Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘ClustIRR/DESCRIPTION’ ... OK
* preparing ‘ClustIRR’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘ClustIRR_0.99.5.tar.gz’

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 BiocCheckGitClone('ClustIRR')

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─ BiocCheckVersion: 1.37.8
─ BiocVersion: 3.18
─ Package: ClustIRR
─ PackageVersion: 0.99.5
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3087/68bd6e7d1d34f02d9a983081100db08cbcf83dbe/ClustIRR
─ 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/3087/68bd6e7d1d34f02d9a983081100db08cbcf83dbe/ClustIRR.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* 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 ‘ClustIRR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClustIRR’ version ‘0.99.5’
* 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 ‘ClustIRR’ can be installed ... OK
* 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] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [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/4s] NOTE
configure_network: no visible global function definition for ‘%>%’
Undefined global functions or variables:
  %>%
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/2s] ERROR
Running examples in ‘ClustIRR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cluster_irr
> ### Title: Clustering of immune receptor repertoires
> ### Aliases: cluster_irr
> 
> ### ** Examples
> 
> # load package input data
> data("CDR3ab")
> s <- data.frame(CDR3b = CDR3ab[1:1000, "CDR3b"])
> r <- data.frame(CDR3b = CDR3ab[1:5000, "CDR3b"])
> 
> # artificially enrich motif 'RQWW' inside sample dataset
> base::substr(x = s$CDR3b[1:20], start = 6, stop = 9) <- "RQWW"
> 
> # add an artificial clonal expansion of two sequences to the sample dataset
> s <- base::rbind(s, base::data.frame(CDR3b = rep(x = c("CATSRAAKPDGLRALETQYF",
+                                     "CATSRAAKPDRQWWLSTQYF"),
+                                     times = 15)))
> 
> # run analysis
> out <- cluster_irr( s = s,
+                     r = r,
+                     version = 3,
+                     ks = 4,
+                     cores = 1,
+                     control = list(
+                         B = 1000,
+                         global_max_dist = 1,
+                         local_max_fdr = 0.05,
+                         local_min_ove = 2,
+                         local_min_o = 1,
+                         trim_flank_aa = 3,
+                         global_pairs = NULL,
+                         low_mem = FALSE))
> 
> # output class
> base::class(out)
[1] "clust_irr"
> 
> # output structure
> utils::str(out)
List of 2
 $ clust :List of 1
  ..$ CDR3b:List of 2
  .. ..$ local :List of 2
  .. .. ..$ m :'data.frame':	4141 obs. of  12 variables:
  .. .. .. ..$ motif     : chr [1:4141] "AAAS" "AAEN" "AAGE" "AAGG" ...
  .. .. .. ..$ f_s       : num [1:4141] 1 1 1 3 1 30 1 2 1 1 ...
  .. .. .. ..$ n_s       : num [1:4141] 5942 5942 5942 5942 5942 ...
  .. .. .. ..$ f_r       : num [1:4141] 2 1 4 9 3 0 1 5 1 2 ...
  .. .. .. ..$ n_r       : num [1:4141] 28256 28256 28256 28256 28256 ...
  .. .. .. ..$ k         : num [1:4141] 4 4 4 4 4 4 4 4 4 4 ...
  .. .. .. ..$ ove       : num [1:4141] 2.38 4.76 1.19 1.59 1.59 ...
  .. .. .. ..$ ove_ci_l95: num [1:4141] 0.082 0.1235 0.049 0.3682 0.0614 ...
  .. .. .. ..$ ove_ci_h95: num [1:4141] Inf Inf Inf Inf Inf ...
  .. .. .. ..$ p_value   : num [1:4141] 0.436 0.317 0.615 0.348 0.534 ...
  .. .. .. ..$ fdr       : num [1:4141] 0.599 0.599 0.695 0.599 0.652 ...
  .. .. .. ..$ pass      : logi [1:4141] FALSE FALSE FALSE FALSE FALSE TRUE ...
  .. .. ..$ lp:'data.frame':	363 obs. of  3 variables:
  .. .. .. ..$ cdr3     : chr [1:363] "CATSRAAKPDGLRALETQYF" "CATSRAAKPDRQWWLSTQYF" "CATSRAAKPDGLRALETQYF" "CATSRAAKPDRQWWLSTQYF" ...
  .. .. .. ..$ cdr3_core: chr [1:363] "SRAAKPDGLRALET" "SRAAKPDRQWWLST" "SRAAKPDGLRALET" "SRAAKPDRQWWLST" ...
  .. .. .. ..$ motif    : chr [1:363] "AAKP" "AAKP" "AAKP" "AAKP" ...
  .. ..$ global: chr [1:3, 1:2] "CATSRAAKPDGLRALETQYF" "CATSRAAKPDRQWWLSTQYF" "CASSPRQWWGYTF" "CATSRAAKPDGLRALETQYF" ...
 $ inputs:List of 6
  ..$ s      :'data.frame':	1030 obs. of  2 variables:
  .. ..$ CDR3b: chr [1:1030] "CASTVRQWWNEKLFF" "CASSLRQWWYTF" "CSALTRQWWYNEQFF" "CSARARQWWNEKLFF" ...
  .. ..$ id   : int [1:1030] 1 2 3 4 5 6 7 8 9 10 ...
  ..$ r      :'data.frame':	5000 obs. of  1 variable:
  .. ..$ CDR3b: chr [1:5000] "CASTVTSGSNEKLFF" "CASSLTGTGYTF" "CSALTPGLIYNEQFF" "CSARASWGTNEKLFF" ...
  ..$ version: num 3
  ..$ ks     : num 4
  ..$ cores  : num 1
  ..$ control:List of 7
  .. ..$ B              : num 1000
  .. ..$ global_max_dist: num 1
  .. ..$ local_max_fdr  : num 0.05
  .. ..$ local_min_ove  : num 2
  .. ..$ local_min_o    : num 1
  .. ..$ trim_flank_aa  : num 3
  .. ..$ low_mem        : logi FALSE
 - attr(*, "class")= chr "clust_irr"
> 
> # inspect motif enrichment results
> knitr::kable(utils::head(out$clust$CDR3b$local$m))


|motif | f_s|  n_s| f_r|   n_r|  k|      ove| ove_ci_l95| ove_ci_h95|   p_value|       fdr|pass  |
|:-----|---:|----:|---:|-----:|--:|--------:|----------:|----------:|---------:|---------:|:-----|
|AAAS  |   1| 5942|   2| 28256|  4| 2.377806|  0.0819980|        Inf| 0.4359444| 0.5993512|FALSE |
|AAEN  |   1| 5942|   1| 28256|  4| 4.755669|  0.1235303|        Inf| 0.3173198| 0.5993512|FALSE |
|AAGE  |   1| 5942|   4| 28256|  4| 1.188820|  0.0490266|        Inf| 0.6149447| 0.6946224|FALSE |
|AAGG  |   3| 5942|   9| 28256|  4| 1.585368|  0.3681890|        Inf| 0.3478369| 0.5993512|FALSE |
|AAGY  |   1| 5942|   3| 28256|  4| 1.585171|  0.0613645|        Inf| 0.5339593| 0.6518648|FALSE |
|AAKP  |  30| 5942|   0| 28256|  4|      Inf| 45.5102237|        Inf| 0.0000000| 0.0000000|TRUE  |
> 
> # inspect which CDR3bs are globally similar
> knitr::kable(utils::head(out$clust$CDR3b$global))


|                     |                     |
|:--------------------|:--------------------|
|CATSRAAKPDGLRALETQYF |CATSRAAKPDGLRALETQYF |
|CATSRAAKPDRQWWLSTQYF |CATSRAAKPDRQWWLSTQYF |
|CASSPRQWWGYTF        |CASRPRQWWGYTF        |
> 
> # plot graph
> plot_graph(out)
Error in visNetwork::visNetwork(nodes = nodes, edges = edges) %>% visNetwork::visIgraphLayout(layout = "layout_components",  : 
  could not find function "%>%"
Calls: plot_graph -> configure_network
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [24s/47s]
 [24s/47s] 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 ERROR, 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3087/68bd6e7d1d34f02d9a983081100db08cbcf83dbe/ClustIRR.Rcheck/00check.log’
for details.





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 BiocCheck('ClustIRR_0.99.5.tar.gz')

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─ BiocCheckVersion: 1.37.8
─ BiocVersion: 3.18
─ Package: ClustIRR
─ PackageVersion: 0.99.5
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp55UW9D/file5ca4543402e4/ClustIRR
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp55UW9D/file5ca44349cebb
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3087/68bd6e7d1d34f02d9a983081100db08cbcf83dbe/ClustIRR.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...
    * NOTE: Update R version dependency from 4.2.0 to 4.3.0.
* 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...
* 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 recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of ClustIRR...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 10 functions greater than 50 lines.
* Checking man page documentation...
* 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; 3 lines (0%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 64 lines
      (2%) 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 | 0 WARNINGS | 4 NOTES

See the ClustIRR.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 ClustIRR_0.99.5.tar.gz'
>>>>>>> 

* installing *source* package ‘ClustIRR’ ...
** using staged installation
** R
** data
** 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 (ClustIRR)