| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:08 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the InterCellar package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/InterCellar.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 933/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| InterCellar 1.0.0 (landing page) Marta Interlandi
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: InterCellar |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:InterCellar.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings InterCellar_1.0.0.tar.gz |
| StartedAt: 2021-10-15 00:48:30 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 00:53:21 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 291.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: InterCellar.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:InterCellar.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings InterCellar_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/InterCellar.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'InterCellar/DESCRIPTION' ... OK
* this is package 'InterCellar' 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 'InterCellar' 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
buildPairsbyFunctionMatrix: warning in
dcast(as.data.table(functions_df), int_pair ~ functional_term, fun =
function(x) min(sum(x), 1), value.var = "value"): partial argument
match of 'fun' to 'fun.aggregate'
annotateGO: no visible binding for global variable 'go_linkage_type'
annotateGO: no visible binding for global variable 'domain'
annotateGO: no visible binding for global variable 'int_pair'
annotateGO: no visible binding for global variable 'geneA'
annotateGO: no visible binding for global variable 'geneB'
annotateGO: no visible binding for global variable 'gene_symbol'
annotateGO: no visible binding for global variable 'go_id'
annotateGO: no visible binding for global variable 'geneA.1'
annotateGO: no visible binding for global variable 'geneB.4'
annotatePathways: no visible binding for global variable 'int_pair'
annotatePathways: no visible binding for global variable 'geneA'
annotatePathways: no visible binding for global variable 'geneB'
combineAnnotations: no visible binding for global variable 'int_pair'
combineAnnotations: no visible binding for global variable
'functional_term'
createBarPlot1_ggplot: no visible binding for global variable
'clusters'
createBarPlot1_ggplot: no visible binding for global variable 'n_int'
createBarPlot1_ggplot: no visible binding for global variable 'type'
createBarPlot2_ggplot: no visible binding for global variable
'Clusters'
createBarPlot2_ggplot: no visible binding for global variable 'Num_int'
getBack2BackBarplot: no visible binding for global variable 'condition'
getBack2BackBarplot: no visible binding for global variable 'n_int'
getBack2BackBarplot: no visible binding for global variable 'clusters'
getBack2BackBarplot: no visible binding for global variable 'type'
getBack2BackBarplot: no visible binding for global variable
'diff_c1_c2'
getBarplotDF : <anonymous>: no visible binding for global variable
'clustA'
getBarplotDF : <anonymous>: no visible binding for global variable
'clustB'
getBarplotDF : <anonymous>: no visible binding for global variable
'int.type'
getBarplotDF2: no visible binding for global variable 'clustA'
getBarplotDF2: no visible binding for global variable 'clustB'
getClusterNetwork: no visible binding for global variable 'clustA'
getClusterNetwork: no visible binding for global variable 'clustB'
getClusterSize: no visible binding for global variable 'clustA'
getClusterSize: no visible binding for global variable 'clustB'
getDotPlot_selInt: no visible binding for global variable 'clustA'
getDotPlot_selInt: no visible binding for global variable 'clustB'
getDotPlot_selInt: no visible binding for global variable 'int_pair'
getDotPlot_selInt: no visible binding for global variable
'cluster_pair'
getDotPlot_selInt: no visible binding for global variable 'score'
getGeneTable: no visible binding for global variable 'int_pair'
getGeneTable: no visible binding for global variable 'geneA'
getGeneTable: no visible binding for global variable 'geneB'
getGeneTable: no visible binding for global variable 'typeA'
getGeneTable: no visible binding for global variable 'typeB'
getGeneTable: no visible binding for global variable
'annotation_strategy'
getGeneTable: no visible binding for global variable 'uniprotswissprot'
getGeneTable: no visible binding for global variable 'ensembl_gene_id'
getIntFlow: no visible binding for global variable 'typeA'
getIntFlow: no visible binding for global variable 'typeB'
getIntFlow: no visible binding for global variable 'clustA'
getIntFlow: no visible binding for global variable 'clustB'
getRadarPlot: no visible global function definition for 'legend'
getRankedTerms: no visible binding for global variable
'functional_term'
getRankedTerms: no visible binding for global variable 'uniq_score'
getRankedTerms: no visible binding for global variable 'int_pair'
getRankedTerms: no visible binding for global variable 'avg_uniqueness'
getSunburst: no visible binding for global variable 'clustA'
getSunburst: no visible binding for global variable 'int_pair'
getSunburst: no visible binding for global variable 'clustB'
getUniqueDotplot: no visible binding for global variable 'int_pair'
getUniqueDotplot: no visible binding for global variable 'cluster_pair'
getUniqueDotplot: no visible binding for global variable 'condition'
mod_cluster_verse_server : <anonymous>: no visible binding for global
variable 'clustA'
mod_cluster_verse_server : <anonymous>: no visible binding for global
variable 'clustB'
mod_cluster_verse_server : <anonymous>: no visible binding for global
variable 'score'
mod_cluster_verse_server : <anonymous>: no visible binding for global
variable 'int.type'
mod_function_verse_server : <anonymous>: no visible binding for global
variable 'GO_id'
mod_function_verse_server : <anonymous>: no visible binding for global
variable 'int_pair'
mod_gene_verse_server : <anonymous>: no visible binding for global
variable 'scSignalR_specific'
mod_gene_verse_server : <anonymous>: no visible binding for global
variable 'int_pair'
mod_gene_verse_server : <anonymous>: no visible binding for global
variable 'clustA'
mod_gene_verse_server : <anonymous>: no visible binding for global
variable 'clustB'
mod_int_pair_modules_server : <anonymous>: no visible binding for
global variable 'int_pair'
mod_int_pair_modules_server : <anonymous>: no visible binding for
global variable 'int_pairModule'
mod_int_pair_modules_server : <anonymous>: no visible binding for
global variable 'p_value'
read.CPDBv2: no visible binding for global variable 'cluster_pair'
read.CPDBv2: no visible binding for global variable 'mean_value'
read.CPDBv2: no visible binding for global variable 'interacting_pair'
read.CPDBv2: no visible binding for global variable 'p_value'
updateInputLR: no visible binding for global variable 'typeA'
updateInputLR: no visible binding for global variable 'typeB'
updateInputLR: no visible binding for global variable 'int_pair'
Undefined global functions or variables:
Clusters GO_id Num_int annotation_strategy avg_uniqueness clustA
clustB cluster_pair clusters condition diff_c1_c2 domain
ensembl_gene_id functional_term geneA geneA.1 geneB geneB.4
gene_symbol go_id go_linkage_type int.type int_pair int_pairModule
interacting_pair legend mean_value n_int p_value scSignalR_specific
score type typeA typeB uniprotswissprot uniq_score
Consider adding
importFrom("graphics", "legend")
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 R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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-3.13-bioc/meat/InterCellar.Rcheck/00check.log'
for details.
InterCellar.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/InterCellar_1.0.0.tar.gz && rm -rf InterCellar.buildbin-libdir && mkdir InterCellar.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=InterCellar.buildbin-libdir InterCellar_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL InterCellar_1.0.0.zip && rm InterCellar_1.0.0.tar.gz InterCellar_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
59 2416k 59 1447k 0 0 2229k 0 0:00:01 --:--:-- 0:00:01 2230k
100 2416k 100 2416k 0 0 2553k 0 --:--:-- --:--:-- --:--:-- 2551k
install for i386
* installing *source* package 'InterCellar' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'InterCellar'
finding HTML links ... done
annotateGO html
annotatePathways html
buildPairsbyFunctionMatrix html
checkLL_RR html
circlePlot html
combineAnnotations html
createBarPlot1_ggplot html
createBarPlot2_CV html
createBarPlot2_ggplot html
createBarPlot_CV html
createNetwork html
dendroIntPairModules html
elbowPoint html
ensemblLink html
getBack2BackBarplot html
getBarplotDF html
getBarplotDF2 html
getClusterNames html
getClusterNetwork html
getClusterSize html
getDotPlot_selInt html
getGObiomaRt html
getGeneTable html
getHitsf html
getIntFlow html
getNtermsBYdb html
getNumLR html
getRadarPlot html
getRankedTerms html
getSignificantFunctions html
getSunburst html
getUMAPipModules html
getUniqueDotplot html
goLink html
input.data html
read.CPDBv2 html
read.SCsignalR html
read.customInput html
run_app html
subsetFuncMatBYFlow html
swap.RLint html
uniprotLink html
updateInputLR 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 'InterCellar' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'InterCellar' as InterCellar_1.0.0.zip
* DONE (InterCellar)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'InterCellar' successfully unpacked and MD5 sums checked
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InterCellar.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(InterCellar)
>
> test_check("InterCellar")
== Skipped tests ===============================================================
* interactive() is not TRUE (1)
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 6 ]
>
> proc.time()
user system elapsed
7.81 0.84 8.95
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InterCellar.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(InterCellar)
>
> test_check("InterCellar")
== Skipped tests ===============================================================
* interactive() is not TRUE (1)
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 6 ]
>
> proc.time()
user system elapsed
9.14 0.57 9.70
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InterCellar.Rcheck/examples_i386/InterCellar-Ex.timings
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InterCellar.Rcheck/examples_x64/InterCellar-Ex.timings
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