| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:07:20 -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 scTreeViz package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scTreeViz.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 1750/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scTreeViz 1.0.0 (landing page) Jayaram Kancherla
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: scTreeViz |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scTreeViz.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings scTreeViz_1.0.0.tar.gz |
| StartedAt: 2022-04-13 02:38:40 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 02:49:30 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 649.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scTreeViz.Rcheck |
| Warnings: 0 |
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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:scTreeViz.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings scTreeViz_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/scTreeViz.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 'scTreeViz/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scTreeViz' version '1.0.0'
* 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 whether package 'scTreeViz' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.generate_hierarchy_tree: no visible binding for global variable
'otu_index'
.generate_leaf_of_table: no visible binding for global variable 'leaf'
.generate_leaf_of_table: no visible binding for global variable
'otu_index'
.generate_leaf_of_table: no visible binding for global variable 'id'
.generate_node_ids : <anonymous>: no visible global function definition
for '.'
.generate_node_ids : <anonymous>: no visible binding for global
variable 'otu_index'
.generate_nodes_table: no visible binding for global variable 'id'
.generate_nodes_table: no visible binding for global variable 'lineage'
.generate_nodes_table: no visible binding for global variable
'node_label'
.generate_nodes_table: no visible binding for global variable 'level'
.preprocessAndCreateTreeViz: no visible global function definition for
'chracter'
getNodes,TreeIndex: no visible binding for global variable 'level'
getNodes,TreeIndex: no visible binding for global variable 'id'
splitAt,TreeIndex: no visible binding for global variable 'level'
splitAt,TreeIndex: no visible binding for global variable 'id'
splitAt,TreeIndex: no visible binding for global variable 'lineage'
splitAt,TreeIndex: no visible binding for global variable 'leaf'
splitAt,TreeIndex: no visible binding for global variable 'otu_index'
splitAt,TreeIndex: no visible global function definition for '.'
splitAt,TreeIndex: no visible binding for global variable 'node_label'
Undefined global functions or variables:
. chracter id leaf level lineage node_label otu_index
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
TreeIndex-methods 20.32 0.87 21.16
TreeViz 9.88 0.15 10.01
createFromSCE 9.69 0.22 9.91
TreeIndex 9.64 0.13 9.74
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
TreeIndex-methods 23.81 0.17 23.94
TreeIndex 10.69 0.04 10.72
TreeViz 9.53 0.13 9.64
createFromSCE 9.54 0.00 9.55
* 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 NOTE
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/scTreeViz.Rcheck/00check.log'
for details.
scTreeViz.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/scTreeViz_1.0.0.tar.gz && rm -rf scTreeViz.buildbin-libdir && mkdir scTreeViz.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scTreeViz.buildbin-libdir scTreeViz_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL scTreeViz_1.0.0.zip && rm scTreeViz_1.0.0.tar.gz scTreeViz_1.0.0.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
7 1491k 7 118k 0 0 264k 0 0:00:05 --:--:-- 0:00:05 263k
66 1491k 66 999k 0 0 691k 0 0:00:02 0:00:01 0:00:01 690k
100 1491k 100 1491k 0 0 838k 0 0:00:01 0:00:01 --:--:-- 838k
install for i386
* installing *source* package 'scTreeViz' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'scTreeViz'
finding HTML links ... done
ClusterHierarchy-class html
ClusterHierarchy html
EpivizTreeData-class html
TreeIndex-class html
TreeIndex-methods html
TreeIndex html
TreeViz-class html
TreeViz-methods html
TreeViz html
TreeVizApp-class html
createFromSCE html
createFromSeurat html
createTreeViz html
dot-generate_hierarchy_tree html
dot-generate_leaf_of_table html
dot-generate_node_ids html
dot-generate_nodes_table html
dot-replaceNAFeatures html
set_gene_list html
startTreeviz 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 'scTreeViz' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scTreeViz' as scTreeViz_1.0.0.zip
* DONE (scTreeViz)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'scTreeViz' successfully unpacked and MD5 sums checked
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scTreeViz.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(scTreeViz)
Loading required package: epivizr
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
>
> test_check("scTreeViz")
[1] "root" "3.cluster3" "5.cluster5" "6.cluster6" "samples"
[1] "root" "3.cluster3" "5.cluster5"
[1] "1.cluster1" "2.cluster2" "3.cluster3" "samples"
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 7 ]
== Skipped tests ===============================================================
* conflict between new Seurat and Summarized Experiment (1)
* need data here (1)
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 7 ]
>
> proc.time()
user system elapsed
23.00 2.18 25.17
|
scTreeViz.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(scTreeViz)
Loading required package: epivizr
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
>
> test_check("scTreeViz")
[1] "root" "3.cluster3" "5.cluster5" "6.cluster6" "samples"
[1] "root" "3.cluster3" "5.cluster5"
[1] "1.cluster1" "2.cluster2" "3.cluster3" "samples"
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 7 ]
== Skipped tests ===============================================================
* conflict between new Seurat and Summarized Experiment (1)
* need data here (1)
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 7 ]
>
> proc.time()
user system elapsed
25.59 1.04 26.62
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scTreeViz.Rcheck/examples_i386/scTreeViz-Ex.timings
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scTreeViz.Rcheck/examples_x64/scTreeViz-Ex.timings
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