Ghislain FIEVET
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/adverSCarial |
| git_branch: RELEASE_3_20 |
| git_last_commit: c51e636 |
| git_last_commit_date: 2024-10-29 11:21:39 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 21/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| adverSCarial 1.4.0 (landing page) Ghislain FIEVET
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: 1.4.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:adverSCarial.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings adverSCarial_1.4.0.tar.gz |
| StartedAt: 2024-12-19 23:30:11 -0500 (Thu, 19 Dec 2024) |
| EndedAt: 2024-12-19 23:33:19 -0500 (Thu, 19 Dec 2024) |
| EllapsedTime: 188.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: adverSCarial.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:adverSCarial.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings adverSCarial_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/adverSCarial.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘adverSCarial/DESCRIPTION’ ... OK
* this is package ‘adverSCarial’ version ‘1.4.0’
* 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 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 38.935 4.197 51.581
advChar 19.775 1.494 22.175
matrixFromSCE 12.796 1.248 15.485
sceConvertToHGNC 12.819 0.976 15.133
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/adverSCarial.Rcheck/00check.log’
for details.
adverSCarial.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL adverSCarial ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘adverSCarial’ ... ** 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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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
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: 0.000341176986694336
Split number: 8/100
Split time: 0.000346899032592773
Split number: 16/100
Split time: 0.000366926193237305
Split number: 32/100
Split time: 0.000317096710205078
Split number: 64/100
Split time: 0.000322103500366211
Split number: 100/100
Split time: 0.000329017639160156
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: 0.000317096710205078
Split number: 8/100
Split time: 0.000301837921142578
Split number: 16/100
Split time: 0.000313997268676758
Split number: 32/100
Split time: 0.000316143035888672
Split number: 64/100
Split time: 0.00031590461730957
Split number: 100/100
Split time: 0.000323057174682617
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: 0.000325202941894531
Split number: 8/100
Split time: 0.000299930572509766
Split number: 16/100
Split time: 0.000374078750610352
Split number: 32/100
Split time: 0.000335931777954102
Split number: 64/100
Split time: 0.000336885452270508
Split number: 100/100
Split time: 0.0003509521484375
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: 0.000322103500366211
Split number: 8/100
Split time: 0.000300884246826172
Split number: 16/100
Split time: 0.000310897827148438
Split number: 32/100
Split time: 0.000305891036987305
Split number: 64/100
Split time: 0.000308990478515625
Split number: 100/100
Split time: 0.000313997268676758
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: 0.000332832336425781
Split number: 8/100
Split time: 0.000318050384521484
Split number: 16/100
Split time: 0.00032496452331543
Split number: 32/100
Split time: 0.000314950942993164
Split number: 64/100
Split time: 0.000330209732055664
Split number: 100/100
Split time: 0.000337123870849609
RUNIT TEST PROTOCOL -- Thu Dec 19 23:33:04 2024
***********************************************
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
10.306 0.567 11.106
adverSCarial.Rcheck/adverSCarial-Ex.timings
| name | user | system | elapsed | |
| MClassifier | 38.935 | 4.197 | 51.581 | |
| advCGD | 0.055 | 0.003 | 0.058 | |
| advChar | 19.775 | 1.494 | 22.175 | |
| advGridMinChange | 0.682 | 0.128 | 0.825 | |
| advList | 0.029 | 0.003 | 0.044 | |
| advMaxChange | 0.282 | 0.025 | 0.411 | |
| advModifications | 0.280 | 0.024 | 0.320 | |
| advRandWalkMinChange | 0.733 | 0.033 | 0.874 | |
| advSingleGene | 0.304 | 0.026 | 0.388 | |
| getSignGenes | 0.015 | 0.001 | 0.021 | |
| matrixFromSCE | 12.796 | 1.248 | 15.485 | |
| maxChangeOverview | 0.392 | 0.025 | 0.422 | |
| predictWithNewValue | 0.279 | 0.022 | 0.312 | |
| sceConvertToHGNC | 12.819 | 0.976 | 15.133 | |
| singleGeneOverview | 0.469 | 0.033 | 0.506 | |