visible binding for global variable 'gene'
plotDotPlot: no visible binding for global variable 'cell_type'
plotDotPlot: no visible binding for global variable
'average_expression'
plotDotPlot: no visible binding for global variable
'percent_expressing'
plotMetaClusters: no visible global function definition for
'order_sym_matrix'
topHitsByStudy: no visible binding for global variable 'ref_cell_type'
topHitsByStudy: no visible binding for global variable
'target_cell_type'
topHitsByStudy: no visible binding for global variable 'ref_study'
topHitsByStudy: no visible binding for global variable 'target_study'
topHitsByStudy: no visible binding for global variable '.'
topHitsByStudy: no visible binding for global variable 'pair_id'
topHitsByStudy: no visible binding for global variable 'is_reciprocal'
topHitsByStudy: no visible global function definition for 'desc'
topHitsByStudy: no visible binding for global variable 'Match_type'
variableGenes: no visible binding for global variable 'gene'
variableGenes: no visible binding for global variable 'is_hvg'
variableGenes: no visible binding for global variable 'var_quant'
variableGenes: no visible binding for global variable 'recurrence'
variableGenes: no visible global function definition for 'desc'
variableGenes: no visible binding for global variable 'score'
variable_genes_single_exp: no visible binding for global variable
'bin_med'
variable_genes_single_exp: no visible binding for global variable
'variance'
variable_genes_single_exp: no visible binding for global variable
'var_quant'
Undefined global functions or variables:
. Match_type auroc average_expression bin_med cell_type cluster desc
gene is_hvg is_reciprocal order_sym_matrix pair_id percent_expressing
reciprocal_cell_type recurrence ref_cell_type ref_ct ref_study score
target_cell_type target_ct target_study var_quant variance
* 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 ... WARNING
LazyData DB of 7.1 MB without LazyDataCompression set
See ยง1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MetaNeighbor 22.55 0.81 23.36
neighborVoting 15.25 0.51 15.77
plotBPlot 14.66 0.39 15.04
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MetaNeighbor 17.97 0.68 18.64
plotBPlot 12.78 0.43 13.21
neighborVoting 12.42 0.39 12.81
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* 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 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/MetaNeighbor.Rcheck/00check.log'
for details.
MetaNeighbor.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MetaNeighbor_1.14.0.tar.gz && rm -rf MetaNeighbor.buildbin-libdir && mkdir MetaNeighbor.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MetaNeighbor.buildbin-libdir MetaNeighbor_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MetaNeighbor_1.14.0.zip && rm MetaNeighbor_1.14.0.tar.gz MetaNeighbor_1.14.0.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
1 2634k 1 44467 0 0 278k 0 0:00:09 --:--:-- 0:00:09 278k
60 2634k 60 1601k 0 0 1385k 0 0:00:01 0:00:01 --:--:-- 1385k
100 2634k 100 2634k 0 0 1641k 0 0:00:01 0:00:01 --:--:-- 1641k
install for i386
* installing *source* package 'MetaNeighbor' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MetaNeighbor'
finding HTML links ... done
GOhuman html
GOmouse html
MetaNeighbor html
MetaNeighborUS html
extendClusterSet html
extractMetaClusters html
getCellType html
getStudyId html
ggPlotHeatmap html
makeClusterGraph html
makeClusterName html
mergeSCE html
mn_data html
neighborVoting html
orderCellTypes html
plotBPlot html
plotClusterGraph html
plotDotPlot html
plotHeatmap html
plotHeatmapPretrained html
plotMetaClusters html
plotUpset html
scoreMetaClusters html
splitClusters html
splitTestClusters html
splitTrainClusters html
standardizeLabel html
subsetClusterGraph html
topHits html
topHitsByStudy html
trainModel html
variableGenes 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 'MetaNeighbor' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MetaNeighbor' as MetaNeighbor_1.14.0.zip
* DONE (MetaNeighbor)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MetaNeighbor' successfully unpacked and MD5 sums checked
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MetaNeighbor.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(MetaNeighbor)
>
> test_check("MetaNeighbor")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
>
> proc.time()
user system elapsed
0.87 0.06 0.92
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MetaNeighbor.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(MetaNeighbor)
>
> test_check("MetaNeighbor")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
>
> proc.time()
user system elapsed
0.68 0.10 0.78
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MetaNeighbor.Rcheck/examples_i386/MetaNeighbor-Ex.timings
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MetaNeighbor.Rcheck/examples_x64/MetaNeighbor-Ex.timings
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