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_0.99.30.tar.gz’

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 BiocCheckGitClone('adverSCarial')

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─ BiocCheckVersion: 1.37.0
─ BiocVersion: 3.18
─ Package: adverSCarial
─ PackageVersion: 0.99.30
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2983/c065fe0421299d1110f95a6478bfaa2e6cc057f2/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')




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2983/c065fe0421299d1110f95a6478bfaa2e6cc057f2/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 ‘0.99.30’
* 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 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/c065fe0421299d1110f95a6478bfaa2e6cc057f2/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] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] NOTE
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)

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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [3s/3s] 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'.

.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’
.randWalkTryNewVector: no visible global function definition for
  ‘SingleCellExperiment’
MClassifier: no visible global function definition for ‘is’
advGridMinChange: no visible global function definition for ‘is’
advGridMinChange: no visible global function definition for ‘counts’
advGridMinChange: no visible global function definition for
  ‘SingleCellExperiment’
advMaxChange: no visible global function definition for ‘is’
advMaxChange: no visible global function definition for ‘counts’
advMaxChange: no visible global function definition for ‘new’
advMinChange: no visible global function definition for ‘is’
advMinChange: no visible global function definition for ‘counts’
advMinChange: no visible binding for '<<-' assignment to
  ‘lastResLength’
advMinChange : <anonymous>: no visible binding for global variable
  ‘lastResLength’
advMinChange : <anonymous>: no visible binding for '<<-' assignment to
  ‘lastResLength’
advMinChange: 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’
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’
minChangeOverview: no visible global function definition for ‘is’
minChangeOverview: 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’
Undefined global functions or variables:
  SingleCellExperiment colData counts is lastResLength new
Consider adding
  importFrom("methods", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
* checking Rd \usage sections ... OK
* 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 ... [49s/51s] OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
MClassifier      17.363  1.931  20.281
matrixFromSCE     9.692  1.661  11.929
sceConvertToHGNC  9.480  1.410  11.414
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [1s/1s]
 [1s/1s] OK
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2983/c065fe0421299d1110f95a6478bfaa2e6cc057f2/adverSCarial.Rcheck/00check.log’
for details.






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 BiocCheck('adverSCarial_0.99.30.tar.gz')

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─ BiocCheckVersion: 1.37.0
─ BiocVersion: 3.18
─ Package: adverSCarial
─ PackageVersion: 0.99.30
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpHjuQm1/file1677027186238/adverSCarial
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpHjuQm1/file167707429a1c3
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2983/c065fe0421299d1110f95a6478bfaa2e6cc057f2/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.
        35 code chunks / 70 total = 50% percent unevaluated
        34 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.

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir adverSCarial_0.99.30.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)