| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:06:45 -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 InterCellar package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/InterCellar.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 944/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| InterCellar 2.0.0 (landing page) Marta Interlandi
| 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: InterCellar |
| Version: 2.0.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:InterCellar.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings InterCellar_2.0.0.tar.gz |
| StartedAt: 2022-04-12 21:33:51 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 21:39:24 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 333.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: InterCellar.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:InterCellar.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings InterCellar_2.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/InterCellar.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 'InterCellar/DESCRIPTION' ... OK
* this is package 'InterCellar' version '2.0.0'
* 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 ... NOTE
Found the following hidden files and directories:
.dockerignore
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* 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
'cluster_names'
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 'n_int'
getBack2BackBarplot: no visible binding for global variable
'cluster_names'
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'
getBarplotDF : <anonymous>: no visible binding for global variable
'score'
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'
getClusterNetwork: no visible binding for global variable 'score'
getClusterSize: no visible binding for global variable 'clustA'
getClusterSize: no visible binding for global variable 'clustB'
getDistinctCouplets: no visible binding for global variable 'clustA'
getDistinctCouplets: no visible binding for global variable 'clustB'
getDistinctCouplets: no visible binding for global variable 'int_pair'
getDistinctCouplets: no visible binding for global variable
'cluster_pair'
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 'pathway_cellchat'
getGeneTable: no visible binding for global variable
'annotation_cellchat'
getGeneTable: no visible binding for global variable
'evidence_cellchat'
getGeneTable: no visible binding for global variable 'uniprotswissprot'
getGeneTable: no visible binding for global variable 'ensembl_gene_id'
getGeneTable: no visible binding for global variable 'hgnc_symbol'
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'
getPieChart: no visible binding for global variable 'condition'
getPieChart: no visible binding for global variable 'value'
getPieChart: no visible binding for global variable 'prop'
getPieChart: no visible binding for global variable 'ypos'
getPieChart: no visible binding for global variable 'perc'
getRankedTerms: no visible binding for global variable
'functional_term'
getRankedTerms: no visible binding for global variable 'int_pair'
getRankedTerms: no visible binding for global variable 'n_occurrence'
getSignif_table: no visible binding for global variable 'n_int_pair'
getSignif_table: no visible binding for global variable 'n_cond'
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'
getSunburst: no visible binding for global variable 'score'
getSunburst: no visible binding for global variable 'weightedInt'
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'
getUniqueIntpairs_byCond: no visible binding for global variable
'int_pair'
getUniqueIntpairs_byCond: no visible binding for global variable
'condition'
getUniqueIntpairs_byCond: no visible binding for global variable
'n_cond'
getUniqueIntpairs_byCond: no visible binding for global variable
'clustA'
getUniqueIntpairs_byCond: no visible binding for global variable
'clustB'
getUniqueIntpairs_byCond: no visible binding for global variable
'clust_pair'
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 'annotation_cellchat'
mod_gene_verse_server : <anonymous>: no visible binding for global
variable 'pathway_cellchat'
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 'int.type'
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'
mod_multi_cond_server : <anonymous>: no visible global function
definition for 'legend'
mod_multi_cond_server : <anonymous>: no visible binding for global
variable 'clustA'
mod_multi_cond_server : <anonymous>: no visible binding for global
variable 'p_value'
mod_multi_cond_server : <anonymous>: no visible binding for global
variable 'condition'
mod_multi_cond_server : <anonymous>: no visible binding for global
variable 'int_pair'
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'
read.icellnet: no visible binding for global variable 'X'
read.icellnet: no visible binding for global variable 'score'
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 X annotation_cellchat annotation_strategy
clustA clustB clust_pair cluster_names cluster_pair condition
diff_c1_c2 domain ensembl_gene_id evidence_cellchat functional_term
geneA geneA.1 geneB geneB.4 gene_symbol go_id go_linkage_type
hgnc_symbol int.type int_pair int_pairModule interacting_pair legend
mean_value n_cond n_int n_int_pair n_occurrence p_value
pathway_cellchat perc prop scSignalR_specific score type typeA typeB
uniprotswissprot value weightedInt ypos
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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-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://155.52.207.166/BBS/3.14/bioc/src/contrib/InterCellar_2.0.0.tar.gz && rm -rf InterCellar.buildbin-libdir && mkdir InterCellar.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=InterCellar.buildbin-libdir InterCellar_2.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL InterCellar_2.0.0.zip && rm InterCellar_2.0.0.tar.gz InterCellar_2.0.0.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 2382k 7 171k 0 0 640k 0 0:00:03 --:--:-- 0:00:03 641k
73 2382k 73 1743k 0 0 1373k 0 0:00:01 0:00:01 --:--:-- 1373k
100 2382k 100 2382k 0 0 1354k 0 0:00:01 0:00:01 --:--:-- 1355k
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
getClusterA_Names html
getClusterColors html
getClusterNames html
getClusterNetwork html
getClusterSize html
getDistinctCouplets html
getDotPlot_selInt html
getGObiomaRt html
getGeneTable html
getHitsf html
getIntFlow html
getNtermsBYdb html
getNumLR html
getPieChart html
getRadar_df html
getRankedTerms html
getSignif_table html
getSignificantFunctions html
getSignificantFunctions_multiCond html
getSunburst html
getUMAPipModules html
getUniqueDotplot html
getUniqueIntpairs_byCond html
goLink html
input.data html
read.CPDBv2 html
read.SCsignalR html
read.cellchat html
read.customInput html
read.icellnet html
run_app html
subsetAnnot_multiCond 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_2.0.0.zip
* DONE (InterCellar)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'InterCellar' successfully unpacked and MD5 sums checked
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InterCellar.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (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(InterCellar)
>
> test_check("InterCellar")
[ FAIL 0 | WARN 2 | SKIP 1 | PASS 6 ]
== Skipped tests ===============================================================
* interactive() is not TRUE (1)
[ FAIL 0 | WARN 2 | SKIP 1 | PASS 6 ]
>
> proc.time()
user system elapsed
7.87 0.64 8.76
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InterCellar.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(InterCellar)
>
> test_check("InterCellar")
[ FAIL 0 | WARN 2 | SKIP 1 | PASS 6 ]
== Skipped tests ===============================================================
* interactive() is not TRUE (1)
[ FAIL 0 | WARN 2 | SKIP 1 | PASS 6 ]
>
> proc.time()
user system elapsed
9.20 0.73 9.90
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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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