Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘adverSCarial/DESCRIPTION’ ... OK
* preparing ‘adverSCarial’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘adverSCarial_0.99.26.tar.gz’

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 BiocCheckGitClone('adverSCarial')

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─ BiocCheckVersion: 1.37.0
─ BiocVersion: 3.18
─ Package: adverSCarial
─ PackageVersion: 0.99.26
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2983/07ec83cd171f7f2f3370fe0809e7e22a7fad52e1/adverSCarial
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




===============================

 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2983/07ec83cd171f7f2f3370fe0809e7e22a7fad52e1/adverSCarial.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84266)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘adverSCarial/DESCRIPTION’ ... OK
* this is package ‘adverSCarial’ version ‘0.99.26’
* 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 ... WARNING
Found the following file with a non-portable file name:
  vignettes/figure/chetah dimplot-1.png
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘adverSCarial’ can be installed ... WARNING
Found the following significant warnings:
  Warning: For function ‘show’, signature ‘advChar’: argument in method definition changed from (x) to (object)
  Warning: For function ‘show’, signature ‘advList’: argument in method definition changed from (x) to (object)
See ‘/Users/pkgbuild/packagebuilder/workers/jobs/2983/07ec83cd171f7f2f3370fe0809e7e22a7fad52e1/adverSCarial.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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
* checking whether the package can be loaded ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] WARNING
Error: package or namespace load failed for ‘adverSCarial’:
 .onLoad failed in loadNamespace() for 'adverSCarial', details:
  call: setMethod("show", "advChar", function(x) {
  error: could not find function "setMethod"
Execution halted

It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package.  All dependencies must be
declared in DESCRIPTION.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* checking whether the package can be unloaded cleanly ... [0s/0s] WARNING
Error: package or namespace load failed for ‘adverSCarial’:
 .onLoad failed in loadNamespace() for 'adverSCarial', details:
  call: setMethod("show", "advChar", function(x) {
  error: could not find function "setMethod"
Execution halted
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] WARNING
Error: .onLoad failed in loadNamespace() for 'adverSCarial', details:
  call: setMethod("show", "advChar", function(x) {
  error: could not find function "setMethod"
Execution halted

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking startup messages can be suppressed ... [0s/0s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Error: .onLoad failed in loadNamespace() for 'adverSCarial', details:
  call: setMethod("show", "advChar", function(x) {
  error: could not find function "setMethod"
Call sequence:
3: stop(gettextf("%s failed in %s() for '%s', details:\n  call: %s\n  error: %s", 
       hookname, "loadNamespace", pkgname, deparse(conditionCall(res))[1L], 
       conditionMessage(res)), call. = FALSE, domain = NA)
2: runHook(".onLoad", env, package.lib, package)
1: loadNamespace(package, lib.loc)
Execution halted
* checking S3 generic/method consistency ... WARNING
Error: .onLoad failed in loadNamespace() for 'adverSCarial', details:
  call: setMethod("show", "advChar", function(x) {
  error: could not find function "setMethod"
Call sequence:
3: stop(gettextf("%s failed in %s() for '%s', details:\n  call: %s\n  error: %s", 
       hookname, "loadNamespace", pkgname, deparse(conditionCall(res))[1L], 
       conditionMessage(res)), call. = FALSE, domain = NA)
2: runHook(".onLoad", env, package.lib, package)
1: loadNamespace(package, lib.loc)
Execution halted
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Error: .onLoad failed in loadNamespace() for 'adverSCarial', details:
  call: setMethod("show", "advChar", function(x) {
  error: could not find function "setMethod"
Call sequence:
3: stop(gettextf("%s failed in %s() for '%s', details:\n  call: %s\n  error: %s", 
       hookname, "loadNamespace", pkgname, deparse(conditionCall(res))[1L], 
       conditionMessage(res)), call. = FALSE, domain = NA)
2: runHook(".onLoad", env, package.lib, package)
1: loadNamespace(package, lib.loc)
Execution halted
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Error: .onLoad failed in loadNamespace() for 'adverSCarial', details:
  call: setMethod("show", "advChar", function(x) {
  error: could not find function "setMethod"
Call sequence:
3: stop(gettextf("%s failed in %s() for '%s', details:\n  call: %s\n  error: %s", 
       hookname, "loadNamespace", pkgname, deparse(conditionCall(res))[1L], 
       conditionMessage(res)), call. = FALSE, domain = NA)
2: runHook(".onLoad", env, package.lib, package)
1: loadNamespace(package, lib.loc)
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [2s/2s] NOTE
File ‘adverSCarial/R/onLoad.R’:
  .onLoad calls:
    print(x@values)
    print(paste0("Vector with ", length(x@values), " values:"))
    print(paste0(paste(x@values[1:10], collapse = ", "), " ..."))
    print(paste0(paste(paste0(names(x@values[1:5]), ": ", x@values[1:5]),     collapse = ", "), " ..."))
    print(x@values)
    print(paste0("Vector with ", length(x@values), " values:"))
    print(paste0(paste(x@values[1:10], collapse = ", "), " ..."))
    print(paste0(paste(paste0(names(x@values[1:5]), ": ", x@values[1:5]),     collapse = ", "), " ..."))

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.

Error: .onLoad failed in loadNamespace() for 'adverSCarial', details:
  call: setMethod("show", "advChar", function(x) {
  error: could not find function "setMethod"
Execution halted
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Error: package or namespace load failed for ‘adverSCarial’:
 .onLoad failed in loadNamespace() for 'adverSCarial', details:
  call: setMethod("show", "advChar", function(x) {
  error: could not find function "setMethod"
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   }
Execution halted
Error: package or namespace load failed for ‘adverSCarial’:
 .onLoad failed in loadNamespace() for 'adverSCarial', details:
  call: setMethod("show", "advChar", function(x) {
  error: could not find function "setMethod"
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   }
Execution halted
Error: package or namespace load failed for ‘adverSCarial’:
 .onLoad failed in loadNamespace() for 'adverSCarial', details:
  call: setMethod("show", "advChar", function(x) {
  error: could not find function "setMethod"
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   }
Execution halted
* checking Rd \usage sections ... NOTE
Error: .onLoad failed in loadNamespace() for 'adverSCarial', details:
  call: setMethod("show", "advChar", function(x) {
  error: could not find function "setMethod"
Call sequence:
3: stop(gettextf("%s failed in %s() for '%s', details:\n  call: %s\n  error: %s", 
       hookname, "loadNamespace", pkgname, deparse(conditionCall(res))[1L], 
       conditionMessage(res)), call. = FALSE, domain = NA)
2: runHook(".onLoad", env, package.lib, package)
1: loadNamespace(package, lib.loc)
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
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 ... [20s/27s] ERROR
Running examples in ‘adverSCarial-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: advGridMinChange
> ### Title: Grid search of min change adversarial attack. Tries each
> ###   combination on a cluster, given a list of genes and a list of
> ###   modifications.
> ### Aliases: advGridMinChange
> 
> ### ** Examples
> 
> MyClassifier <- function(expr, clusters, target) {
+    c("T cell", 0.9)
+ }
> 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","B cell","T cell","T cell")
> 
> advGridMinChange(rna_expression, clusters_id, "T cell",
+ MyClassifier, genes=genes,
+ modifications = list(c("perc1"), c("perc99")))
Running combination: 1 on 9
Running combination: 2 on 9
Running combination: 3 on 9
Running combination: 4 on 9
Running combination: 5 on 9
Running combination: 6 on 9
Running combination: 7 on 9
Running combination: 8 on 9
Running combination: 9 on 9
DataFrame with 9 rows and 6 columns
   prediction         odd genesModified typeModified         CD4        CD8A
  <character> <character>     <integer>    <logical> <character> <character>
1      T cell         0.9             0        FALSE          NA          NA
2      T cell         0.9             1        FALSE       perc1          NA
3      T cell         0.9             1        FALSE      perc99          NA
4      T cell         0.9             1        FALSE          NA       perc1
5      T cell         0.9             1        FALSE          NA      perc99
6      T cell         0.9             2        FALSE       perc1       perc1
7      T cell         0.9             2        FALSE       perc1      perc99
8      T cell         0.9             2        FALSE      perc99       perc1
9      T cell         0.9             2        FALSE      perc99      perc99
> 
> myModif = function(x){
+    return(sample(1:10,1))
+ }
> 
> my_modifications = list(c("perc1"),
+                         c("fixed", 1000),
+                         c("full_matrix_fct", myModif))
> advGridMinChange(rna_expression, clusters_id, "T cell",
+ MyClassifier, genes=genes, modifications = my_modifications)
Running combination: 1 on 16
Running combination: 2 on 16
Error in FUN(X[[i]], ...) : object 'numGenes' not found
Calls: advGridMinChange ... .advModificationsNotFunction -> unlist -> lapply -> FUN -> append
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [1s/1s]
 [1s/1s] ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 20 lines of output:
  FAILURE in test_advMaxChange: Error in checkTrue(length(advMaxChange(exprs, clusters, "b", MyClassifier)) ==  : 
    Test not TRUE
  
  FAILURE in test_advMinChange: Error in checkTrue(length(advMinChange(exprs, clusters, "b", MyClassifier)) ==  : 
    Test not TRUE
  
  ERROR in test_advModifications: Error in FUN(X[[i]], ...) : object 'numGenes' not found
  ERROR in test_maxChangeOverview: Error in validObject(.Object) : 
    invalid class "advChar" object: invalid object for slot "values" in class "advChar": got class "NULL", should be or extend class "character"
  
  Test files with failing tests
  
     test_adv.R 
       test_advMaxChange 
       test_advMinChange 
       test_advModifications 
       test_maxChangeOverview 
  
  
  Error in BiocGenerics:::testPackage("adverSCarial") : 
    unit tests failed for package adverSCarial
  Execution halted
* 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 ... [4s/4s] OK
* DONE

Status: 2 ERRORs, 8 WARNINGs, 5 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2983/07ec83cd171f7f2f3370fe0809e7e22a7fad52e1/adverSCarial.Rcheck/00check.log’
for details.





===============================

 BiocCheck('adverSCarial_0.99.26.tar.gz')

===============================

─ BiocCheckVersion: 1.37.0
─ BiocVersion: 3.18
─ Package: adverSCarial
─ PackageVersion: 0.99.26
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpTwXYC6/file14a7ba05cb2/adverSCarial
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpTwXYC6/file14a7b8d8af8d
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2983/07ec83cd171f7f2f3370fe0809e7e22a7fad52e1/adverSCarial.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
    * NOTE: Consider adding these automatically suggested biocViews:
      GeneExpression, ATACSeq, GeneTarget
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
Warning: For function ‘show’, signature ‘advChar’: argument in method definition changed from (x) to (object)
Warning: For function ‘show’, signature ‘advList’: argument in method definition changed from (x) to (object)
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
    * WARNING: Evaluate more vignette chunks.
        41 code chunks / 73 total = 56% percent unevaluated
        40 non-exec code chunks (e.g., '``` r')
    * NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of adverSCarial...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid using '=' for assignment and use '<-' instead
    * NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
    Found @ in vignettes/vign01_adverSCarial.Rmd
    * NOTE: Use accessors; don't access S4 class slots via '@' in
      examples/vignettes.
    * NOTE: Avoid '<<-' if possible (found 2 times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 11 functions greater than 50 lines.
* Checking man page documentation...
Warning: For function ‘show’, signature ‘advChar’: argument in method definition changed from (x) to (object)
Warning: For function ‘show’, signature ‘advList’: argument in method definition changed from (x) to (object)
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 156 lines (4%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 168 lines
      (4%) are not.
    See https://contributions.bioconductor.org/r-code.html
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
    Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.

─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 10 NOTES

See the adverSCarial.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

===============================

 R CMD BUILD

===============================

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir adverSCarial_0.99.26.tar.gz'
>>>>>>> 

* 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
Warning: For function ‘show’, signature ‘advChar’: argument in method definition changed from (x) to (object)
Warning: For function ‘show’, signature ‘advList’: argument in method definition changed from (x) to (object)
** testing if installed package can be loaded from final location
Warning: For function ‘show’, signature ‘advChar’: argument in method definition changed from (x) to (object)
Warning: For function ‘show’, signature ‘advList’: argument in method definition changed from (x) to (object)
** testing if installed package keeps a record of temporary installation path
* DONE (adverSCarial)