Multiple platform build/check report for BioC 3.20 - CHECK results for adverSCarial on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"	4690
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life"	4404
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life"	4353
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*

CHECK results for adverSCarial on kjohnson3

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.

raw results

Summary

Package: adverSCarial

Version: 1.3.1

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_1.3.1.tar.gz

StartedAt: 2024-06-20 18:58:47 -0400 (Thu, 20 Jun 2024)

EndedAt: 2024-06-20 18:59:14 -0400 (Thu, 20 Jun 2024)

EllapsedTime: 27.3 seconds

RetCode: 1

Status: ERROR

CheckDir: adverSCarial.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/adverSCarial.Rcheck’
* using R version 4.4.1 RC (2024-06-06 r86719)
* using platform: aarch64-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 Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘adverSCarial/DESCRIPTION’ ... OK
* this is package ‘adverSCarial’ version ‘1.3.1’
* 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 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’
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’
MClassifier: no visible global function definition for ‘is’
MClassifier: 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:
  colData combn counts is lastResLength new SingleCellExperiment 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) advGridMinChange.Rd:34-37: Lost braces
    34 | classifier = function(expr, clusters, target){
       |                                              ^
checkRd: (-1) advIGD4C.Rd:31-34: Lost braces
    31 | 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 ... ERROR
Running examples in ‘adverSCarial-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: advIGD4C
> ### Title: Implementation of the IDG4C algorithm.
> ### Aliases: advIGD4C
> 
> ### ** Examples
> 
> MyClassifier <- function(expr, clusters, target) {
+    typePredictions <- as.data.frame(matrix(nrow=nrow(expr), ncol=length(unique(clusters))))
+    colnames(typePredictions) <- unique(clusters)
+    typePredictions[unique(clusters)[1]] <- c(1,0,0,0)
+    typePredictions[unique(clusters)[2]] <- c(0,1,1,1)
+    rownames(typePredictions) <- 1:4
+ 
+    list(prediction="T cell", odd=1,
+                      typePredictions=t(typePredictions),
+                      cellTypes=c("B cell","T cell","T cell","T cell"))
+ }
> rna_expression <- data.frame(CD4=c(0,0,0,0), CD8A=c(1,1,1,1),
+     CD8B=c(2,2,3,3))
> genes <- c("CD4", "CD8A")
> clusters_id <- c("B cell","T cell","T cell","T cell")
> 
> advIGD4C(rna_expression, clusters_id, "T cell",
+   MyClassifier, genes=genes, verbose=T)
Error in advIGD4C(rna_expression, clusters_id, "T cell", MyClassifier,  : 
  T used instead of TRUE
Execution halted
* 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: 1 ERROR, 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/adverSCarial.Rcheck/00check.log’
for details.

Installation output

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-arm64/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)

Tests output

adverSCarial.Rcheck/tests/runTests.Rout


R version 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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: 3.48091125488281e-05
Split number: 8/100
Split time: 3.09944152832031e-05
Split number: 16/100
Split time: 3.09944152832031e-05
Split number: 32/100
Split time: 3.19480895996094e-05
Split number: 64/100
Split time: 3.09944152832031e-05
Split number: 100/100
Split time: 3.29017639160156e-05
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: 3.21865081787109e-05
Split number: 8/100
Split time: 3.00407409667969e-05
Split number: 16/100
Split time: 2.81333923339844e-05
Split number: 32/100
Split time: 2.88486480712891e-05
Split number: 64/100
Split time: 2.71797180175781e-05
Split number: 100/100
Split time: 2.78949737548828e-05
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: 2.88486480712891e-05
Split number: 8/100
Split time: 2.78949737548828e-05
Split number: 16/100
Split time: 3.21865081787109e-05
Split number: 32/100
Split time: 2.69412994384766e-05
Split number: 64/100
Split time: 2.81333923339844e-05
Split number: 100/100
Split time: 3.38554382324219e-05
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: 2.90870666503906e-05
Split number: 8/100
Split time: 2.78949737548828e-05
Split number: 16/100
Split time: 2.69412994384766e-05
Split number: 32/100
Split time: 2.59876251220703e-05
Split number: 64/100
Split time: 2.81333923339844e-05
Split number: 100/100
Split time: 2.78949737548828e-05
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: 2.69412994384766e-05
Split number: 8/100
Split time: 2.59876251220703e-05
Split number: 16/100
Split time: 2.59876251220703e-05
Split number: 32/100
Split time: 2.59876251220703e-05
Split number: 64/100
Split time: 2.69412994384766e-05
Split number: 100/100
Split time: 2.59876251220703e-05


RUNIT TEST PROTOCOL -- Thu Jun 20 18:59:10 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 
  1.762   0.080   1.838

Example timings

adverSCarial.Rcheck/adverSCarial-Ex.timings

name	user	system	elapsed
MClassifier	8.145	0.540	9.361
advChar	2.278	0.443	2.721
advGridMinChange	0.077	0.005	0.083