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 12:04 -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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:adverSCarial.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings adverSCarial_1.4.0.tar.gz |
| StartedAt: 2024-12-19 22:45:45 -0500 (Thu, 19 Dec 2024) |
| EndedAt: 2024-12-19 22:47:51 -0500 (Thu, 19 Dec 2024) |
| EllapsedTime: 126.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: adverSCarial.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:adverSCarial.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings adverSCarial_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/adverSCarial.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 26.76 4.01 31.19
advChar 11.88 1.76 13.61
sceConvertToHGNC 11.05 1.61 12.88
matrixFromSCE 8.98 1.38 10.54
* 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
'F:/biocbuild/bbs-3.20-bioc/meat/adverSCarial.Rcheck/00check.log'
for details.
adverSCarial.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL adverSCarial ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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: 0.000195026397705078
Split number: 8/100
Split time: 0.000193119049072266
Split number: 16/100
Split time: 0.000243902206420898
Split number: 32/100
Split time: 0.000204086303710938
Split number: 64/100
Split time: 0.000228166580200195
Split number: 100/100
Split time: 0.000225067138671875
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: 0.000196933746337891
Split number: 8/100
Split time: 0.000185966491699219
Split number: 16/100
Split time: 0.00018310546875
Split number: 32/100
Split time: 0.000192880630493164
Split number: 64/100
Split time: 0.000228166580200195
Split number: 100/100
Split time: 0.000248908996582031
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: 0.000217914581298828
Split number: 8/100
Split time: 0.000205039978027344
Split number: 16/100
Split time: 0.000196933746337891
Split number: 32/100
Split time: 0.000221967697143555
Split number: 64/100
Split time: 0.000230073928833008
Split number: 100/100
Split time: 0.000226020812988281
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: 0.000216960906982422
Split number: 8/100
Split time: 0.000224113464355469
Split number: 16/100
Split time: 0.000206947326660156
Split number: 32/100
Split time: 0.000236034393310547
Split number: 64/100
Split time: 0.000247001647949219
Split number: 100/100
Split time: 0.000244140625
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: 0.000246047973632812
Split number: 8/100
Split time: 0.000249147415161133
Split number: 16/100
Split time: 0.000226020812988281
Split number: 32/100
Split time: 0.000263214111328125
Split number: 64/100
Split time: 0.000293970108032227
Split number: 100/100
Split time: 0.000272989273071289
RUNIT TEST PROTOCOL -- Thu Dec 19 22:47:39 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
5.96 0.42 6.32
adverSCarial.Rcheck/adverSCarial-Ex.timings
| name | user | system | elapsed | |
| MClassifier | 26.76 | 4.01 | 31.19 | |
| advCGD | 0.02 | 0.02 | 0.03 | |
| advChar | 11.88 | 1.76 | 13.61 | |
| advGridMinChange | 0.34 | 0.08 | 0.43 | |
| advList | 0.02 | 0.00 | 0.01 | |
| advMaxChange | 0.17 | 0.03 | 0.20 | |
| advModifications | 0.19 | 0.03 | 0.22 | |
| advRandWalkMinChange | 0.37 | 0.04 | 0.41 | |
| advSingleGene | 0.21 | 0.01 | 0.23 | |
| getSignGenes | 0.02 | 0.00 | 0.02 | |
| matrixFromSCE | 8.98 | 1.38 | 10.54 | |
| maxChangeOverview | 0.30 | 0.04 | 0.34 | |
| predictWithNewValue | 0.18 | 0.02 | 0.20 | |
| sceConvertToHGNC | 11.05 | 1.61 | 12.88 | |
| singleGeneOverview | 0.35 | 0.01 | 0.36 | |