Ghislain FIEVET
| Snapshot Date: 2025-12-21 13:40 -0500 (Sun, 21 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/adverSCarial |
| git_branch: devel |
| git_last_commit: a19db67 |
| git_last_commit_date: 2025-10-29 11:23:46 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-22 11:34 -0500 (Mon, 22 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4878 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 | ||||
| Package 21/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| adverSCarial 1.9.0 (landing page) Ghislain FIEVET
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the adverSCarial package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/adverSCarial.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: adverSCarial |
| Version: 1.9.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:adverSCarial.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings adverSCarial_1.9.0.tar.gz |
| StartedAt: 2025-12-21 20:43:42 -0500 (Sun, 21 Dec 2025) |
| EndedAt: 2025-12-21 20:45:06 -0500 (Sun, 21 Dec 2025) |
| EllapsedTime: 84.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: adverSCarial.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:adverSCarial.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings adverSCarial_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/adverSCarial.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘adverSCarial/DESCRIPTION’ ... OK
* this is package ‘adverSCarial’ version ‘1.9.0’
* 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:
vignettes/.RData
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘adverSCarial’ 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 loading without being on the library search path ... 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
.advModificationsFunction: no visible global function definition for
‘is’
.advModificationsFunction : <anonymous>: no visible global function
definition for ‘is’
.advModificationsNotFunction: no visible global function definition for
‘is’
.advModificationsNotFunction: no visible global function definition for
‘counts’
.advModificationsNotFunction : <anonymous>: no visible global function
definition for ‘is’
.randWalkGetSeed: no visible global function definition for
‘SingleCellExperiment’
.randWalkGetSeed: no visible global function definition for ‘is’
.randWalkTryNewVector: no visible global function definition for
‘SingleCellExperiment’
.randWalkTryNewVector: no visible global function definition for ‘is’
MClassifier: no visible global function definition for ‘is’
MClassifier: no visible global function definition for ‘counts’
advChar: no visible global function definition for ‘new’
advGridMinChange: no visible global function definition for ‘is’
advGridMinChange: no visible global function definition for ‘counts’
advGridMinChange: no visible global function definition for
‘SingleCellExperiment’
advList: no visible global function definition for ‘new’
advMaxChange: no visible global function definition for ‘is’
advMaxChange: no visible global function definition for ‘counts’
advMaxChange: no visible global function definition for ‘new’
advModifications: no visible global function definition for ‘is’
advModifications: no visible global function definition for ‘counts’
advModifications: no visible global function definition for
‘SingleCellExperiment’
advRandWalkMinChange: no visible global function definition for ‘is’
advRandWalkMinChange: no visible global function definition for
‘counts’
advSingleGene: no visible global function definition for ‘is’
advSingleGene: no visible global function definition for ‘counts’
advSingleGene: no visible binding for '<<-' assignment to
‘lastResLength’
advSingleGene : <anonymous>: no visible binding for global variable
‘lastResLength’
advSingleGene : <anonymous>: no visible binding for '<<-' assignment to
‘lastResLength’
advSingleGene: no visible global function definition for ‘new’
getDistantCouples: no visible global function definition for ‘combn’
getSignGenes : <anonymous>: no visible global function definition for
‘wilcox.test’
getSignGenes : <anonymous>: no visible global function definition for
‘t.test’
matrixFromSCE: no visible global function definition for ‘is’
matrixFromSCE: no visible global function definition for ‘colData’
maxChangeOverview: no visible global function definition for ‘is’
maxChangeOverview: no visible global function definition for ‘counts’
predictWithNewValue: no visible global function definition for ‘is’
sceConvertToHGNC: no visible global function definition for ‘is’
sceConvertToHGNC: no visible global function definition for
‘SingleCellExperiment’
sceConvertToHGNC: no visible global function definition for ‘colData’
singleGeneOverview: no visible global function definition for ‘is’
singleGeneOverview: no visible global function definition for ‘counts’
Undefined global functions or variables:
SingleCellExperiment colData combn counts is lastResLength new t.test
wilcox.test
Consider adding
importFrom("methods", "is", "new")
importFrom("stats", "t.test", "wilcox.test")
importFrom("utils", "combn")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) advCGD.Rd:31-34: Lost braces
31 | classifier = function(expr, clusters, target){
| ^
checkRd: (-1) advGridMinChange.Rd:34-37: Lost braces
34 | classifier = function(expr, clusters, target){
| ^
checkRd: (-1) advMaxChange.Rd:39-42: Lost braces
39 | classifier = function(expr, clusters, target){
| ^
checkRd: (-1) advRandWalkMinChange.Rd:36-39: Lost braces
36 | classifier = function(expr, clusters, target){
| ^
checkRd: (-1) advSingleGene.Rd:43-46: Lost braces
43 | classifier = function(expr, clusters, target){
| ^
checkRd: (-1) maxChangeOverview.Rd:35-38: Lost braces
35 | classifier = function(expr, clusters, target){
| ^
checkRd: (-1) predictWithNewValue.Rd:36-39: Lost braces
36 | classifier = function(expr, clusters, target){
| ^
checkRd: (-1) singleGeneOverview.Rd:37-40: Lost braces
37 | classifier = function(expr, clusters, target){
| ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘advTraining’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'advMaxChange.Rd'
‘slot’
Undocumented arguments in Rd file 'advModifications.Rd'
‘slot’
Undocumented arguments in Rd file 'advSingleGene.Rd'
‘slot’
Undocumented arguments in Rd file 'predictWithNewValue.Rd'
‘slot’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
‘figure’
Please remove from your package.
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MClassifier 20.903 2.662 24.090
sceConvertToHGNC 7.020 1.095 8.439
advChar 7.486 0.522 8.020
matrixFromSCE 7.088 0.800 8.253
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/adverSCarial.Rcheck/00check.log’
for details.
adverSCarial.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL adverSCarial ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘adverSCarial’ ... ** this is package ‘adverSCarial’ version ‘1.9.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (adverSCarial)
adverSCarial.Rcheck/tests/runTests.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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.
> BiocGenerics:::testPackage("adverSCarial")
Running combination: 1 on 3
Running combination: 2 on 3
Running combination: 3 on 3
Warning: stack imbalance in 'dim', 33 then 35
Warning: stack imbalance in '==', 32 then 34
Warning: stack imbalance in 'all', 31 then 33
Warning: stack imbalance in '{', 21 then 23
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
result length: 3
Running first batch to determine walk seed: 1 on 3
Running first batch to determine walk seed: 2 on 3
Running first batch to determine walk seed: 3 on 3
No modified type, try with a higher firstBatch argument
predictWithNewValue data.frame data.frame
Split number: 1/100
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: b
Split number: 2/100
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: b
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: b
Split number: 4/100
Split time: 0.000134706497192383
Split number: 8/100
Split time: 0.000161886215209961
Split number: 16/100
Split time: 0.000131845474243164
Split number: 32/100
Split time: 0.000138044357299805
Split number: 64/100
Split time: 0.000134468078613281
Split number: 100/100
Split time: 0.000135421752929688
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
result length: 3
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
result length: 3
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
result length: 3
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
result length: 3
predictWithNewValue data.frame data.frame
predictWithNewValue data.frame data.frame
Split number: 1/100
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: b
Split number: 2/100
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: b
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: b
Split number: 4/100
Split time: 0.000129222869873047
Split number: 8/100
Split time: 0.000124931335449219
Split number: 16/100
Split time: 0.000117063522338867
Split number: 32/100
Split time: 0.000132083892822266
Split number: 64/100
Split time: 0.000123977661132812
Split number: 100/100
Split time: 0.000137090682983398
predictWithNewValue data.frame data.frame
Split number: 1/100
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: t
Split number: 2/100
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: t
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: t
Split number: 4/100
Split time: 0.000132560729980469
Split number: 8/100
Split time: 0.000121831893920898
Split number: 16/100
Split time: 0.000120401382446289
Split number: 32/100
Split time: 0.000120639801025391
Split number: 64/100
Split time: 0.000131845474243164
Split number: 100/100
Split time: 0.000130891799926758
predictWithNewValue data.frame data.frame
Split number: 1/100
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: b
Split number: 2/100
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: b
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: b
Split number: 4/100
Split time: 0.000128507614135742
Split number: 8/100
Split time: 0.000118732452392578
Split number: 16/100
Split time: 0.000136852264404297
Split number: 32/100
Split time: 0.000126838684082031
Split number: 64/100
Split time: 0.000134944915771484
Split number: 100/100
Split time: 0.000131845474243164
predictWithNewValue data.frame data.frame
Split number: 1/100
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: t
Split number: 2/100
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: t
predictWithNewValue data.frame data.frame
cellType: b
classifTarget: b
target: t
Split number: 4/100
Split time: 0.000131130218505859
Split number: 8/100
Split time: 0.000138759613037109
Split number: 16/100
Split time: 0.000127077102661133
Split number: 32/100
Split time: 0.000138282775878906
Split number: 64/100
Split time: 0.000128030776977539
Split number: 100/100
Split time: 0.000127315521240234
RUNIT TEST PROTOCOL -- Sun Dec 21 20:45:00 2025
***********************************************
Number of test functions: 8
Number of errors: 0
Number of failures: 0
1 Test Suite :
adverSCarial RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
4.866 0.260 5.115
adverSCarial.Rcheck/adverSCarial-Ex.timings
| name | user | system | elapsed | |
| MClassifier | 20.903 | 2.662 | 24.090 | |
| advCGD | 0.024 | 0.002 | 0.025 | |
| advChar | 7.486 | 0.522 | 8.020 | |
| advGridMinChange | 0.328 | 0.008 | 0.336 | |
| advList | 0.012 | 0.000 | 0.012 | |
| advMaxChange | 0.163 | 0.003 | 0.165 | |
| advModifications | 0.179 | 0.006 | 0.186 | |
| advRandWalkMinChange | 0.328 | 0.012 | 0.340 | |
| advSingleGene | 0.150 | 0.008 | 0.158 | |
| getSignGenes | 0.007 | 0.000 | 0.007 | |
| matrixFromSCE | 7.088 | 0.800 | 8.253 | |
| maxChangeOverview | 0.166 | 0.017 | 0.182 | |
| predictWithNewValue | 0.117 | 0.013 | 0.130 | |
| sceConvertToHGNC | 7.020 | 1.095 | 8.439 | |
| singleGeneOverview | 0.198 | 0.019 | 0.217 | |